BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716981.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 = 1,605,992 number of mapped reads = 1,426,020 (88.79%) number of supplementary alignments = 6,058 (0.38%) number of secondary alignments = 0 number of mapped bases = 82,190,135 bp number of sequenced bases = 82,168,987 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,174 duplication rate = 2.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7295 >>>>>>> ACTG content number of A's = 20,920,714 bp (25.46%) number of C's = 15,253,899 bp (18.56%) number of T's = 25,113,233 bp (30.56%) number of G's = 20,879,420 bp (25.41%) number of N's = 1,721 bp (0%) GC percentage = 43.97% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 388,388 number of insertions = 4,013 mapped reads with insertion percentage = 0.28% number of deletions = 12,330 mapped reads with deletion percentage = 0.86% homopolymer indels = 43.06% >>>>>>> Coverage mean coverageData = 0.0265X std coverageData = 0.2142X There is a 2.41% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 9107786 0.03654067525873887 0.31856032427297765 chr2 243199373 6839764 0.028124102112713916 0.23585530791396053 chr3 198022430 5370242 0.027119362185384757 0.17759907164987657 chr4 191154276 5195908 0.027181751351458127 0.18962847941275418 chr5 180915260 4131060 0.022834226366532043 0.16498782921672686 chr6 171115067 4250440 0.02483965950233944 0.1788114237308617 chr7 159138663 3516725 0.022098495322912196 0.19087183009800707 chr8 146364022 5132575 0.035067190214272737 0.22629842564136476 chr9 141213431 2957938 0.020946576958391444 0.2123296476090123 chr10 135534747 3807722 0.028094065059198436 0.22344779837941398 chr11 135006516 3184940 0.023591009488756823 0.21399528061762413 chr12 133851895 3603547 0.026921897519642884 0.18007603144048653 chr13 115169878 2504589 0.021746910246792133 0.15746885914264308 chr14 107349540 2219708 0.020677387159740043 0.164471958795672 chr15 102531392 2320363 0.02263075683201492 0.1621698709534745 chr16 90354753 2350779 0.02601721461183121 0.1856148798096117 chr17 81195210 1818082 0.022391493291291444 0.16828680311614058 chr18 78077248 1983277 0.02540147162973777 0.385983031716234 chr19 59128983 1509188 0.025523659015072187 0.23194487415350631 chr20 63025520 3657006 0.05802420987561864 0.2706086408026247 chr21 48129895 1050800 0.02183258450906656 0.17493580841829745 chr22 51304566 944424 0.018408186125188155 0.1468081328174228 chrMT 16571 2323 0.1401846599481021 0.3640862145215579 chrX 155270560 4495905 0.028955295839726475 0.19942354250807537 chrY 59373566 235044 0.003958731399087601 0.09800523890014366