BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716732.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 = 537,161 number of mapped reads = 499,679 (93.02%) number of supplementary alignments = 2,708 (0.5%) number of secondary alignments = 0 number of mapped bases = 29,890,946 bp number of sequenced bases = 29,881,811 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,630 duplication rate = 1.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1735 >>>>>>> ACTG content number of A's = 7,871,882 bp (26.34%) number of C's = 5,884,595 bp (19.69%) number of T's = 8,741,715 bp (29.25%) number of G's = 7,383,244 bp (24.71%) number of N's = 375 bp (0%) GC percentage = 44.4% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 142,607 number of insertions = 1,809 mapped reads with insertion percentage = 0.36% number of deletions = 5,600 mapped reads with deletion percentage = 1.11% homopolymer indels = 42.21% >>>>>>> Coverage mean coverageData = 0.0097X std coverageData = 0.121X There is a 0.92% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 2376530 0.00953470041705533 0.16065003149835164 chr2 243199373 2840775 0.011680848371266154 0.13540426589248641 chr3 198022430 1930857 0.009750698443605606 0.1019329178931124 chr4 191154276 1594152 0.008339609415799833 0.0977076607588268 chr5 180915260 1524829 0.008428415601867969 0.09436067631740994 chr6 171115067 1586428 0.009271118130117672 0.10222755481527275 chr7 159138663 1905686 0.011975003208365524 0.1967687869986624 chr8 146364022 2395253 0.01636503949037421 0.15614171086527565 chr9 141213431 1356611 0.009606812825049198 0.10482037617670721 chr10 135534747 1362486 0.01005266937193604 0.13700825859231844 chr11 135006516 987873 0.0073172245997370974 0.09492627827369195 chr12 133851895 1700636 0.012705356169966812 0.11785268219692858 chr13 115169878 969851 0.008421047385324138 0.09457423035633178 chr14 107349540 940386 0.00876003753718926 0.09714150096943183 chr15 102531392 683866 0.006669820692573841 0.08405796199161347 chr16 90354753 894754 0.009902677726317286 0.10406610298753348 chr17 81195210 1221317 0.015041737067987138 0.1280614602356387 chr18 78077248 647805 0.008296975323720427 0.12945888944033332 chr19 59128983 572233 0.009677707462007253 0.13908963527730608 chr20 63025520 650014 0.010313504751725967 0.10624652169364408 chr21 48129895 224075 0.004655630351988094 0.07331372847775998 chr22 51304566 450803 0.008786800769350627 0.09645963689990039 chrMT 16571 12330 0.7440709673526039 0.9330394505518554 chrX 155270560 994880 0.006407396225015225 0.08546309879777984 chrY 59373566 66516 0.0011202965306143142 0.04219496284370111