BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716955.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 = 2,216,833 number of mapped reads = 1,975,827 (89.13%) number of supplementary alignments = 7,599 (0.34%) number of secondary alignments = 0 number of mapped bases = 113,344,943 bp number of sequenced bases = 113,311,430 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,966 duplication rate = 2.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8308 >>>>>>> ACTG content number of A's = 28,728,661 bp (25.35%) number of C's = 23,701,759 bp (20.92%) number of T's = 34,026,628 bp (30.03%) number of G's = 26,853,403 bp (23.7%) number of N's = 979 bp (0%) GC percentage = 44.62% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 577,604 number of insertions = 8,615 mapped reads with insertion percentage = 0.43% number of deletions = 21,271 mapped reads with deletion percentage = 1.07% homopolymer indels = 40.13% >>>>>>> Coverage mean coverageData = 0.0366X std coverageData = 0.2907X There is a 3.25% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9483723 0.038048944319380454 0.3822424520154948 chr2 243199373 8956919 0.03682953162876781 0.40764926545723423 chr3 198022430 6573874 0.033197623117744796 0.20451268347974133 chr4 191154276 6920495 0.03620371536967345 0.22502575935717223 chr5 180915260 6485404 0.0358477444080726 0.20824489176266517 chr6 171115067 6103260 0.035667578004688505 0.2549390490685704 chr7 159138663 6465670 0.0406291587356116 0.43027281134857637 chr8 146364022 5861336 0.040046289517788734 0.28310183702489666 chr9 141213431 3772540 0.02671516422541989 0.21888669655491522 chr10 135534747 4993955 0.03684630775899851 0.3727581239434636 chr11 135006516 3993188 0.02957774275132024 0.24379205028930653 chr12 133851895 5679318 0.042429866233869906 0.22916451321381268 chr13 115169878 3459806 0.030040893157844622 0.19277667247369204 chr14 107349540 3820691 0.035591125961042774 0.2141155107824665 chr15 102531392 4134700 0.040326186149896415 0.23131993494281375 chr16 90354753 3917958 0.04336194688064722 0.24541027574270058 chr17 81195210 4995184 0.06152067344859383 0.2890397117562608 chr18 78077248 2089664 0.02676405807745683 0.36342524198035703 chr19 59128983 2964072 0.050128919010834334 0.38281434554009963 chr20 63025520 3633845 0.057656723816003425 0.2806995134797281 chr21 48129895 1398903 0.029065157943934845 0.20347822133212046 chr22 51304566 1033489 0.02014419145461634 0.1559604020909547 chrMT 16571 134988 8.146038259610162 6.0711206655377055 chrX 155270560 6141485 0.03955344142508406 0.2360503633404065 chrY 59373566 330476 0.00556604600774695 0.14957278399060187