BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173858.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,430,276 number of mapped reads = 4,319,176 (97.49%) number of supplementary alignments = 413,634 (9.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,161,750 number of mapped paired reads (second in pair) = 2,157,426 number of mapped paired reads (both in pair) = 4,246,938 number of mapped paired reads (singletons) = 72,238 number of mapped bases = 510,266,156 bp number of sequenced bases = 510,001,051 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,315,125 duplication rate = 65.08% >>>>>>> Insert size mean insert size = 784,528.6308 std insert size = 8,294,329.4017 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 52.7855 >>>>>>> ACTG content number of A's = 154,128,966 bp (30.22%) number of C's = 99,576,971 bp (19.52%) number of T's = 153,551,719 bp (30.11%) number of G's = 102,736,765 bp (20.14%) number of N's = 6,630 bp (0%) GC percentage = 39.67% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 5,042,791 number of insertions = 52,125 mapped reads with insertion percentage = 1.17% number of deletions = 102,177 mapped reads with deletion percentage = 2.31% homopolymer indels = 44.01% >>>>>>> Coverage mean coverageData = 0.1648X std coverageData = 2.464X There is a 3.52% of reference with a coverageData >= 1X There is a 2.76% of reference with a coverageData >= 2X There is a 2.1% of reference with a coverageData >= 3X There is a 1.72% of reference with a coverageData >= 4X There is a 1.3% of reference with a coverageData >= 5X There is a 1.05% of reference with a coverageData >= 6X There is a 0.77% of reference with a coverageData >= 7X There is a 0.63% of reference with a coverageData >= 8X There is a 0.46% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 38020163 0.15253788675615776 1.6256884871793844 chr2 243199373 54471045 0.22397691378916507 7.3495347308512535 chr3 198022430 42200584 0.21311012090903036 1.348439970947362 chr4 191154276 23960062 0.12534410687208483 1.1753315657032701 chr5 180915260 30673707 0.16954737262075073 1.1778566846581522 chr6 171115067 26058868 0.15228856498066298 1.2522470036671718 chr7 159138663 29293340 0.18407431260120616 1.5879347219327706 chr8 146364022 30843951 0.2107345137044676 1.63019949303998 chr9 141213431 20648534 0.14622216777666142 1.3117389369265346 chr10 135534747 26975766 0.19903210502912586 2.467957389124421 chr11 135006516 17173171 0.1272025344317455 1.0445849555820335 chr12 133851895 22889900 0.17100915904104308 1.182758395329503 chr13 115169878 12860306 0.11166379806358742 0.9584605233422797 chr14 107349540 15438429 0.14381457992274582 1.0772272915032246 chr15 102531392 17396579 0.16967075800550918 1.170741579792283 chr16 90354753 16301350 0.18041496942612414 1.5031913326450521 chr17 81195210 19454726 0.2396043559712451 1.5165542368466984 chr18 78077248 9527407 0.12202539464505716 1.6259077730648464 chr19 59128983 7578993 0.1281772933588254 1.3875839130826195 chr20 63025520 21199698 0.33636688757189154 1.8113119860576614 chr21 48129895 6305542 0.13101092366812767 1.0693798755541166 chr22 51304566 3562793 0.06944397502553672 0.7224005436485964 chrMT 16571 1138857 68.72590670448373 61.366365157516114 chrX 155270560 15420335 0.09931267717460412 0.8983415632455883 chrY 59373566 872050 0.014687512621357457 0.5651551085694556