BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525041.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 = 1,048,767 number of mapped reads = 962,102 (91.74%) number of supplementary alignments = 3,869 (0.37%) number of secondary alignments = 0 number of mapped bases = 55,891,953 bp number of sequenced bases = 55,874,193 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,939 duplication rate = 2.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3478 >>>>>>> ACTG content number of A's = 13,791,007 bp (24.68%) number of C's = 10,895,247 bp (19.5%) number of T's = 17,477,210 bp (31.28%) number of G's = 13,710,127 bp (24.54%) number of N's = 602 bp (0%) GC percentage = 44.04% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 277,765 number of insertions = 4,279 mapped reads with insertion percentage = 0.44% number of deletions = 10,815 mapped reads with deletion percentage = 1.12% homopolymer indels = 41.31% >>>>>>> Coverage mean coverageData = 0.0181X std coverageData = 0.184X There is a 1.67% of reference with a coverageData >= 1X There is a 0.09% 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 4481251 0.017978896028507788 0.309338155703685 chr2 243199373 4690041 0.01928475777772667 0.2018748965627469 chr3 198022430 3738527 0.018879310793226807 0.14627316261791568 chr4 191154276 3623257 0.01895462176320869 0.15810174239164926 chr5 180915260 3309785 0.018294670112405112 0.1434735278392665 chr6 171115067 3206092 0.01873646813345782 0.16783697743994103 chr7 159138663 3049451 0.019162225838230146 0.20785372549407594 chr8 146364022 2856218 0.019514481502838178 0.19885223414633443 chr9 141213431 2338410 0.01655940220020573 0.1571812761919098 chr10 135534747 2720545 0.02007267553316051 0.19415504222955282 chr11 135006516 2575056 0.01907356827132699 0.17673372813030433 chr12 133851895 2511814 0.01876562151025206 0.14614607968004414 chr13 115169878 1757754 0.015262271963160367 0.1320053082522399 chr14 107349540 1717062 0.01599505689544641 0.13623277989262267 chr15 102531392 1615605 0.0157571741540386 0.1347153726381642 chr16 90354753 1642381 0.01817702938106643 0.1487169094218432 chr17 81195210 1534535 0.018899329159934433 0.1561072790499393 chr18 78077248 1495814 0.01915812913897785 0.25161261034094046 chr19 59128983 1165409 0.019709606708439412 0.21171734298464628 chr20 63025520 1209013 0.019182911937894363 0.14961624085992722 chr21 48129895 727708 0.015119667308644658 0.14403270250219652 chr22 51304566 669146 0.013042620806888805 0.12115081977784306 chrMT 16571 234 0.014121054854866937 0.11799004476926338 chrX 155270560 3083002 0.01985567643988661 0.1596134149361777 chrY 59373566 173843 0.0029279528199468432 0.09896384831275579