BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524619.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,720,063 number of mapped reads = 1,598,599 (92.94%) number of supplementary alignments = 3,706 (0.22%) number of secondary alignments = 0 number of mapped bases = 93,202,247 bp number of sequenced bases = 93,173,273 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,640 duplication rate = 3.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3856 >>>>>>> ACTG content number of A's = 23,071,119 bp (24.76%) number of C's = 18,732,922 bp (20.11%) number of T's = 30,064,068 bp (32.27%) number of G's = 21,304,592 bp (22.87%) number of N's = 572 bp (0%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 440,429 number of insertions = 6,680 mapped reads with insertion percentage = 0.42% number of deletions = 17,400 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.21% >>>>>>> Coverage mean coverageData = 0.0301X std coverageData = 0.2622X There is a 2.65% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9386438 0.03765863435902934 0.4269907684261809 chr2 243199373 8380857 0.03446084953516718 0.3095265849455624 chr3 198022430 6013198 0.03036624689435434 0.19473144845003845 chr4 191154276 4303693 0.022514238708424183 0.1886863307635255 chr5 180915260 5820221 0.03217097883285246 0.2003075186796664 chr6 171115067 6044327 0.0353231723305815 0.2257648507741803 chr7 159138663 5743914 0.036093768112152605 0.3556556750277191 chr8 146364022 8242511 0.05631514416842139 0.34448512283019445 chr9 141213431 3420154 0.024219750032133985 0.24394241953593612 chr10 135534747 3931209 0.029005174591870526 0.2523691757532504 chr11 135006516 4710136 0.034888212358579786 0.26881536976203174 chr12 133851895 3130799 0.023390023727344316 0.1755022760241516 chr13 115169878 2318784 0.02013359777979447 0.15986968233224294 chr14 107349540 1698828 0.015825200555121148 0.1478421459652641 chr15 102531392 2381789 0.023229851400047314 0.17679441885151595 chr16 90354753 2744669 0.03037658682991475 0.2029394913710256 chr17 81195210 2034240 0.02505369466991957 0.181846608245913 chr18 78077248 2487755 0.03186273932195971 0.385806592946514 chr19 59128983 1820975 0.030796656861153862 0.31443119064519365 chr20 63025520 1716146 0.027229382637382445 0.18734605908240062 chr21 48129895 821153 0.01706118411436385 0.15580416597517077 chr22 51304566 1643513 0.032034439195918744 0.20008050170744018 chrMT 16571 4511 0.27222255747993485 0.5520958713285339 chrX 155270560 4178277 0.026909653703831558 0.20714276913099078 chrY 59373566 224150 0.0037752490729628736 0.10499017444925143