BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716357.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 = 1,531,959 number of mapped reads = 1,385,030 (90.41%) number of supplementary alignments = 7,930 (0.52%) number of secondary alignments = 0 number of mapped bases = 80,273,222 bp number of sequenced bases = 80,250,647 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,462 duplication rate = 3.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6951 >>>>>>> ACTG content number of A's = 20,623,215 bp (25.7%) number of C's = 16,070,704 bp (20.03%) number of T's = 24,625,288 bp (30.69%) number of G's = 18,930,869 bp (23.59%) number of N's = 571 bp (0%) GC percentage = 43.62% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 397,807 number of insertions = 5,238 mapped reads with insertion percentage = 0.38% number of deletions = 14,417 mapped reads with deletion percentage = 1.03% homopolymer indels = 42.54% >>>>>>> Coverage mean coverageData = 0.0259X std coverageData = 0.2402X There is a 2.28% of reference with a coverageData >= 1X There is a 0.24% 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 9508944 0.03815013162996292 0.37515313300383885 chr2 243199373 8282524 0.03405651872301496 0.33773205288247143 chr3 198022430 5049568 0.025499979977015735 0.17703517940965988 chr4 191154276 3367266 0.017615436444644327 0.17060546306306298 chr5 180915260 5879633 0.032499375674556144 0.20133492849055526 chr6 171115067 2955506 0.017272038352999036 0.16089268209486585 chr7 159138663 5373502 0.03376616278345885 0.36206670384287426 chr8 146364022 3587622 0.02451163852275117 0.234148081398826 chr9 141213431 2197460 0.015561267681400644 0.17535593933474786 chr10 135534747 3599894 0.02656067229756219 0.22379046189339075 chr11 135006516 3397939 0.02516870370908616 0.2136616914353605 chr12 133851895 3039641 0.022708987422255023 0.16875798576555973 chr13 115169878 2372321 0.020598450230189528 0.1604744996528622 chr14 107349540 1696373 0.015802331337423522 0.14518960885178986 chr15 102531392 3543047 0.03455572903955113 0.20730330252650017 chr16 90354753 2404462 0.026611350484240712 0.1872398064381052 chr17 81195210 3061179 0.03770147278392408 0.23197171877446315 chr18 78077248 2619457 0.03354955594746372 0.3585757073275994 chr19 59128983 1064981 0.018011150301705678 0.2740851715120897 chr20 63025520 2131698 0.03382277528213968 0.20807251028123788 chr21 48129895 1044071 0.021692775353031626 0.1795830621636585 chr22 51304566 905743 0.017654237636470796 0.14681844427494875 chrMT 16571 43570 2.6292921368656086 2.17721281075356 chrX 155270560 2940917 0.018940596337129204 0.16684323285054625 chrY 59373566 205904 0.003467940598346409 0.09715075689102831