BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524796.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 = 1,319,069 number of mapped reads = 1,195,032 (90.6%) number of supplementary alignments = 4,028 (0.31%) number of secondary alignments = 0 number of mapped bases = 67,505,325 bp number of sequenced bases = 67,483,859 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,789 duplication rate = 2.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3756 >>>>>>> ACTG content number of A's = 16,633,654 bp (24.65%) number of C's = 11,086,470 bp (16.43%) number of T's = 22,118,382 bp (32.78%) number of G's = 17,637,308 bp (26.14%) number of N's = 8,045 bp (0.01%) GC percentage = 42.56% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 344,412 number of insertions = 4,885 mapped reads with insertion percentage = 0.41% number of deletions = 13,317 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.33% >>>>>>> Coverage mean coverageData = 0.0218X std coverageData = 0.2077X There is a 1.97% of reference with a coverageData >= 1X There is a 0.15% 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 5393353 0.021638273069738912 0.2709296877595051 chr2 243199373 5650573 0.023234323881254414 0.32505299897061474 chr3 198022430 4400602 0.022222745170837464 0.16444563277230032 chr4 191154276 4277463 0.022377019701092116 0.1864594504692405 chr5 180915260 3959882 0.021888048581418726 0.16032601389109155 chr6 171115067 3877817 0.022662042963171678 0.17799920421502505 chr7 159138663 3784564 0.023781549553423105 0.24627208055658642 chr8 146364022 3340742 0.022824885203004328 0.1944582617533722 chr9 141213431 2861447 0.020263277931403 0.18031577151808456 chr10 135534747 3327140 0.02454824370609553 0.2453368207531344 chr11 135006516 3057273 0.02264537364996516 0.1884743028120229 chr12 133851895 3056748 0.02283679285974995 0.16559917580090908 chr13 115169878 2114395 0.01835892367620638 0.14708545794755779 chr14 107349540 2024140 0.018855600126465377 0.15316748611770825 chr15 102531392 1960648 0.01912241667410504 0.15188321844946123 chr16 90354753 2046312 0.022647530230092045 0.17828756790085115 chr17 81195210 1921520 0.023665435436400744 0.17269751157033716 chr18 78077248 1774238 0.022724135973644973 0.26431106161443096 chr19 59128983 1477281 0.02498404208981575 0.2274258978891274 chr20 63025520 1437134 0.02280241400626286 0.17228085773723018 chr21 48129895 906337 0.018831061235433818 0.1598764252327006 chr22 51304566 851559 0.016598113314124908 0.1418051656574433 chrMT 16571 13302 0.8027276567497436 1.0457151311382205 chrX 155270560 3760783 0.02422083748522579 0.17969440698397438 chrY 59373566 230072 0.003874990429242535 0.11216038299354206