BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524789.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 = 1,648,687 number of mapped reads = 1,501,948 (91.1%) number of supplementary alignments = 5,798 (0.35%) number of secondary alignments = 0 number of mapped bases = 88,295,125 bp number of sequenced bases = 88,265,042 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,979 duplication rate = 2.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4409 >>>>>>> ACTG content number of A's = 22,614,049 bp (25.62%) number of C's = 16,239,952 bp (18.4%) number of T's = 27,153,973 bp (30.76%) number of G's = 22,255,156 bp (25.21%) number of N's = 1,912 bp (0%) GC percentage = 43.61% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 481,621 number of insertions = 5,279 mapped reads with insertion percentage = 0.35% number of deletions = 18,724 mapped reads with deletion percentage = 1.24% homopolymer indels = 45.72% >>>>>>> Coverage mean coverageData = 0.0285X std coverageData = 0.2924X There is a 2.59% of reference with a coverageData >= 1X There is a 0.19% 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 8926020 0.035811425320380647 0.5593011631500202 chr2 243199373 7060419 0.029031402971585785 0.3540730352732843 chr3 198022430 5432535 0.02743393766049634 0.18089002716024505 chr4 191154276 4941283 0.02584971209328323 0.18150501551172865 chr5 180915260 3891024 0.02150743944982861 0.1581240632403687 chr6 171115067 5343935 0.03123006695839356 0.21315777827629334 chr7 159138663 6434576 0.0404337693851305 0.4838775064848702 chr8 146364022 6033038 0.04121940568154105 0.3136759645520892 chr9 141213431 2818699 0.019960558850807896 0.197637698381668 chr10 135534747 6547644 0.0483097076205853 0.3386042423399801 chr11 135006516 3443645 0.025507250331532148 0.22503935690496354 chr12 133851895 3898119 0.0291226284095567 0.1862044440421585 chr13 115169878 2736318 0.0237589728105816 0.1671173449304673 chr14 107349540 2622883 0.02443310888896217 0.17081406164682728 chr15 102531392 2303208 0.022463442220700562 0.16193322698934096 chr16 90354753 2213206 0.024494627305328365 0.1868750828677297 chr17 81195210 1471438 0.018122226668297305 0.14897174077437195 chr18 78077248 1866922 0.023911216747803405 0.4078530344298204 chr19 59128983 1715314 0.029009699016808728 0.37548261729260407 chr20 63025520 1511457 0.023981666474152057 0.16839674689837272 chr21 48129895 1111214 0.023087812678585732 0.17126443613992998 chr22 51304566 919568 0.017923706829524686 0.1430779770310872 chrMT 16571 3209 0.19365155995413674 0.45520703905128773 chrX 155270560 4794099 0.030875775807081524 0.2025825095454684 chrY 59373566 255352 0.004300769133523157 0.11800861562089258