BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716642.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 = 940,026 number of mapped reads = 860,687 (91.56%) number of supplementary alignments = 2,869 (0.31%) number of secondary alignments = 0 number of mapped bases = 49,635,808 bp number of sequenced bases = 49,620,051 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,278 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.37 >>>>>>> ACTG content number of A's = 12,470,416 bp (25.13%) number of C's = 9,594,886 bp (19.34%) number of T's = 15,714,695 bp (31.67%) number of G's = 11,839,132 bp (23.86%) number of N's = 922 bp (0%) GC percentage = 43.2% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 254,493 number of insertions = 3,406 mapped reads with insertion percentage = 0.39% number of deletions = 9,737 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.17% >>>>>>> Coverage mean coverageData = 0.016X std coverageData = 0.1794X There is a 1.49% of reference with a coverageData >= 1X There is a 0.08% 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 4191625 0.016816908953659136 0.25192021131336706 chr2 243199373 3880253 0.015955028798532306 0.2577904372419913 chr3 198022430 2820033 0.014240977650865107 0.12687735377651235 chr4 191154276 3051374 0.015962886438386552 0.1548809096747445 chr5 180915260 2810728 0.015536157646403074 0.13191827890767502 chr6 171115067 2596065 0.015171457695189402 0.14517188060927555 chr7 159138663 2821891 0.01773227791916286 0.21470439767199032 chr8 146364022 2590987 0.01770234901033261 0.23174318999875934 chr9 141213431 1645313 0.011651250085411494 0.13177209219085187 chr10 135534747 2235529 0.016494139322073623 0.19613472373130816 chr11 135006516 1769557 0.013107196988921632 0.14374316649795824 chr12 133851895 2433406 0.018179839740035057 0.14380800666517649 chr13 115169878 1502927 0.013049653486652126 0.12399236326397585 chr14 107349540 1666471 0.015523783334330077 0.13397409288097784 chr15 102531392 1824994 0.017799368216906683 0.14073038583774583 chr16 90354753 1719322 0.019028572852166394 0.15113942056337468 chr17 81195210 2177542 0.026818601737713346 0.177510506330496 chr18 78077248 919658 0.011778821917493814 0.20101854181756715 chr19 59128983 1301350 0.022008665361283146 0.22328615488834744 chr20 63025520 1626846 0.025812496271351668 0.17439291804681614 chr21 48129895 639997 0.01329728643704708 0.1444039532329174 chr22 51304566 475609 0.009270305492887319 0.10178023317837677 chrMT 16571 45593 2.751372880333112 2.314165319467967 chrX 155270560 2697616 0.017373647650913347 0.14644347004138045 chrY 59373566 191122 0.0032189745854240928 0.14274414307536287