BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231780.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,352,198 number of mapped reads = 1,162,598 (85.98%) number of supplementary alignments = 9,253 (0.68%) number of secondary alignments = 0 number of mapped bases = 76,167,397 bp number of sequenced bases = 76,137,075 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,456 duplication rate = 1.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8585 >>>>>>> ACTG content number of A's = 22,193,505 bp (29.15%) number of C's = 14,339,318 bp (18.83%) number of T's = 21,031,390 bp (27.62%) number of G's = 18,567,526 bp (24.39%) number of N's = 5,336 bp (0.01%) GC percentage = 43.22% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 538,040 number of insertions = 6,373 mapped reads with insertion percentage = 0.54% number of deletions = 17,847 mapped reads with deletion percentage = 1.52% homopolymer indels = 42.71% >>>>>>> Coverage mean coverageData = 0.0246X std coverageData = 5.6213X There is a 2.19% of reference with a coverageData >= 1X There is a 0.11% 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 6419618 0.025755675048047322 0.5864659011193057 chr2 243199373 8676515 0.03567655168255718 20.031967875421135 chr3 198022430 6929711 0.03499457611948303 0.19564224918690803 chr4 191154276 2630260 0.01375988052707751 0.13359962832933345 chr5 180915260 3877829 0.021434504751008842 0.15535914164673495 chr6 171115067 5820721 0.03401641422961311 0.24961989799398565 chr7 159138663 4835462 0.030385211920499797 0.42236534617451166 chr8 146364022 4831962 0.03301331798602802 0.3578390480843558 chr9 141213431 3418286 0.02420652182864957 0.22837710228777633 chr10 135534747 3094651 0.022832897603741423 0.2430372177355873 chr11 135006516 2549787 0.01888639952756058 0.22834168255517287 chr12 133851895 2681701 0.02003483775855396 0.15016009944869885 chr13 115169878 2230261 0.019364967982339967 0.14454500205654477 chr14 107349540 3006260 0.028004405049150652 0.22005005726360444 chr15 102531392 1385885 0.013516689600780998 0.12217237900155002 chr16 90354753 1879353 0.02079971376823973 0.17324267063335586 chr17 81195210 1642755 0.02023216640489014 0.1622750995032013 chr18 78077248 1592002 0.020390088544104422 0.44263469957776036 chr19 59128983 1672436 0.028284538565461207 0.36874322601018483 chr20 63025520 1768515 0.028060300018151376 0.17948746453806533 chr21 48129895 1243558 0.025837538187024923 0.17902564908499055 chr22 51304566 690955 0.013467709677146474 0.12039368878921133 chrMT 16571 59943 3.6173435519884136 2.668271475561165 chrX 155270560 3041323 0.019587248220139093 0.1617892453969287 chrY 59373566 187648 0.00316046369860958 0.08303140374691192