BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716439.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 = 1,133,371 number of mapped reads = 1,002,626 (88.46%) number of supplementary alignments = 5,932 (0.52%) number of secondary alignments = 0 number of mapped bases = 58,385,256 bp number of sequenced bases = 58,368,957 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,053 duplication rate = 1.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4278 >>>>>>> ACTG content number of A's = 14,972,544 bp (25.65%) number of C's = 10,745,018 bp (18.41%) number of T's = 17,983,614 bp (30.81%) number of G's = 14,666,932 bp (25.13%) number of N's = 849 bp (0%) GC percentage = 43.54% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 282,090 number of insertions = 3,202 mapped reads with insertion percentage = 0.32% number of deletions = 10,096 mapped reads with deletion percentage = 1% homopolymer indels = 43.27% >>>>>>> Coverage mean coverageData = 0.0189X std coverageData = 0.1979X There is a 1.75% of reference with a coverageData >= 1X There is a 0.1% 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 5112136 0.020510023122469974 0.2736271717113995 chr2 243199373 5254910 0.02160741590398755 0.22968047587925358 chr3 198022430 4357492 0.022005042560077664 0.16273938247893777 chr4 191154276 3361666 0.017586140735873466 0.1468341108042643 chr5 180915260 2996452 0.016562737714883754 0.136182105846623 chr6 171115067 3215582 0.018791927890254106 0.15064581377431402 chr7 159138663 3540182 0.022245895078306648 0.39199098519295883 chr8 146364022 4744650 0.032416777942874515 0.23337454560697304 chr9 141213431 2465555 0.017459776896150907 0.15281906367302595 chr10 135534747 2778568 0.02050077977420801 0.24217267473353976 chr11 135006516 1784009 0.013214243673986817 0.13543859925249188 chr12 133851895 2777385 0.02074968755578694 0.16326639794689496 chr13 115169878 1275987 0.011079172976114467 0.11095901143459463 chr14 107349540 1449352 0.013501240899588391 0.12447687135768616 chr15 102531392 1392055 0.013576866292813034 0.12698663854349138 chr16 90354753 1864435 0.020634609006125 0.15601280418699676 chr17 81195210 2481522 0.030562418645139287 0.18986068895894914 chr18 78077248 1374371 0.01760270802577468 0.2132883527083733 chr19 59128983 1178227 0.019926387030874522 0.24979088672650976 chr20 63025520 1295379 0.02055324573283965 0.156869455423225 chr21 48129895 611726 0.01270989683231181 0.12324437535092521 chr22 51304566 873265 0.017021194565801413 0.13785177413922264 chrMT 16571 5015 0.30263713716734053 0.5901084194905486 chrX 155270560 2063801 0.013291643953625207 0.13269563345392635 chrY 59373566 131534 0.0022153629781980757 0.06466104273783096