diff --git a/README.md b/README.md index 98f0971..7c2ea38 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,6 @@ -# Final Project +# DJM Final Project + +link to final project presentation: https://docs.google.com/presentation/d/1Cj2cMghksd8KFY0QX1QT4nm68gL-UBkqfmLc4fXgGAA/edit?usp=sharing ## Instructions @@ -13,21 +15,30 @@ are from public sources, or track them with [git-lfs](https://git-lfs.github.com ## Introduction -This is a final project for the [Comparative Genomics](https://github.com/Yale-EEB723/syllabus) seminar in the spring of 2019. This project (a very brief, ie 1-2 sentence, overview of the project)... +This is a final project for the [Comparative Genomics](https://github.com/Yale-EEB723/syllabus) seminar in the spring of 2019. +My project is to sequence and assemble the first darter genome using an Oxford Nanopore platform to collect long-read sequence data. ## The goal -The specific problem I/we sought to explore was ... Our goal was... +The long-term goals are to provide genomic resources for many future darter projects, including phylogenomic inference, functional genomics studies, and reference mapping. I will sequence a genome for *Etheostoma perlongum*, a species restricted to single lake in NC. The "sister species" of *E. perlongum* is *Etheostoma maculaticeps*, which can be found in the Waccamaw River that drains the lake. My specific goals are to use the genome to help assemble a large amount of ddRAD data that I have collected along a transect spanning the lake and the river. Our preliminary de novo assemblies and analyses of the ddRAD data indicate a steep cline between the lake and river, with some loci exhibiting particularly sharp breaks. My secondary goal is to map these outlier loci to the genomes to identify candidate regions that are maintaining the species boundary between the lake and river. ## The data -Description of data... - -- Data source (simulated/ published/ unpublished?) -- Data structure +I have not collected the data yet, but plan to use an Oxford Nanopore PromethION platform to sequence one darter species to ~30x coverage. ## Background +Speciation commonly involves geographic isolation of lineages that limits or prevents gene flow1. The prevalence of allopatric speciation is exemplified by darters, a clade of ~250 North American freshwater fishes. Nearly all darter sister species pairs are isolated in different river drainages2. The only exception is *Etheostoma perlongum*. Endemic to the 36 km2 Lake Waccamaw in North Carolina, *E. perlongum* is phylogenetically nested within the widespread Etheostoma olmstedi (Fig. 1A). The closest *E. olmstedi* relatives of *E. perlongum* are found immediately outside of Lake Waccamaw in the Waccamaw River (Fig. 1B). A small spillway dam built in 1926 separates the lake from the river, but the dam is frequently inundated3. Despite the lack of dispersal barriers, my dissertation research indicates that there is a sharp geographic cline in allele frequencies between the lake and the river (Fig. 1C&D). Additionally, *E. perlongum* differs from *E. olmstedi* in the number of vertebrae, lateral line scales, body shape, and breeding habits, including an annual life cycle rarely observed in other darters4,5. + +![](figures/Fig1.png) +*Figure 1.* Analyses of ddRAD-seq data for *E. olmstedi* and *E. perlongum*. A) Maximum likelihood phylogeny identified by IQTree, nodes <95% bootstrap support collapsed, red = *E. perlongum*, blue = *E. olmstedi* in the Waccamaw River. B) Sampling map, localities 1-4 in Lake Waccamaw, 5-11 in the Waccamaw River. C) Ancestry coefficients estimated using the “snmf” function in the R package LEA, locality numbers are indicated above the plot. D) PCA, with points color coded by species designation. + +However, there is still debate whether *E. perlongum* is a distinct species or a lake ecomorph of *E. olmstedi*6. Lake Waccamaw is only 15,000-32,000 years old3, requiring very rapid ecological speciation between *E. perlongum* and *E. olmstedi*. Alternatively, the divergence between *E. olmstedi* and *E. perlongum* could be explained by local adaptation and/or phenotypic plasticity. Intraspecific lake-stream divergence is well-documented in many other fish species including sticklebacks7, minnows8, and cichlids9. If the divergence between *E. perlongum* and *E. olmstedi* represents intraspecific variation, we should observe similar genetic, phenotypic, and ecological divergence between other lake-stream populations of *E. olmstedi*. While there are many museum records of *E. olmstedi* in other lake-stream systems, there has been no detailed study of these populations. + +**Research Questions:** Is *E. perlongum* a unique case of recent ecological speciation in a clade dominated by allopatric speciation? Or is differentiation between *E. perlongum* and *E. olmstedi* typical of intraspecific variation between other *E. olmstedi* lake-stream populations? + + + Motivation for the project.... How it fits in with other work... @@ -37,6 +48,9 @@ What the reader needs to know to understand the project ## Methods +I plan to perform the DNA extraction and sequencing in mid-March in the lab of Trevor Krabbenhoft, a collaborator at the University of Buffalo (http://arts-sciences.buffalo.edu/biological-sciences/faculty/faculty-directory/trevor-krabbenhoft.html). I will use a variety of base-calling and assembly methods, including Scrappie and Canu (outlined in Jain et al. 2018). I will hopefully perform genome annotation using several additional sources of data, including exon-capture sequences and transcriptomic data from a closely related darter species. + + ## Results @@ -51,3 +65,21 @@ What would you have done differently? What are future directions this could go in? ## References + +1. Coyne J.A. & Orr H.A. Speciation. Sunderland, MA: Sinauer Associates, Inc. 2004. + +2. Near T.J., Bossu C.M., Bradburd G.S., Carlson R.L., Harrington R.C., Hollingsworth, P.R., Keck, B.P., & Etnier, D.A. Phylogeny and temporal diversification of Darters (Percidae: Etheostomatinae). Syst. Biol. 60:565–595. 2011. + +3. Stager J.C. & Cahoon L.B. The Age and Trophic History of Lake Waccamaw, North Carolina. J. Elisha Mitchell Scientific Society. 103:1-13. 1987. + +4. Shute, P.W., Shute J.R., Lindquist D.G. Age, growth, and early life history of the Waccamaw Darter, Etheostoma perlongum. Copeia. 1982:561–567. 1982. + +5. Shute, J. R. A Systematic Evaluation of the Waccamaw Darter, Etheostoma perlongum Hubbs and Raney, with Comments on Relationships within the Subgenus Boleosoma Percidae: Etheostomatinae. University of Tennessee, Knoxville. 1984. + +6. Berner D., Adams D.C., Grandchamp A.C., & Hendry A.P. Natural selection drives patterns of lake-stream divergence in stickleback foraging morphology. J. Evol. Biol. 21:1653–1665. 2008. + +7. Collin H. & Fumagalli L. Evidence for morphological and adaptive genetic divergence between lake and stream habitats in European minnows (Phoxinus phoxinus, Cyprinidae). Mol. Ecol. 20:4490-4502. 2011 + +8. Theis A., Ronco F., Indermaur A., Salzburger W., Egger B. Adaptive divergence between lake and stream populations of an East African cichlid fish. Mol. Ecol. 23:5304-5322. 2014. + +9. Wainwright P.C. & Richard B.A., Predicting patterns of prey use from morphology of fishes. EnvironBiolFish. 44:97-113. 1994. diff --git a/assemblies/v0.1/assemblyPipeline.md b/assemblies/v0.1/assemblyPipeline.md new file mode 100644 index 0000000..a2c4a98 --- /dev/null +++ b/assemblies/v0.1/assemblyPipeline.md @@ -0,0 +1,40 @@ +# Etheostoma perlongum genome assebly +*v0.1* + +Running genome assembly with data from two Nanopore flow cells + +Excluding reads < 1 kb + +## pipeline + +combine fastq files + +`cat ~/scratch60/Eper_genome/nanoporeData/Eper_*/*/*/fastq_pass/*.fastq > Eper_nanopore.fastq` + +convert fastq to fasta (we don't actually need to do this) + +`paste - - - - < Eper_nanopore.fastq | cut -f 1,2 | sed 's/^@/>/' | tr "\t" "\n" > Eper_nanopore.fasta` + +remove reads < 1kb + +`bioawk -c fastx 'length($seq) > 1000{print "@"$name"\n"$seq"\n+\n"$qual}' Eper_nanopore.fastq > Eper_nanopore_1kb.fastq` + +run minimap2 to map each read against all other reads + +`minimap2 -x ava-ont -t 20 Eper_nanopore_1kb.fastq Eper_nanopore_1kb.fastq > Eper_nanopore_1kb_ovlp.paf 2> minimap.log` + +run miniasm to assmble the reads using the mapping from previous step + +`miniasm -f Eper_nanopore_1kb.fastq Eper_nanopore_1kb_ovlp.paf > Eper_nanopore_1kb.gfa 2> miniasm.log` + +convert gfa file from miniasm to fasta format + +`awk '/^S/{print ">"$2"\n"$3}' Eper_nanopore_1kb.gfa | fold > Eper_nanopore_1kb.gfa.fasta` + +run minimap2 again to map reads to the assembled contigs + +` minimap2 -x ava-ont -t 10 Eper_nanopore_1kb.gfa.fasta Eper_nanopore_1kb.fastq > Eper_nanopore_1kb_ovlp_genome.paf 2> minimap_genome.log` + +run racon to polish the assembly and create consensus sequences + +`racon -t 10 Eper_nanopore_1kb.fastq Eper_nanopore_1kb_ovlp_genome.paf Eper_nanopore_1kb.gfa.fasta > Eper_nanopore_1kb.racon.fasta` diff --git a/assemblies/v0.1/assemblyStats.txt b/assemblies/v0.1/assemblyStats.txt new file mode 100644 index 0000000..b6c787c --- /dev/null +++ b/assemblies/v0.1/assemblyStats.txt @@ -0,0 +1,9 @@ +# Assembly stats +v0.1 + +contig n50 = 872,654 bps +median contig length = 314,004 bp +shortest contig = 4,308 bp +longest contig = 3,968,385 bp +number of contigs = 1,416 +total assembly length = 717,512,980 bp diff --git a/assemblies/v0.1/bandageGraph.png b/assemblies/v0.1/bandageGraph.png new file mode 100644 index 0000000..ac1ff61 Binary files /dev/null and b/assemblies/v0.1/bandageGraph.png differ diff --git a/assemblies/v0.1/contigLengths.txt b/assemblies/v0.1/contigLengths.txt new file mode 100644 index 0000000..11039a3 --- /dev/null +++ b/assemblies/v0.1/contigLengths.txt @@ -0,0 +1,1416 @@ +utg000001l 575571 +utg000002l 1359645 +utg000003l 428403 +utg000004l 125071 +utg000005c 16599 +utg000006l 274472 +utg000007l 336386 +utg000008l 197300 +utg000009l 1169657 +utg000010l 135260 +utg000011l 469546 +utg000012l 1135354 +utg000013l 771329 +utg000014l 293731 +utg000015l 59686 +utg000016l 300351 +utg000017l 763794 +utg000018l 115466 +utg000019l 204865 +utg000020l 113427 +utg000021l 315953 +utg000022l 945291 +utg000023l 1937087 +utg000024l 207356 +utg000025l 355862 +utg000026l 175402 +utg000027l 798991 +utg000028l 55459 +utg000029l 274607 +utg000030l 983276 +utg000031l 159768 +utg000032l 1626735 +utg000033l 677902 +utg000034l 1445349 +utg000035l 239506 +utg000036l 526308 +utg000037l 1621279 +utg000038l 337451 +utg000039l 314535 +utg000040l 1458846 +utg000041l 120722 +utg000042l 1387471 +utg000043l 410297 +utg000044l 780723 +utg000045l 3252905 +utg000046l 1204585 +utg000047l 1644080 +utg000048l 321751 +utg000049l 498763 +utg000050l 1057520 +utg000051l 246257 +utg000052l 284029 +utg000053l 159484 +utg000054l 982798 +utg000055l 1340964 +utg000056l 180963 +utg000057l 570051 +utg000058l 758962 +utg000059l 1022455 +utg000060l 204107 +utg000061l 380571 +utg000062l 262003 +utg000063l 609740 +utg000064l 213870 +utg000065l 202205 +utg000066l 567295 +utg000067l 894359 +utg000068l 137595 +utg000069l 235959 +utg000070l 1602073 +utg000071l 977347 +utg000072l 123130 +utg000073l 2764241 +utg000074l 221265 +utg000075l 1111803 +utg000076l 204909 +utg000077l 849162 +utg000078l 585405 +utg000079l 1042362 +utg000080l 480191 +utg000081l 1672384 +utg000082l 1446854 +utg000083l 1112871 +utg000084l 4035490 +utg000085l 1418693 +utg000086l 231814 +utg000087l 249312 +utg000088l 600580 +utg000089l 963744 +utg000090l 151459 +utg000091l 881387 +utg000092l 2379970 +utg000093l 1027626 +utg000094l 527264 +utg000095l 172599 +utg000096l 975951 +utg000097l 432264 +utg000098l 2720264 +utg000099l 137149 +utg000100l 1561446 +utg000101l 1216177 +utg000102l 870250 +utg000103l 595711 +utg000104l 1470908 +utg000105l 555381 +utg000106l 778502 +utg000107l 367519 +utg000108l 273399 +utg000109l 378159 +utg000110l 805998 +utg000111l 968657 +utg000112l 1976739 +utg000113l 442865 +utg000114l 2123306 +utg000115l 1701577 +utg000116l 1608345 +utg000117l 664395 +utg000118l 376609 +utg000119l 2157162 +utg000120l 1696908 +utg000121l 938576 +utg000122l 450807 +utg000123l 1237547 +utg000124l 574621 +utg000125l 879666 +utg000126l 823370 +utg000127l 1950823 +utg000128l 242896 +utg000129l 240703 +utg000130l 679260 +utg000131l 181688 +utg000132l 1071063 +utg000133l 2381066 +utg000134l 407908 +utg000135l 735583 +utg000136l 89224 +utg000137l 163925 +utg000138l 948968 +utg000139l 247436 +utg000140l 971303 +utg000141l 284439 +utg000142l 334253 +utg000143l 456250 +utg000144l 306651 +utg000145l 156342 +utg000146l 872773 +utg000147l 1277781 +utg000148l 831540 +utg000149l 314783 +utg000150l 668611 +utg000151l 1357650 +utg000152l 474862 +utg000153l 370916 +utg000154l 308600 +utg000155l 199512 +utg000156l 588760 +utg000157l 172175 +utg000158l 602495 +utg000159l 98374 +utg000160l 1283710 +utg000161l 148360 +utg000162l 224319 +utg000163l 1269638 +utg000164l 356355 +utg000165l 940873 +utg000166l 459110 +utg000167l 75651 +utg000168l 340620 +utg000169l 381723 +utg000170l 846197 +utg000171l 226191 +utg000172l 1090963 +utg000173l 1207687 +utg000174l 656699 +utg000175l 453680 +utg000176l 131539 +utg000177l 578112 +utg000178l 479418 +utg000179l 1105127 +utg000180l 399962 +utg000181l 1384306 +utg000182l 1286419 +utg000183l 272522 +utg000184l 2320155 +utg000185l 544822 +utg000186l 353146 +utg000187l 629477 +utg000188l 128640 +utg000189l 182436 +utg000190l 684153 +utg000191l 2284787 +utg000192l 2574370 +utg000193l 861666 +utg000194l 49861 +utg000195l 496173 +utg000196l 200682 +utg000197l 146404 +utg000198l 940730 +utg000199l 1214622 +utg000200l 563216 +utg000201l 68336 +utg000202l 188427 +utg000203l 440356 +utg000204l 897777 +utg000205l 701622 +utg000206l 435509 +utg000207l 1668910 +utg000208l 354320 +utg000209l 882077 +utg000210l 531768 +utg000211l 652257 +utg000212l 653978 +utg000213l 367930 +utg000214l 602105 +utg000215l 1764031 +utg000216l 1194124 +utg000217l 76261 +utg000218l 262588 +utg000219l 154652 +utg000220l 1935952 +utg000221l 2332175 +utg000222l 843408 +utg000223l 885723 +utg000224l 877758 +utg000225l 334701 +utg000226l 3187558 +utg000227l 829768 +utg000228l 583553 +utg000229l 1273898 +utg000230l 388106 +utg000231l 356491 +utg000232l 600842 +utg000233l 1097254 +utg000234l 3040842 +utg000235l 227274 +utg000236l 1823113 +utg000237l 951897 +utg000238l 966734 +utg000239l 227323 +utg000240c 36193 +utg000241l 145597 +utg000242l 37640 +utg000243l 2074373 +utg000244l 142499 +utg000245l 1288439 +utg000246l 826807 +utg000247l 1492567 +utg000248l 1064951 +utg000249l 338416 +utg000250l 492421 +utg000251l 1793664 +utg000252l 2448801 +utg000253l 960885 +utg000254l 603812 +utg000255l 438918 +utg000256l 123338 +utg000257l 520734 +utg000258l 967362 +utg000259l 306727 +utg000260l 512384 +utg000261l 1569048 +utg000262l 982367 +utg000263l 303194 +utg000264l 110243 +utg000265l 2298942 +utg000266l 86001 +utg000267l 500100 +utg000268l 283972 +utg000269l 1291807 +utg000270l 248939 +utg000271l 212991 +utg000272l 192315 +utg000273l 160094 +utg000274l 403582 +utg000275l 614509 +utg000276l 228080 +utg000277l 1033277 +utg000278l 434346 +utg000279l 1323004 +utg000280l 363567 +utg000281l 132746 +utg000282l 1101316 +utg000283l 35215 +utg000284l 1421542 +utg000285l 528665 +utg000286l 932648 +utg000287l 374774 +utg000288l 420855 +utg000289l 1792978 +utg000290l 1263367 +utg000291l 216481 +utg000292l 154555 +utg000293l 514800 +utg000294l 1845766 +utg000295l 129719 +utg000296l 716038 +utg000297l 94600 +utg000298l 2015055 +utg000299l 242872 +utg000300l 752753 +utg000301l 808290 +utg000302l 4326 +utg000303l 404656 +utg000304l 1239858 +utg000305l 266713 +utg000306l 295633 +utg000307l 833944 +utg000308l 273089 +utg000309l 623203 +utg000310l 3377816 +utg000311l 315960 +utg000312l 929011 +utg000313l 2857021 +utg000314l 1043859 +utg000315l 2156514 +utg000316l 474212 +utg000317l 165340 +utg000318l 505764 +utg000319l 1581219 +utg000320l 272633 +utg000321l 820792 +utg000322l 385612 +utg000323l 682056 +utg000324l 282205 +utg000325l 96425 +utg000326l 343999 +utg000327l 1583544 +utg000328l 1034676 +utg000329l 597080 +utg000330c 86473 +utg000331l 470804 +utg000332l 1656014 +utg000333l 1861088 +utg000334l 1397071 +utg000335l 376158 +utg000336l 286010 +utg000337l 208187 +utg000338l 1154618 +utg000339l 556352 +utg000340l 252767 +utg000341l 1565574 +utg000342l 377868 +utg000343l 380159 +utg000344l 214341 +utg000345l 540626 +utg000346l 1077883 +utg000347l 3849580 +utg000348l 467597 +utg000349l 1258043 +utg000350l 1214844 +utg000351l 1014654 +utg000352l 304485 +utg000353l 577153 +utg000354l 649225 +utg000355l 1561302 +utg000356l 243141 +utg000357l 80935 +utg000358l 531715 +utg000359l 141554 +utg000360l 554968 +utg000361l 534893 +utg000362l 277521 +utg000363l 139472 +utg000364l 169780 +utg000365l 326114 +utg000366l 744362 +utg000367l 721138 +utg000368l 1027535 +utg000369l 1807231 +utg000370l 1275656 +utg000371l 806321 +utg000372l 600318 +utg000373l 1887933 +utg000374l 958903 +utg000375l 921345 +utg000376l 349752 +utg000377l 198134 +utg000378l 2283962 +utg000379l 426333 +utg000380l 745506 +utg000381l 230609 +utg000382l 63290 +utg000383l 680762 +utg000384l 375316 +utg000385l 84685 +utg000386l 668733 +utg000387l 792420 +utg000388l 1572420 +utg000389l 2040348 +utg000390l 2258938 +utg000391l 586496 +utg000392l 1022597 +utg000393l 975247 +utg000394l 482285 +utg000395l 341500 +utg000396l 745740 +utg000397l 207596 +utg000398l 389765 +utg000399l 711586 +utg000400l 104395 +utg000401l 221431 +utg000402l 433816 +utg000403l 106532 +utg000404l 287748 +utg000405l 562458 +utg000406l 199924 +utg000407l 2078057 +utg000408l 75936 +utg000409l 269340 +utg000410l 217767 +utg000411l 87307 +utg000412l 2089997 +utg000413l 320723 +utg000414l 1253014 +utg000415l 763394 +utg000416l 449363 +utg000417l 2491400 +utg000418l 332561 +utg000419l 1496454 +utg000420c 69174 +utg000421l 290718 +utg000422l 26063 +utg000423l 1089328 +utg000424l 802892 +utg000425l 808083 +utg000426l 263225 +utg000427l 849433 +utg000428l 1581556 +utg000429l 514636 +utg000430l 919938 +utg000431l 1032808 +utg000432l 980417 +utg000433l 985903 +utg000434l 275990 +utg000435l 886581 +utg000436l 1929834 +utg000437l 294573 +utg000438l 823525 +utg000439l 63020 +utg000440l 606836 +utg000441l 314122 +utg000442l 103940 +utg000443l 292471 +utg000444l 1755098 +utg000445l 896507 +utg000446l 1770874 +utg000447l 2372765 +utg000448l 196607 +utg000449l 73875 +utg000450l 1421977 +utg000451l 485260 +utg000452l 386795 +utg000453l 814739 +utg000454l 119322 +utg000455l 565501 +utg000456l 1481346 +utg000457l 1207174 +utg000458l 75612 +utg000459l 461105 +utg000460l 396188 +utg000461l 285350 +utg000462l 934368 +utg000463l 294070 +utg000464l 365709 +utg000465l 748131 +utg000466l 470333 +utg000467l 567590 +utg000468l 2828037 +utg000469l 48475 +utg000470l 899370 +utg000471l 390505 +utg000472l 768920 +utg000473l 660086 +utg000474l 1596004 +utg000475l 607878 +utg000476l 939075 +utg000477l 225318 +utg000478l 707700 +utg000479l 1239434 +utg000480l 1706095 +utg000481l 888451 +utg000482l 1258596 +utg000483l 485805 +utg000484l 1345025 +utg000485l 384937 +utg000486l 1480648 +utg000487l 535276 +utg000488l 345747 +utg000489l 759187 +utg000490l 985521 +utg000491l 333909 +utg000492l 433690 +utg000493l 1116530 +utg000494l 195494 +utg000495l 234405 +utg000496l 213867 +utg000497l 751917 +utg000498l 1056537 +utg000499l 663567 +utg000500l 676951 +utg000501l 154165 +utg000502l 349775 +utg000503l 42372 +utg000504l 282415 +utg000505l 976867 +utg000506l 473185 +utg000507l 513682 +utg000508l 218095 +utg000509l 955945 +utg000510l 1315429 +utg000511l 591522 +utg000512l 1494232 +utg000513l 663841 +utg000514l 777741 +utg000515l 417837 +utg000516l 460080 +utg000517l 182393 +utg000518l 257239 +utg000519l 534669 +utg000520l 184636 +utg000521l 2017134 +utg000522l 1168496 +utg000523l 1279986 +utg000524l 251344 +utg000525l 1765351 +utg000526l 89945 +utg000527l 768535 +utg000528l 1748031 +utg000529l 416818 +utg000530l 799486 +utg000531l 360448 +utg000532l 138676 +utg000533l 1070624 +utg000534l 792418 +utg000535l 157118 +utg000536l 171474 +utg000537l 1466467 +utg000538l 246659 +utg000539l 297810 +utg000540l 394221 +utg000541l 1474238 +utg000542l 219980 +utg000543l 1798265 +utg000544l 1814084 +utg000545l 669388 +utg000546l 2157314 +utg000547l 103742 +utg000548l 793646 +utg000549l 161928 +utg000550l 752643 +utg000551l 1089534 +utg000552l 549321 +utg000553l 270805 +utg000554l 187527 +utg000555l 1800423 +utg000556l 390424 +utg000557l 801972 +utg000558l 206179 +utg000559l 95618 +utg000560l 1800595 +utg000561l 311709 +utg000562l 764951 +utg000563l 979094 +utg000564l 320638 +utg000565l 193753 +utg000566l 339695 +utg000567l 626880 +utg000568l 264415 +utg000569l 612847 +utg000570l 211456 +utg000571l 239485 +utg000572l 763908 +utg000573l 2537688 +utg000574l 864546 +utg000575l 1240202 +utg000576l 352456 +utg000577l 559373 +utg000578l 873118 +utg000579l 639452 +utg000580l 925226 +utg000581l 334427 +utg000582l 185716 +utg000583l 668048 +utg000584l 234969 +utg000585l 108025 +utg000586l 1438944 +utg000587l 725392 +utg000588l 720750 +utg000589l 1349825 +utg000590l 775831 +utg000591l 405408 +utg000592l 223916 +utg000593l 341806 +utg000594l 873370 +utg000595l 783871 +utg000596l 791923 +utg000597l 231915 +utg000598l 338753 +utg000599l 1761398 +utg000600l 693508 +utg000601l 1090098 +utg000602l 227964 +utg000603l 320531 +utg000604l 402687 +utg000605l 374218 +utg000606l 495394 +utg000607c 27665 +utg000608l 331168 +utg000609l 835234 +utg000610l 212031 +utg000611l 686455 +utg000612l 2111933 +utg000613l 1223545 +utg000614l 418208 +utg000615l 223280 +utg000616l 528294 +utg000617l 167799 +utg000618l 283136 +utg000619l 297764 +utg000620l 108311 +utg000621l 641944 +utg000622l 2399644 +utg000623l 973747 +utg000624l 242814 +utg000625l 735487 +utg000626l 685765 +utg000627l 991481 +utg000628l 529796 +utg000629l 321401 +utg000630l 405611 +utg000631l 114417 +utg000632l 1214945 +utg000633l 1982169 +utg000634l 1610814 +utg000635l 309275 +utg000636l 1336021 +utg000637l 386646 +utg000638l 85221 +utg000639l 731867 +utg000640l 739915 +utg000641l 442558 +utg000642l 598047 +utg000643l 321597 +utg000644l 352421 +utg000645l 550211 +utg000646l 1581451 +utg000647l 2346738 +utg000648l 367122 +utg000649l 221617 +utg000650l 175935 +utg000651l 1053406 +utg000652l 927498 +utg000653l 864593 +utg000654l 883154 +utg000655l 99536 +utg000656l 492911 +utg000657l 154629 +utg000658l 257762 +utg000659l 1099223 +utg000660l 390774 +utg000661l 483456 +utg000662l 113653 +utg000663l 479209 +utg000664l 94068 +utg000665l 322306 +utg000666l 531958 +utg000667l 550088 +utg000668l 48666 +utg000669l 578174 +utg000670l 354883 +utg000671l 418128 +utg000672l 220801 +utg000673l 146567 +utg000674l 2034043 +utg000675l 689966 +utg000676l 642948 +utg000677l 482926 +utg000678l 141184 +utg000679l 989615 +utg000680l 589511 +utg000681l 100083 +utg000682l 1504268 +utg000683l 315254 +utg000684l 8500 +utg000685l 463254 +utg000686l 398431 +utg000687l 453414 +utg000688l 379946 +utg000689l 1098753 +utg000690l 557960 +utg000691l 461902 +utg000692l 418014 +utg000693l 923503 +utg000694l 507836 +utg000695l 259332 +utg000696l 151276 +utg000697l 142218 +utg000698l 574905 +utg000699l 238215 +utg000700l 1210199 +utg000701l 34586 +utg000702l 2250165 +utg000703l 370256 +utg000704l 422712 +utg000705l 484420 +utg000706l 50436 +utg000707l 1179720 +utg000708l 822198 +utg000709l 18776 +utg000710l 394704 +utg000711l 1299661 +utg000712l 326345 +utg000713l 330704 +utg000714l 453349 +utg000715l 168153 +utg000716l 336412 +utg000717l 1705536 +utg000718l 412361 +utg000719l 276169 +utg000720l 493586 +utg000721l 477491 +utg000722l 939009 +utg000723l 300389 +utg000724l 457837 +utg000725l 649461 +utg000726l 23051 +utg000727l 105025 +utg000728l 761873 +utg000729l 57311 +utg000730l 429292 +utg000731l 167374 +utg000732l 1028250 +utg000733l 1108299 +utg000734l 683135 +utg000735l 173781 +utg000736l 830312 +utg000737l 1312682 +utg000738l 554396 +utg000739l 318589 +utg000740l 474521 +utg000741l 814883 +utg000742l 179592 +utg000743l 347324 +utg000744l 382606 +utg000745l 514292 +utg000746l 621313 +utg000747l 235670 +utg000748l 225699 +utg000749l 1094590 +utg000750l 210149 +utg000751l 1390659 +utg000752l 194158 +utg000753l 956562 +utg000754l 596152 +utg000755l 748394 +utg000756l 1471007 +utg000757l 182841 +utg000758l 99244 +utg000759l 1233952 +utg000760l 870148 +utg000761l 257473 +utg000762l 537025 +utg000763l 250719 +utg000764l 1434012 +utg000765l 499813 +utg000766l 164108 +utg000767l 745850 +utg000768l 227623 +utg000769l 284253 +utg000770l 54949 +utg000771l 564030 +utg000772l 715243 +utg000773l 1890701 +utg000774l 322794 +utg000775l 796077 +utg000776l 500256 +utg000777l 219605 +utg000778l 233551 +utg000779l 541539 +utg000780l 178412 +utg000781l 151297 +utg000782l 11814 +utg000783l 699209 +utg000784l 693125 +utg000785l 838611 +utg000786l 116269 +utg000787l 1185510 +utg000788l 191264 +utg000789l 498771 +utg000790l 391537 +utg000791l 347971 +utg000792l 98261 +utg000793l 452266 +utg000794l 149905 +utg000795l 257043 +utg000796l 196343 +utg000797l 2161195 +utg000798l 1348684 +utg000799l 130715 +utg000800l 988920 +utg000801l 353664 +utg000802l 1043893 +utg000803l 155826 +utg000804l 136361 +utg000805l 404662 +utg000806l 502709 +utg000807l 387151 +utg000808l 137774 +utg000809l 477648 +utg000810l 320387 +utg000811l 658107 +utg000812l 236023 +utg000813l 881035 +utg000814l 30243 +utg000815l 511375 +utg000816l 337414 +utg000817l 712095 +utg000818l 1150565 +utg000819l 132287 +utg000820l 784216 +utg000821l 303708 +utg000822l 78316 +utg000823l 936260 +utg000824l 902299 +utg000825l 118869 +utg000826l 946344 +utg000827l 1287316 +utg000828l 163082 +utg000829l 1233121 +utg000830l 470714 +utg000831l 1980292 +utg000832l 149188 +utg000833l 252409 +utg000834l 360763 +utg000835l 602135 +utg000836l 277603 +utg000837l 171036 +utg000838l 95041 +utg000839l 233750 +utg000840l 624910 +utg000841l 231048 +utg000842l 305749 +utg000843l 1770779 +utg000844l 108557 +utg000845l 183074 +utg000846l 174619 +utg000847l 186005 +utg000848l 247733 +utg000849l 483076 +utg000850l 191591 +utg000851l 240115 +utg000852l 231601 +utg000853l 983426 +utg000854l 481686 +utg000855l 460408 +utg000856l 175008 +utg000857l 283819 +utg000858l 32229 +utg000859l 285157 +utg000860l 402233 +utg000861l 546322 +utg000862l 373515 +utg000863l 208711 +utg000864l 225737 +utg000865l 179360 +utg000866l 848513 +utg000867l 87687 +utg000868l 193214 +utg000869l 726106 +utg000870l 156269 +utg000871l 490937 +utg000872l 275033 +utg000873l 689380 +utg000874l 101579 +utg000875l 346835 +utg000876l 51964 +utg000877l 1246785 +utg000878l 640954 +utg000879l 777790 +utg000880l 52646 +utg000881l 35219 +utg000882l 260776 +utg000883l 526776 +utg000884l 252670 +utg000885l 173180 +utg000886l 109610 +utg000887l 310599 +utg000888l 760025 +utg000889l 1230928 +utg000890l 80644 +utg000891l 256948 +utg000892l 1162401 +utg000893l 339656 +utg000894l 111615 +utg000895l 669474 +utg000896l 344859 +utg000897l 353635 +utg000898l 240602 +utg000899l 387745 +utg000900l 34938 +utg000901l 190524 +utg000902l 194102 +utg000903l 217553 +utg000904l 207550 +utg000905l 150093 +utg000906l 531009 +utg000907l 947399 +utg000908l 198406 +utg000909l 343681 +utg000910l 262620 +utg000911l 489280 +utg000912l 595580 +utg000913l 466675 +utg000914l 292752 +utg000915l 49405 +utg000916l 748881 +utg000917l 880190 +utg000918l 767437 +utg000919l 582979 +utg000920l 582280 +utg000921l 440676 +utg000922l 353454 +utg000923l 513506 +utg000924l 60957 +utg000925l 324483 +utg000926l 368147 +utg000927l 378734 +utg000928l 386621 +utg000929l 375614 +utg000930l 258303 +utg000931l 38361 +utg000932l 221606 +utg000933l 165324 +utg000934l 18555 +utg000935l 629354 +utg000936l 235366 +utg000937l 63801 +utg000938l 583489 +utg000939l 70103 +utg000940l 371513 +utg000941l 237529 +utg000942l 460939 +utg000943l 182132 +utg000944l 431682 +utg000945l 879848 +utg000946l 148099 +utg000947l 484541 +utg000948l 1014519 +utg000949l 312442 +utg000950c 15181 +utg000951l 409228 +utg000952l 170335 +utg000953l 107253 +utg000954l 852473 +utg000955l 320005 +utg000956l 143122 +utg000957l 170261 +utg000958l 772451 +utg000959l 67522 +utg000960l 34088 +utg000961l 252209 +utg000962l 345054 +utg000963l 664778 +utg000964l 172992 +utg000965l 88521 +utg000966l 100774 +utg000967l 171006 +utg000968l 75833 +utg000969l 149549 +utg000970l 358141 +utg000971l 246932 +utg000972l 236624 +utg000973c 111614 +utg000974l 168265 +utg000975l 375605 +utg000976l 277743 +utg000977l 765464 +utg000978l 254716 +utg000979l 312123 +utg000980l 77610 +utg000981l 15387 +utg000982l 604610 +utg000983l 903461 +utg000984l 423001 +utg000985l 329090 +utg000986l 574162 +utg000987l 314300 +utg000988l 15220 +utg000989l 784009 +utg000990l 51009 +utg000991l 820440 +utg000992l 121670 +utg000993l 262143 +utg000994l 422118 +utg000995l 100521 +utg000996l 300023 +utg000997l 281040 +utg000998l 105900 +utg000999l 585694 +utg001000l 202837 +utg001001l 123620 +utg001002l 36849 +utg001003l 680687 +utg001004l 226386 +utg001005l 227286 +utg001006l 72726 +utg001007l 90227 +utg001008l 1435974 +utg001009l 352164 +utg001010l 169307 +utg001011l 158749 +utg001012l 91592 +utg001013l 304203 +utg001014l 107548 +utg001015l 370360 +utg001016l 10589 +utg001017l 115628 +utg001018l 552871 +utg001019l 6962 +utg001020l 422926 +utg001021l 23888 +utg001022l 211458 +utg001023l 400216 +utg001024l 148841 +utg001025l 238541 +utg001026l 111091 +utg001027l 427789 +utg001028l 149508 +utg001029l 79707 +utg001030l 460815 +utg001031l 65028 +utg001032l 741892 +utg001033l 325838 +utg001034l 385216 +utg001035l 328451 +utg001036l 81810 +utg001037l 342582 +utg001038l 232360 +utg001039l 381013 +utg001040l 245084 +utg001041l 1012819 +utg001042l 267127 +utg001043l 583703 +utg001044l 43922 +utg001045l 146407 +utg001046l 90771 +utg001047l 170965 +utg001048l 156945 +utg001049l 298595 +utg001050l 376358 +utg001051l 559059 +utg001052l 258027 +utg001053l 140741 +utg001054l 185100 +utg001055l 269535 +utg001056l 120290 +utg001057l 224744 +utg001058l 72377 +utg001059l 486692 +utg001060l 104546 +utg001061l 96028 +utg001062l 111128 +utg001063l 696340 +utg001064l 395642 +utg001065l 323993 +utg001066l 367772 +utg001067l 260978 +utg001068l 722270 +utg001069l 100558 +utg001070l 140225 +utg001071l 225719 +utg001072l 368699 +utg001073l 83094 +utg001074l 331444 +utg001075l 284839 +utg001076l 426655 +utg001077l 386783 +utg001078l 233680 +utg001079l 366702 +utg001080l 225094 +utg001081l 174640 +utg001082l 80846 +utg001083l 94786 +utg001084l 203711 +utg001085l 1169456 +utg001086l 306151 +utg001087l 51423 +utg001088l 140783 +utg001089l 365064 +utg001090l 461575 +utg001091l 42687 +utg001092l 712492 +utg001093l 171801 +utg001094l 114122 +utg001095l 126789 +utg001096l 132238 +utg001097l 155435 +utg001098l 179490 +utg001099l 253630 +utg001100l 53224 +utg001101l 291131 +utg001102l 182408 +utg001103l 260685 +utg001104l 153643 +utg001105l 96297 +utg001106l 120914 +utg001107l 428740 +utg001108l 254992 +utg001109l 422663 +utg001110l 44620 +utg001111l 119540 +utg001112l 207364 +utg001113l 99779 +utg001114l 210912 +utg001115l 105773 +utg001116l 395502 +utg001117l 99313 +utg001118l 84390 +utg001119l 266271 +utg001120l 145591 +utg001121l 184783 +utg001122l 234507 +utg001123l 113765 +utg001124l 190163 +utg001125l 459658 +utg001126l 491326 +utg001127l 288680 +utg001128l 258412 +utg001129l 378915 +utg001130l 120734 +utg001131l 119039 +utg001132l 136965 +utg001133l 396942 +utg001134l 303518 +utg001135l 206981 +utg001136l 127441 +utg001137l 13034 +utg001138l 250432 +utg001139c 45615 +utg001140l 90557 +utg001141l 266573 +utg001142l 349935 +utg001143l 175605 +utg001144l 340876 +utg001145l 408077 +utg001146l 232972 +utg001147l 82818 +utg001148l 318240 +utg001149l 290430 +utg001150l 309240 +utg001151l 135883 +utg001152l 91311 +utg001153l 594340 +utg001154l 401408 +utg001155l 36480 +utg001156l 528500 +utg001157l 246658 +utg001158l 427053 +utg001159l 103381 +utg001160l 164406 +utg001161l 115643 +utg001162l 188225 +utg001163l 93258 +utg001164l 88956 +utg001165l 209920 +utg001166l 215564 +utg001167l 247220 +utg001168l 283002 +utg001169l 314269 +utg001170l 204512 +utg001171l 225465 +utg001172l 216399 +utg001173l 230419 +utg001174l 321305 +utg001175l 711121 +utg001176l 222336 +utg001177l 249862 +utg001178l 111324 +utg001179l 160048 +utg001180l 476107 +utg001181l 287859 +utg001182l 265447 +utg001183l 248382 +utg001184c 20136 +utg001185l 689554 +utg001186l 256779 +utg001187l 177570 +utg001188l 231348 +utg001189l 457162 +utg001190l 101282 +utg001191l 378642 +utg001192l 268940 +utg001193l 215700 +utg001194l 294370 +utg001195l 125395 +utg001196l 68110 +utg001197l 368428 +utg001198l 570215 +utg001199l 135080 +utg001200l 113801 +utg001201l 161803 +utg001202l 106415 +utg001203l 126106 +utg001204l 75798 +utg001205l 219202 +utg001206l 258831 +utg001207l 70198 +utg001208l 314969 +utg001209l 139600 +utg001210l 16903 +utg001211l 162719 +utg001212l 52525 +utg001213l 108241 +utg001214l 129002 +utg001215l 79100 +utg001216l 291650 +utg001217l 464984 +utg001218l 546129 +utg001219l 230975 +utg001220l 143827 +utg001221l 266580 +utg001222l 71961 +utg001223l 232641 +utg001224c 9953 +utg001225c 22464 +utg001226l 87728 +utg001227l 140430 +utg001228l 97919 +utg001229l 79046 +utg001230l 165481 +utg001231l 227359 +utg001232l 298911 +utg001233l 135117 +utg001234l 92086 +utg001235l 155501 +utg001236l 453898 +utg001237l 378520 +utg001238l 153297 +utg001239l 97867 +utg001240l 311703 +utg001241l 199038 +utg001242l 149763 +utg001243l 136273 +utg001244l 556972 +utg001245l 277131 +utg001246l 134717 +utg001247l 261928 +utg001248l 239652 +utg001249l 239147 +utg001250l 255288 +utg001251l 303552 +utg001252c 45799 +utg001253l 419107 +utg001254l 96478 +utg001255c 35399 +utg001256l 103819 +utg001257l 127253 +utg001258l 304340 +utg001259l 380840 +utg001260l 95398 +utg001261l 122837 +utg001262l 101379 +utg001263l 301582 +utg001264l 147124 +utg001265l 208261 +utg001266l 136180 +utg001267l 344378 +utg001268l 84502 +utg001269c 55043 +utg001270l 230247 +utg001271l 47879 +utg001272c 26300 +utg001273l 201218 +utg001274l 166900 +utg001275l 237749 +utg001276l 206540 +utg001277l 193580 +utg001278l 136352 +utg001279c 80020 +utg001280l 285506 +utg001281l 190427 +utg001282l 140808 +utg001283l 125990 +utg001284l 105852 +utg001285l 240041 +utg001286l 235744 +utg001287l 154720 +utg001288l 66982 +utg001289l 95127 +utg001290l 88872 +utg001291l 171576 +utg001292l 88375 +utg001293l 96265 +utg001294l 143536 +utg001295l 156430 +utg001296l 105816 +utg001297l 132431 +utg001298l 91560 +utg001299l 279777 +utg001300l 118518 +utg001301l 181558 +utg001302l 197624 +utg001303l 174303 +utg001304l 70246 +utg001305l 102923 +utg001306l 117223 +utg001307l 123676 +utg001308l 213925 +utg001309l 110249 +utg001310l 448211 +utg001311l 133553 +utg001312l 253909 +utg001313l 90451 +utg001314c 38139 +utg001315l 128303 +utg001316l 114113 +utg001317c 21444 +utg001318l 165706 +utg001319l 207880 +utg001320l 47581 +utg001321l 167282 +utg001322l 116538 +utg001323l 106984 +utg001324l 117126 +utg001325l 128009 +utg001326l 188105 +utg001327l 149161 +utg001328l 107983 +utg001329c 57673 +utg001330l 84297 +utg001331l 110154 +utg001332l 99041 +utg001333l 108484 +utg001334l 159295 +utg001335l 67267 +utg001336l 133140 +utg001337l 122552 +utg001338l 62439 +utg001339l 120577 +utg001340l 102998 +utg001341l 141444 +utg001342l 116004 +utg001343l 199227 +utg001344l 51279 +utg001345c 28457 +utg001346l 134557 +utg001347l 194197 +utg001348l 126467 +utg001349l 135781 +utg001350l 284996 +utg001351l 192258 +utg001352l 225428 +utg001353l 165037 +utg001354l 161524 +utg001355l 179716 +utg001356l 78856 +utg001357l 115792 +utg001358c 30243 +utg001359l 69857 +utg001360l 208295 +utg001361l 78678 +utg001362l 144817 +utg001363l 298591 +utg001364l 84641 +utg001365l 83984 +utg001366l 53431 +utg001367c 57287 +utg001368l 120119 +utg001369c 60873 +utg001370l 141411 +utg001371l 198329 +utg001372l 105500 +utg001373l 67968 +utg001374l 161373 +utg001375l 128957 +utg001376c 32494 +utg001377l 92939 +utg001378l 57475 +utg001379l 116025 +utg001380l 116712 +utg001381l 77824 +utg001382l 100816 +utg001383l 100933 +utg001384l 134577 +utg001385l 101548 +utg001386l 119387 +utg001387l 65970 +utg001388l 84675 +utg001389l 67099 +utg001390l 67216 +utg001391c 52022 +utg001392l 80830 +utg001393l 92614 +utg001394l 146508 +utg001395l 157139 +utg001396l 70248 +utg001397l 91249 +utg001398l 86940 +utg001399c 15191 +utg001400l 76227 +utg001401l 71737 +utg001402l 134010 +utg001403l 86346 +utg001404l 75710 +utg001405l 51574 +utg001406l 81107 +utg001407l 71440 +utg001408l 106471 +utg001409l 114483 +utg001410l 57072 +utg001411l 68723 +utg001412l 57025 +utg001413l 34933 +utg001414l 61930 +utg001415l 64010 +utg001416l 58322 diff --git a/ddRAD/iPyrad/EperRef_c88_m65_WCMWOnly_stats.txt b/ddRAD/iPyrad/EperRef_c88_m65_WCMWOnly_stats.txt new file mode 100644 index 0000000..a1568a5 --- /dev/null +++ b/ddRAD/iPyrad/EperRef_c88_m65_WCMWOnly_stats.txt @@ -0,0 +1,265 @@ + + +## The number of loci caught by each filter. +## ipyrad API location: [assembly].stats_dfs.s7_filters + + total_filters applied_order retained_loci +total_prefiltered_loci 277755 0 277755 +filtered_by_rm_duplicates 15756 15756 261999 +filtered_by_max_indels 252 252 261747 +filtered_by_max_snps 1218 0 261747 +filtered_by_max_shared_het 751 600 261147 +filtered_by_min_sample 262927 248826 12321 +filtered_by_max_alleles 28627 4237 8084 +total_filtered_loci 8084 0 8084 + + +## The number of loci recovered for each Sample. +## ipyrad API location: [assembly].stats_dfs.s7_samples + + sample_coverage +EolmJV_WCMW_NC 7955 +EolmJW_WCMW_NC 7299 +EolmJX_WCMW_NC 7941 +EolmJY_WCMW_NC 7986 +EolmKX_WCMW_NC 8054 +EolmKY_WCMW_NC 8028 +EolmKZ_WCMW_NC 8032 +EolmLA_WCMW_NC 8027 +EolmLB_WCMW_NC 8058 +EolmLC_WCMW_NC 8002 +EolmLD_WCMW_NC 8043 +EolmLE_WCMW_NC 8029 +EolmLF_WCMW_NC 8039 +EolmLG_WCMW_NC 6321 +EolmLH_WCMW_NC 7939 +EolmLI_WCMW_NC 7713 +EolmLJ_WCMW_NC 8060 +EolmLK_WCMW_NC 7769 +EolmLL_WCMW_NC 8027 +EolmLN_WCMW_NC 8042 +EolmLO_WCMW_NC 8062 +EolmLP_WCMW_NC 8028 +EolmLQ_WCMW_NC 8047 +EolmLR_WCMW_NC 8020 +EolmLS_WCMW_NC 8038 +EolmLT_WCMW_NC 8055 +EolmLU_WCMW_NC 8025 +EolmLV_WCMW_NC 8030 +EolmLW_WCMW_NC 6368 +EolmLX_WCMW_NC 8058 +EolmLY_WCMW_NC 8022 +EolmLZ_WCMW_NC 8050 +EolmMA_WCMW_NC 8056 +EolmMB_WCMW_NC 8036 +EolmMC_WCMW_NC 8038 +EolmMD_WCMW_NC 8053 +EolmMF_WCMW_NC 8032 +EolmMG_WCMW_NC 8022 +EolmMI_WCMW_NC 5269 +EolmMJ_WCMW_NC 8007 +EolmMN_WCMW_NC 8061 +EolmMO_WCMW_NC 6680 +EolmMP_WCMW_NC 7565 +EolmMQ_WCMW_NC 4079 +EolmMS_WCMW_NC 8038 +EolmMT_WCMW_NC 8057 +EolmMU_WCMW_NC 8032 +EolmMV_WCMW_NC 8051 +EolmMW_WCMW_NC 8048 +EolmMX_WCMW_NC 7857 +EolmMY_WCMW_NC 7413 +EperAA_WCMW_NC 8024 +EperE_WCMW_NC 8055 +EperG_WCMW_NC 8056 +EperH_WCMW_NC 8051 +EperI_WCMW_NC 8039 +EperJ_WCMW_NC 8032 +EperKL_WCMW_NC 7987 +EperMN_WCMW_NC 8047 +EperO_WCMW_NC 8057 +EperP_WCMW_NC 8032 +EperQ_WCMW_NC 8066 +EperR_WCMW_NC 8042 +EperS_WCMW_NC 8051 +EperT_WCMW_NC 8060 +EperU_WCMW_NC 4803 +EperW_WCMW_NC 6131 +EperX_WCMW_NC 8061 +EperY_WCMW_NC 7767 +EperZ_WCMW_NC 7609 + + +## The number of loci for which N taxa have data. +## ipyrad API location: [assembly].stats_dfs.s7_loci + + locus_coverage sum_coverage +1 0 0 +2 0 0 +3 0 0 +4 0 0 +5 0 0 +6 0 0 +7 0 0 +8 0 0 +9 0 0 +10 0 0 +11 0 0 +12 0 0 +13 0 0 +14 0 0 +15 0 0 +16 0 0 +17 0 0 +18 0 0 +19 0 0 +20 0 0 +21 0 0 +22 0 0 +23 0 0 +24 0 0 +25 0 0 +26 0 0 +27 0 0 +28 0 0 +29 0 0 +30 0 0 +31 0 0 +32 0 0 +33 0 0 +34 0 0 +35 0 0 +36 0 0 +37 0 0 +38 0 0 +39 0 0 +40 0 0 +41 0 0 +42 0 0 +43 0 0 +44 0 0 +45 0 0 +46 0 0 +47 0 0 +48 0 0 +49 0 0 +50 0 0 +51 0 0 +52 0 0 +53 0 0 +54 0 0 +55 0 0 +56 0 0 +57 0 0 +58 0 0 +59 0 0 +60 0 0 +61 0 0 +62 0 0 +63 0 0 +64 0 0 +65 1686 1686 +66 1663 3349 +67 1481 4830 +68 1309 6139 +69 1206 7345 +70 739 8084 + + +## The distribution of SNPs (var and pis) per locus. +## var = Number of loci with n variable sites (pis + autapomorphies) +## pis = Number of loci with n parsimony informative site (minor allele in >1 sample) +## ipyrad API location: [assembly].stats_dfs.s7_snps + + var sum_var pis sum_pis +0 2706 0 4776 0 +1 2479 2479 2244 2244 +2 1430 5339 702 3648 +3 715 7484 227 4329 +4 370 8964 79 4645 +5 189 9909 33 4810 +6 94 10473 12 4882 +7 46 10795 8 4938 +8 28 11019 1 4946 +9 12 11127 1 4955 +10 10 11227 0 4955 +11 2 11249 1 4966 +12 0 11249 0 4966 +13 2 11275 0 4966 +14 0 11275 0 4966 +15 1 11290 0 4966 + + +## Final Sample stats summary + + state reads_raw reads_passed_filter refseq_mapped_reads refseq_unmapped_reads clusters_total clusters_hidepth hetero_est error_est reads_consens loci_in_assembly +EolmJV_WCMW_NC 7 2051819 1849102 418614 38051 242710 80599 0.020292 0.001596 75028 7955 +EolmJW_WCMW_NC 7 1184327 1083458 329969 29132 219014 45583 0.012185 0.001792 43395 7299 +EolmJX_WCMW_NC 7 2364668 2156994 525456 49950 311256 84348 0.014059 0.001858 79760 7941 +EolmJY_WCMW_NC 7 3074505 2827866 508909 45645 267065 95466 0.020066 0.001534 89174 7986 +EolmKX_WCMW_NC 7 2157458 1978569 356630 32476 179463 83807 0.015986 0.001395 79157 8054 +EolmKY_WCMW_NC 7 1586234 1449643 299882 22499 167876 68469 0.011796 0.001288 65707 8028 +EolmKZ_WCMW_NC 7 1660643 1526538 294360 21311 160129 64799 0.009943 0.001394 62643 8032 +EolmLA_WCMW_NC 7 2842609 2597602 473629 49562 206759 93574 0.026828 0.002038 84935 8027 +EolmLB_WCMW_NC 7 2045548 1870330 349897 29593 177185 78208 0.020086 0.001423 72964 8058 +EolmLC_WCMW_NC 7 1671903 1535348 306854 28716 166014 64928 0.016089 0.001419 61282 8002 +EolmLD_WCMW_NC 7 2261484 2068367 376368 39020 183826 82619 0.023397 0.001441 76232 8043 +EolmLE_WCMW_NC 7 2763663 2528004 484501 42289 213230 95257 0.017603 0.001926 89385 8029 +EolmLF_WCMW_NC 7 2926877 2687602 491501 41298 218802 100160 0.016942 0.001738 94345 8039 +EolmLG_WCMW_NC 7 748127 684737 215587 16428 140906 31178 0.009035 0.001574 30180 6321 +EolmLH_WCMW_NC 7 1797625 1655981 343546 29959 192179 69855 0.014267 0.001434 66379 7939 +EolmLI_WCMW_NC 7 1471801 1311904 358889 31337 199985 64988 0.010909 0.002009 62365 7713 +EolmLJ_WCMW_NC 7 2931357 2690951 421029 34724 201558 97134 0.019260 0.001385 91000 8060 +EolmLK_WCMW_NC 7 1227310 1130833 243692 15560 152274 53354 0.007112 0.001222 52096 7769 +EolmLL_WCMW_NC 7 1759564 1635072 293802 20849 170607 66269 0.007871 0.001178 64672 8027 +EolmLN_WCMW_NC 7 3082393 2825847 468535 48163 213389 99570 0.027984 0.001610 90512 8042 +EolmLO_WCMW_NC 7 2777170 2538029 426076 46753 198593 91663 0.031191 0.001476 82433 8062 +EolmLP_WCMW_NC 7 2330339 2150063 391872 31855 195977 78985 0.017568 0.001644 74236 8028 +EolmLQ_WCMW_NC 7 2955543 2673880 451417 44364 210482 104233 0.022122 0.001582 96908 8047 +EolmLR_WCMW_NC 7 1600662 1474591 294198 22170 174513 62859 0.007387 0.001417 61199 8020 +EolmLS_WCMW_NC 7 12348552 11338121 1003147 122951 258695 149873 0.045580 0.001262 133863 8038 +EolmLT_WCMW_NC 7 6811462 6240526 739542 95074 245414 134238 0.047394 0.001400 116970 8055 +EolmLU_WCMW_NC 7 3114584 2856700 512804 53636 243151 96953 0.029646 0.001765 87499 8025 +EolmLV_WCMW_NC 7 3364399 3083366 505259 53849 231166 102448 0.034275 0.001496 91457 8030 +EolmLW_WCMW_NC 7 763608 703344 231070 37898 151360 29655 0.010051 0.001827 28522 6368 +EolmLX_WCMW_NC 7 3450214 3166275 475334 52397 201046 102036 0.034792 0.001417 91217 8058 +EolmLY_WCMW_NC 7 4347170 3934125 571333 75037 245708 123214 0.037467 0.001465 110583 8022 +EolmLZ_WCMW_NC 7 3582355 3280981 499162 56832 210466 105995 0.033347 0.001549 94953 8050 +EolmMA_WCMW_NC 7 3730349 3396364 496573 52018 220125 114544 0.030021 0.001390 104243 8056 +EolmMB_WCMW_NC 7 7031232 6438601 772685 101858 258860 135825 0.046583 0.001501 118952 8036 +EolmMC_WCMW_NC 7 1953702 1801754 356929 30015 197751 71820 0.010436 0.001635 69083 8038 +EolmMD_WCMW_NC 7 4040938 3709855 497039 49533 199010 112486 0.033874 0.001336 101095 8053 +EolmMF_WCMW_NC 7 4018535 3690339 523876 56347 209877 107667 0.029743 0.001593 97818 8032 +EolmMG_WCMW_NC 7 2688915 2439878 437630 40109 220801 97936 0.017341 0.001541 92449 8022 +EolmMI_WCMW_NC 7 563010 516826 174332 13368 121878 23073 0.007524 0.001532 22461 5269 +EolmMJ_WCMW_NC 7 5805459 5324136 691701 116952 254259 128199 0.042117 0.001581 113313 8007 +EolmMN_WCMW_NC 7 5316821 4895149 581104 80000 215038 120324 0.038721 0.001302 107196 8061 +EolmMO_WCMW_NC 7 777268 708757 229247 19549 149504 32263 0.009137 0.001763 31246 6680 +EolmMP_WCMW_NC 7 1174428 1078910 237733 22555 145232 46604 0.007486 0.001502 45489 7565 +EolmMQ_WCMW_NC 7 461745 423166 161231 13382 117169 16839 0.008260 0.001586 16326 4079 +EolmMS_WCMW_NC 7 4457089 4082667 595444 72263 235838 115409 0.032414 0.001951 103485 8038 +EolmMT_WCMW_NC 7 3383232 3111263 478144 52378 206771 101691 0.025203 0.001718 93290 8057 +EolmMU_WCMW_NC 7 1896544 1739889 332082 30300 184825 70689 0.016747 0.001389 66756 8032 +EolmMV_WCMW_NC 7 3743855 3432558 499563 53516 208526 106514 0.034862 0.001519 95277 8051 +EolmMW_WCMW_NC 7 3855911 3492175 524882 62658 212462 120040 0.036080 0.001608 107935 8048 +EolmMX_WCMW_NC 7 4816192 4283473 810321 111893 231041 133723 0.016889 0.001588 128284 7857 +EolmMY_WCMW_NC 7 2839998 2461527 735579 98020 265431 110452 0.012389 0.002536 105437 7413 +EperAA_WCMW_NC 7 1493453 1372985 270959 20697 160248 61226 0.008532 0.001423 59277 8024 +EperE_WCMW_NC 7 3187395 2894257 469937 40116 199675 105461 0.034172 0.001576 94691 8055 +EperG_WCMW_NC 7 4780273 4365780 569303 71279 209803 125031 0.039442 0.001444 111266 8056 +EperH_WCMW_NC 7 2285582 2077412 358285 28351 180096 87807 0.015976 0.001425 82993 8051 +EperI_WCMW_NC 7 2062254 1896607 360712 34278 183036 76430 0.012755 0.001712 72862 8039 +EperJ_WCMW_NC 7 3791514 3456737 553714 63083 224823 109402 0.032272 0.002105 97661 8032 +EperKL_WCMW_NC 7 1573080 1433357 316888 32940 179717 66220 0.018166 0.001567 61922 7987 +EperMN_WCMW_NC 7 5254781 4807394 595235 76413 214663 121716 0.044859 0.001394 106302 8047 +EperO_WCMW_NC 7 3824641 3496061 500642 68558 202551 110735 0.038566 0.001477 98004 8057 +EperP_WCMW_NC 7 5353342 4878320 603741 56578 244147 130771 0.037219 0.001349 117394 8032 +EperQ_WCMW_NC 7 5447862 4986762 599083 58077 219918 127256 0.037972 0.001379 113459 8066 +EperR_WCMW_NC 7 3009157 2777344 435511 44763 201077 93646 0.013835 0.001863 88666 8042 +EperS_WCMW_NC 7 4004514 3677287 497063 45573 210097 109598 0.028749 0.001544 99792 8051 +EperT_WCMW_NC 7 2850187 2617596 391659 34201 186275 91060 0.022450 0.001434 84320 8060 +EperU_WCMW_NC 7 543512 498565 203782 16606 132377 19405 0.016804 0.001980 18474 4803 +EperW_WCMW_NC 7 620771 575081 192973 13963 128184 26757 0.008386 0.001765 25947 6131 +EperX_WCMW_NC 7 3932315 3572287 487930 47071 205087 117471 0.034657 0.001345 105384 8061 +EperY_WCMW_NC 7 3678454 3052491 604187 77255 206894 114235 0.012446 0.001507 110816 7767 +EperZ_WCMW_NC 7 4370271 3641533 742293 121385 260762 111887 0.017340 0.001811 107572 7609 \ No newline at end of file diff --git a/ddRAD/iPyrad/params-EperRef_c88_m65_WCMWOnly.txt b/ddRAD/iPyrad/params-EperRef_c88_m65_WCMWOnly.txt new file mode 100644 index 0000000..ef8a071 --- /dev/null +++ b/ddRAD/iPyrad/params-EperRef_c88_m65_WCMWOnly.txt @@ -0,0 +1,30 @@ +------- ipyrad params file (v.0.7.23)------------------------------------------- +EperRef_c88_m65_WCMWOnly ## [0] [assembly_name]: Assembly name. Used to name output directories for assembly steps +/gpfs/ysm/project/dm733/BoleosomaProject/ddRAD/WCMW/ipyrad ## [1] [project_dir]: Project dir (made in curdir if not present) + ## [2] [raw_fastq_path]: Location of raw non-demultiplexed fastq files + ## [3] [barcodes_path]: Location of barcodes file +/gpfs/ysm/project/dm733/BoleosomaProject/ddRAD/WCMW/ipyrad/fastqs/*.fastq.gz ## [4] [sorted_fastq_path]: Location of demultiplexed/sorted fastq files +reference ## [5] [assembly_method]: Assembly method (denovo, reference, denovo+reference, denovo-reference) +/home/dm733/scratch60/Eper_genome/assemblies/v0.1/Eper_nanopore_1kb.racon.fasta ## [6] [reference_sequence]: Location of reference sequence file +ddrad ## [7] [datatype]: Datatype (see docs): rad, gbs, ddrad, etc. +TGCAG, CCG ## [8] [restriction_overhang]: Restriction overhang (cut1,) or (cut1, cut2) +5 ## [9] [max_low_qual_bases]: Max low quality base calls (Q<20) in a read +33 ## [10] [phred_Qscore_offset]: phred Q score offset (33 is default and very standard) +6 ## [11] [mindepth_statistical]: Min depth for statistical base calling +6 ## [12] [mindepth_majrule]: Min depth for majority-rule base calling +10000 ## [13] [maxdepth]: Max cluster depth within samples +0.88 ## [14] [clust_threshold]: Clustering threshold for de novo assembly +0 ## [15] [max_barcode_mismatch]: Max number of allowable mismatches in barcodes +2 ## [16] [filter_adapters]: Filter for adapters/primers (1 or 2=stricter) +35 ## [17] [filter_min_trim_len]: Min length of reads after adapter trim +2 ## [18] [max_alleles_consens]: Max alleles per site in consensus sequences +5, 5 ## [19] [max_Ns_consens]: Max N's (uncalled bases) in consensus (R1, R2) +8, 8 ## [20] [max_Hs_consens]: Max Hs (heterozygotes) in consensus (R1, R2) +65 ## [21] [min_samples_locus]: Min # samples per locus for output +20, 20 ## [22] [max_SNPs_locus]: Max # SNPs per locus (R1, R2) +8, 8 ## [23] [max_Indels_locus]: Max # of indels per locus (R1, R2) +0.5 ## [24] [max_shared_Hs_locus]: Max # heterozygous sites per locus (R1, R2) +0, 0, 0, 0 ## [25] [trim_reads]: Trim raw read edges (R1>, , , , + + + + + NanoPlot Report + + +

NanoPlot report

+

Summary statistics

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
General summary:
Mean read length: 4,286.2
Mean read quality: 10.2
Median read length: 1,845.0
Median read quality: 10.5
Number of reads: 3,991,650.0
Read length N50: 10,140.0
Total bases: 17,109,161,879.0
Number, percentage and megabases of reads above quality cutoffs
>Q5:3991650 (100.0%) 17109.2Mb
>Q7:3991649 (100.0%) 17109.2Mb
>Q10:2473495 (62.0%) 11731.4Mb
>Q12:244872 (6.1%) 789.4Mb
>Q15:0 (0.0%) 0.0Mb
Top 5 highest mean basecall quality scores and their read lengths
1:14.9 (196)
2:14.8 (649)
3:14.7 (607)
4:14.7 (363)
5:14.6 (620)
Top 5 longest reads and their mean basecall quality score
1:301857 (10.7)
2:265670 (9.4)
3:250054 (10.4)
4:238373 (10.0)
5:230377 (10.3)
+ +
+
+
+
+

Plots

+ +

Histogram of read lengths

+ + +
+
+
+
+ +

Histogram of read lengths after log transformation

+ + +
+
+
+
+ +

Weighted Histogram of read lengths

+ + +
+
+
+
+ +

Weighted Histogram of read lengths after log transformation

+ + +
+
+
+
+ +

Yield by length

+ + +
+
+
+
+ +

Read lengths vs Average read quality plot using dots

+ + +
+
+
+
+ +

Read lengths vs Average read quality plot using a kernel density estimation

+ + +
+
+
+
\ No newline at end of file diff --git a/sequencing/nanopore/QC/NanoStats.txt b/sequencing/nanopore/QC/NanoStats.txt new file mode 100644 index 0000000..c961e80 --- /dev/null +++ b/sequencing/nanopore/QC/NanoStats.txt @@ -0,0 +1,26 @@ +General summary: +Mean read length: 4,286.2 +Mean read quality: 10.2 +Median read length: 1,845.0 +Median read quality: 10.5 +Number of reads: 3,991,650.0 +Read length N50: 10,140.0 +Total bases: 17,109,161,879.0 +Number, percentage and megabases of reads above quality cutoffs +>Q5: 3991650 (100.0%) 17109.2Mb +>Q7: 3991649 (100.0%) 17109.2Mb +>Q10: 2473495 (62.0%) 11731.4Mb +>Q12: 244872 (6.1%) 789.4Mb +>Q15: 0 (0.0%) 0.0Mb +Top 5 highest mean basecall quality scores and their read lengths +1: 14.9 (196) +2: 14.8 (649) +3: 14.7 (607) +4: 14.7 (363) +5: 14.6 (620) +Top 5 longest reads and their mean basecall quality score +1: 301857 (10.7) +2: 265670 (9.4) +3: 250054 (10.4) +4: 238373 (10.0) +5: 230377 (10.3) diff --git a/sequencing/nanopore/QC/Weighted_HistogramReadlength.pdf b/sequencing/nanopore/QC/Weighted_HistogramReadlength.pdf new file mode 100644 index 0000000..147a53b Binary files /dev/null and b/sequencing/nanopore/QC/Weighted_HistogramReadlength.pdf differ diff --git a/sequencing/nanopore/QC/Weighted_LogTransformed_HistogramReadlength.pdf b/sequencing/nanopore/QC/Weighted_LogTransformed_HistogramReadlength.pdf new file mode 100644 index 0000000..32a655b Binary files /dev/null and b/sequencing/nanopore/QC/Weighted_LogTransformed_HistogramReadlength.pdf differ diff --git a/sequencing/nanopore/QC/Yield_By_Length.pdf b/sequencing/nanopore/QC/Yield_By_Length.pdf new file mode 100644 index 0000000..f5007c5 Binary files /dev/null and b/sequencing/nanopore/QC/Yield_By_Length.pdf differ