BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525002.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 = 977,859 number of mapped reads = 891,845 (91.2%) number of supplementary alignments = 2,808 (0.29%) number of secondary alignments = 0 number of mapped bases = 51,386,559 bp number of sequenced bases = 51,369,587 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,865 duplication rate = 1.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5795 >>>>>>> ACTG content number of A's = 12,106,293 bp (23.57%) number of C's = 9,604,382 bp (18.7%) number of T's = 16,457,473 bp (32.04%) number of G's = 13,200,885 bp (25.7%) number of N's = 554 bp (0%) GC percentage = 44.39% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 254,653 number of insertions = 3,330 mapped reads with insertion percentage = 0.37% number of deletions = 10,098 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.64% >>>>>>> Coverage mean coverageData = 0.0166X std coverageData = 0.1756X There is a 1.56% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5397203 0.0216537193702719 0.3089863679093248 chr2 243199373 4870142 0.020025306561954007 0.19867619065250197 chr3 198022430 2766147 0.013968856962314825 0.12575878356900294 chr4 191154276 3282240 0.017170633420724526 0.14425507939299842 chr5 180915260 2229430 0.012323062189447148 0.11716654987348371 chr6 171115067 3380708 0.019756927658509463 0.1780397014628378 chr7 159138663 3225942 0.02027126494081454 0.22587075618923125 chr8 146364022 3197443 0.02184582629192849 0.1776014050711156 chr9 141213431 1420531 0.010059460987106814 0.13603049333285636 chr10 135534747 2614696 0.019291702370610543 0.18338136359885085 chr11 135006516 2138067 0.015836768945285573 0.15888162549411217 chr12 133851895 2783223 0.020793302926342582 0.15178426611470675 chr13 115169878 1397475 0.012134032129477466 0.11437332664990768 chr14 107349540 1191464 0.011098920405248127 0.11203490395945653 chr15 102531392 1431555 0.013962114159144548 0.12703691738752332 chr16 90354753 1562332 0.01729108816223536 0.1442350519673349 chr17 81195210 1384227 0.017048136213946612 0.16631300316038983 chr18 78077248 1020247 0.013067148575728488 0.2116977579017785 chr19 59128983 1283525 0.021707205753902448 0.202720976792668 chr20 63025520 1053973 0.01672295603431753 0.13626353705029198 chr21 48129895 728470 0.015135499464521997 0.13299117372254304 chr22 51304566 701545 0.01367412405359788 0.12137992156736649 chrMT 16571 3078 0.185746183090942 0.4295995168553961 chrX 155270560 2185664 0.014076486875554515 0.13724079012039817 chrY 59373566 137232 0.0023113316117815796 0.07002113231492126