BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716837.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 = 2,085,941 number of mapped reads = 1,916,691 (91.89%) number of supplementary alignments = 11,144 (0.53%) number of secondary alignments = 0 number of mapped bases = 112,214,648 bp number of sequenced bases = 112,182,988 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 133,231 duplication rate = 5.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8557 >>>>>>> ACTG content number of A's = 28,532,693 bp (25.43%) number of C's = 22,407,915 bp (19.97%) number of T's = 34,510,291 bp (30.76%) number of G's = 26,731,201 bp (23.83%) number of N's = 888 bp (0%) GC percentage = 43.8% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 552,004 number of insertions = 7,705 mapped reads with insertion percentage = 0.4% number of deletions = 19,897 mapped reads with deletion percentage = 1.03% homopolymer indels = 42.71% >>>>>>> Coverage mean coverageData = 0.0362X std coverageData = 0.3173X There is a 2.98% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 13796163 0.05535056620781699 0.5022845876659339 chr2 243199373 11628347 0.047814050079808386 0.47585884117779004 chr3 198022430 7217582 0.0364483053763152 0.22493272819876695 chr4 191154276 4901994 0.025644176539372836 0.23272138795639102 chr5 180915260 8271056 0.04571784602360243 0.25311346711189914 chr6 171115067 4352566 0.02543648596414949 0.20806072843039142 chr7 159138663 6100583 0.038335014791471514 0.42865632000472903 chr8 146364022 5186228 0.03543376254035981 0.32701548443166456 chr9 141213431 3198566 0.022650579178973423 0.23466289617724154 chr10 135534747 5230645 0.03859264960298336 0.3009161698802522 chr11 135006516 3532960 0.02616881099279682 0.25564997660282046 chr12 133851895 4383968 0.03275237903804051 0.21556728668201233 chr13 115169878 3321324 0.02883847806107774 0.2003710051975426 chr14 107349540 2501672 0.023303984348698653 0.18872514630449397 chr15 102531392 5087691 0.04962081271655806 0.2633643133330372 chr16 90354753 3531268 0.03908226056464346 0.24538125521068002 chr17 81195210 4595950 0.05660370851925871 0.30674767171266726 chr18 78077248 2861599 0.03665086914948642 0.5062156018907573 chr19 59128983 1869930 0.031624592629979784 0.35759904097194045 chr20 63025520 3142448 0.04985992975543875 0.2725081561872878 chr21 48129895 1482041 0.030792525103160936 0.22705209329237744 chr22 51304566 1402236 0.02733160241527041 0.19655173236381598 chrMT 16571 2186 0.1319172047552954 0.4074934004696056 chrX 155270560 4323909 0.027847577802256912 0.219560970176848 chrY 59373566 291736 0.004913567091456154 0.14170404317541763