BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716167.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 = 3,545,466 number of mapped reads = 3,241,750 (91.43%) number of supplementary alignments = 19,186 (0.54%) number of secondary alignments = 0 number of mapped bases = 188,337,459 bp number of sequenced bases = 188,286,592 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 172,145 duplication rate = 3.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0185 >>>>>>> ACTG content number of A's = 49,352,554 bp (26.21%) number of C's = 33,835,971 bp (17.97%) number of T's = 58,541,173 bp (31.09%) number of G's = 46,553,806 bp (24.72%) number of N's = 3,088 bp (0%) GC percentage = 42.7% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 985,631 number of insertions = 12,041 mapped reads with insertion percentage = 0.37% number of deletions = 30,874 mapped reads with deletion percentage = 0.95% homopolymer indels = 41.48% >>>>>>> Coverage mean coverageData = 0.0608X std coverageData = 0.5101X There is a 5.08% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 13775513 0.0552677178685946 0.9246966314583766 chr2 243199373 16342340 0.06719729495355237 0.5662631342088026 chr3 198022430 12191724 0.061567389108395446 0.2828205888859164 chr4 191154276 12048313 0.06302926229073735 0.33643996942815485 chr5 180915260 10257962 0.056700369001487214 0.28199202647984223 chr6 171115067 9393567 0.0548962003445319 0.3167628405954278 chr7 159138663 11674043 0.07335767927119005 0.7084862372881894 chr8 146364022 8704976 0.05947483460108796 0.5271102033351293 chr9 141213431 8651389 0.06126463282377156 0.5230717282996312 chr10 135534747 6721827 0.049594861456449986 0.48304312461806415 chr11 135006516 7206384 0.053378045841876255 0.4185993019965956 chr12 133851895 13192877 0.09856324409900959 0.4305437368924419 chr13 115169878 7307644 0.06345100061667167 0.28783310731813955 chr14 107349540 6656108 0.06200406634252927 0.33888816000402444 chr15 102531392 4779520 0.04661518688832392 0.24882023535716574 chr16 90354753 5412796 0.059906046115803115 0.32910413443431114 chr17 81195210 5704801 0.07026031461708147 0.3269715658503012 chr18 78077248 5658234 0.07246969053007606 1.0681855108544938 chr19 59128983 3327096 0.056268446220358634 0.7087480696165852 chr20 63025520 5598062 0.08882214696522932 0.36097312710771706 chr21 48129895 2380134 0.049452299864772196 0.3224982038674772 chr22 51304566 1933662 0.03768986175616416 0.22027524333233042 chrMT 16571 11504 0.694224850642689 1.0292223341590323 chrX 155270560 8892757 0.05727265361830343 0.3753283572452707 chrY 59373566 514226 0.008660857594438576 0.19769490729489017