BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525237.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 = 1,889,064 number of mapped reads = 1,741,974 (92.21%) number of supplementary alignments = 6,655 (0.35%) number of secondary alignments = 0 number of mapped bases = 101,115,447 bp number of sequenced bases = 101,083,986 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,650 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6521 >>>>>>> ACTG content number of A's = 24,733,280 bp (24.47%) number of C's = 18,727,509 bp (18.53%) number of T's = 32,785,518 bp (32.43%) number of G's = 24,835,717 bp (24.57%) number of N's = 1,962 bp (0%) GC percentage = 43.1% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 506,822 number of insertions = 8,324 mapped reads with insertion percentage = 0.48% number of deletions = 19,590 mapped reads with deletion percentage = 1.12% homopolymer indels = 41.1% >>>>>>> Coverage mean coverageData = 0.0327X std coverageData = 0.307X There is a 2.91% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% 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 8717219 0.03497371025607194 0.4958990447798047 chr2 243199373 7999989 0.03289477641868756 0.46100797414520167 chr3 198022430 5829651 0.02943934684570834 0.19266072220203964 chr4 191154276 6360822 0.03327585515272491 0.2402025366692236 chr5 180915260 5653472 0.031249282122469933 0.19353122917581345 chr6 171115067 5474161 0.031991110402919694 0.23096034581881147 chr7 159138663 5650616 0.03550749951945996 0.38004675684447714 chr8 146364022 5278675 0.03606538634200692 0.41733805340015984 chr9 141213431 3333259 0.02360440488128923 0.207928613996534 chr10 135534747 4473619 0.033007174167669344 0.325726224482532 chr11 135006516 3515982 0.0260430540996999 0.22975714164401226 chr12 133851895 4945092 0.03694450496946644 0.21225122088312276 chr13 115169878 2993334 0.025990597992992578 0.177019012806339 chr14 107349540 3346719 0.031175904433311964 0.19772055019086707 chr15 102531392 3641138 0.035512421405534025 0.20816856759463756 chr16 90354753 3389457 0.037512769250777546 0.22534915400912892 chr17 81195210 4318766 0.05318991107972995 0.2648236445278963 chr18 78077248 1871709 0.02397252782270195 0.3531654223325276 chr19 59128983 2596890 0.04391907095713112 0.3794610108466065 chr20 63025520 3409405 0.0540956266604385 0.2674255235572545 chr21 48129895 1331152 0.02765748813705079 0.22492842843697364 chr22 51304566 937855 0.01828014683917217 0.1483104665299976 chrMT 16571 114605 6.915997827530022 4.809681545022003 chrX 155270560 5562286 0.03582318502618913 0.22876230430188074 chrY 59373566 369574 0.006224554543346782 0.26359559121670095