BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524812.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 = 1,851,110 number of mapped reads = 1,665,952 (90%) number of supplementary alignments = 6,445 (0.35%) number of secondary alignments = 0 number of mapped bases = 94,632,442 bp number of sequenced bases = 94,603,002 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,209 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4635 >>>>>>> ACTG content number of A's = 22,648,569 bp (23.94%) number of C's = 18,097,083 bp (19.13%) number of T's = 31,683,234 bp (33.49%) number of G's = 22,162,418 bp (23.43%) number of N's = 11,698 bp (0.01%) GC percentage = 42.56% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 487,622 number of insertions = 6,469 mapped reads with insertion percentage = 0.39% number of deletions = 18,552 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.13% >>>>>>> Coverage mean coverageData = 0.0306X std coverageData = 0.2681X There is a 2.68% of reference with a coverageData >= 1X There is a 0.27% 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 7514365 0.03014782859858953 0.35245573309899747 chr2 243199373 8163815 0.033568404800122575 0.4544525272150285 chr3 198022430 6181848 0.03121791809140005 0.20101030940076858 chr4 191154276 6169596 0.032275479937472075 0.23104952681961669 chr5 180915260 5540651 0.030625669719624535 0.19556572546946246 chr6 171115067 5480184 0.03202630893982001 0.2273067311502654 chr7 159138663 5204840 0.03270631977095346 0.3124011123718669 chr8 146364022 4711146 0.032187869229229026 0.25020080381095927 chr9 141213431 3953106 0.027993838631397604 0.2265764259619335 chr10 135534747 4680438 0.034533122343896064 0.314954907366042 chr11 135006516 4248303 0.031467392284976824 0.2337243435201587 chr12 133851895 4161089 0.03108726252997763 0.20029337087023777 chr13 115169878 2954511 0.025653504642941447 0.17979440335383617 chr14 107349540 2831619 0.026377560630441454 0.18802868630686156 chr15 102531392 2783965 0.02715231838459776 0.185692325825407 chr16 90354753 2834871 0.031374896238164696 0.22230143289227774 chr17 81195210 2658241 0.03273888940000278 0.2140141735168148 chr18 78077248 2421218 0.03101054483887547 0.34487390409924246 chr19 59128983 2075149 0.03509529328451328 0.2947635643184732 chr20 63025520 2038966 0.03235143478387802 0.21053207319718906 chr21 48129895 1264777 0.026278407630018725 0.20131788543895132 chr22 51304566 1160605 0.02262186566396449 0.169499694524437 chrMT 16571 20077 1.2115744372699293 1.3639416865297378 chrX 155270560 5250129 0.033812778159620215 0.223386123260481 chrY 59373566 328933 0.005540058011674758 0.15464037535086983