BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525210.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 = 2,047,002 number of mapped reads = 1,880,733 (91.88%) number of supplementary alignments = 5,386 (0.26%) number of secondary alignments = 0 number of mapped bases = 108,499,096 bp number of sequenced bases = 108,465,815 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,042 duplication rate = 2.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4576 >>>>>>> ACTG content number of A's = 25,698,939 bp (23.69%) number of C's = 20,641,889 bp (19.03%) number of T's = 36,151,559 bp (33.33%) number of G's = 25,970,814 bp (23.94%) number of N's = 2,614 bp (0%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 552,840 number of insertions = 7,791 mapped reads with insertion percentage = 0.41% number of deletions = 21,235 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.89% >>>>>>> Coverage mean coverageData = 0.035X std coverageData = 0.3476X There is a 3.12% 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 0.01% 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 11559005 0.04637502989410807 0.6509099097922874 chr2 243199373 8940847 0.03676344593207483 0.4388937579199637 chr3 198022430 8023588 0.04051858165764353 0.2291636021870276 chr4 191154276 4985243 0.026079683407134454 0.19056101776328035 chr5 180915260 4898038 0.027073658684181753 0.18159736858609604 chr6 171115067 6883367 0.04022653948994451 0.25034097983203785 chr7 159138663 8029255 0.05045445807220336 0.6630150814722171 chr8 146364022 6191885 0.04230469288415701 0.30549390027740064 chr9 141213431 3625583 0.025674491259970872 0.2328636125163491 chr10 135534747 5787659 0.0427024001454033 0.37367875772374415 chr11 135006516 4914386 0.036401102299388276 0.26453228226081943 chr12 133851895 4776518 0.03568509807052041 0.21109433255608526 chr13 115169878 3354228 0.029124177764606123 0.18905293255140468 chr14 107349540 3975278 0.037031160077630514 0.21686563068214237 chr15 102531392 3072277 0.02996425719061729 0.1938944443426505 chr16 90354753 2938498 0.03252178665133421 0.2248669787855637 chr17 81195210 1962676 0.024172312627801566 0.17852563193338233 chr18 78077248 2062927 0.026421615167583776 0.41976032069729885 chr19 59128983 1757169 0.02971755830808049 0.4335294909165911 chr20 63025520 1966261 0.03119785445641702 0.19819046571856277 chr21 48129895 1375399 0.028576812810416477 0.19820991868676907 chr22 51304566 886144 0.01727222485421668 0.14268426081726368 chrMT 16571 116657 7.039828616257317 4.50593121192976 chrX 155270560 6095282 0.0392558769672757 0.23876445315093497 chrY 59373566 320926 0.005405200017799166 0.14274302176891626