BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717038.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 = 1,769,600 number of mapped reads = 1,534,458 (86.71%) number of supplementary alignments = 7,564 (0.43%) number of secondary alignments = 0 number of mapped bases = 87,181,573 bp number of sequenced bases = 87,155,123 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,610 duplication rate = 1.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1649 >>>>>>> ACTG content number of A's = 23,000,018 bp (26.39%) number of C's = 16,534,859 bp (18.97%) number of T's = 26,525,584 bp (30.43%) number of G's = 21,093,422 bp (24.2%) number of N's = 1,240 bp (0%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 442,202 number of insertions = 6,937 mapped reads with insertion percentage = 0.45% number of deletions = 16,690 mapped reads with deletion percentage = 1.08% homopolymer indels = 39.6% >>>>>>> Coverage mean coverageData = 0.0282X std coverageData = 0.2534X There is a 2.54% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% 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 6459601 0.025916087888101992 0.30029323288770954 chr2 243199373 8685686 0.03571426148372513 0.34780137923202326 chr3 198022430 6255990 0.031592330222389456 0.1996220263638934 chr4 191154276 5047226 0.026403939820838745 0.1822854102507536 chr5 180915260 4808907 0.026580991564780106 0.17684894470550191 chr6 171115067 4925367 0.028783946886453898 0.1999166554545985 chr7 159138663 4355883 0.02737161993122941 0.4952646058539724 chr8 146364022 7203325 0.04921513430397533 0.27986802230982444 chr9 141213431 3613434 0.025588458366966525 0.20148629914546387 chr10 135534747 4142548 0.030564472149713754 0.31158658184566584 chr11 135006516 2962135 0.021940681737168892 0.19724251835850068 chr12 133851895 4073165 0.030430387257498297 0.19594419021581555 chr13 115169878 2371664 0.020592745613570936 0.15471073555813156 chr14 107349540 2829719 0.026359861439555307 0.1810412304715195 chr15 102531392 2046833 0.01996298850599824 0.1570420286568338 chr16 90354753 2644235 0.029265034900820327 0.19411192474286743 chr17 81195210 3554230 0.043773887646820546 0.23719618888691157 chr18 78077248 2004722 0.025676135511333596 0.3052519086319281 chr19 59128983 1741360 0.029450193655453198 0.3061788235846341 chr20 63025520 1898713 0.030126098126600144 0.1925120909368563 chr21 48129895 898686 0.018672095586329453 0.15323123023029814 chr22 51304566 1239668 0.02416291758515217 0.17035219850632893 chrMT 16571 63551 3.8350733208617465 3.143849676409364 chrX 155270560 3166652 0.020394413467691493 0.1771964763419397 chrY 59373566 188273 0.0031709902686323406 0.08282265842829935