BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716176.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 = 3,471,991 number of mapped reads = 3,136,197 (90.33%) number of supplementary alignments = 78,419 (2.26%) number of secondary alignments = 0 number of mapped bases = 234,741,524 bp number of sequenced bases = 234,656,115 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,942 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7562 >>>>>>> ACTG content number of A's = 61,795,085 bp (26.33%) number of C's = 46,693,993 bp (19.9%) number of T's = 71,925,419 bp (30.65%) number of G's = 54,214,416 bp (23.1%) number of N's = 27,202 bp (0.01%) GC percentage = 43% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,704,503 number of insertions = 20,869 mapped reads with insertion percentage = 0.66% number of deletions = 50,287 mapped reads with deletion percentage = 1.58% homopolymer indels = 39.02% >>>>>>> Coverage mean coverageData = 0.0758X std coverageData = 0.5921X There is a 6.11% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 19879459 0.07975690860966801 0.8085108506978831 chr2 243199373 21533431 0.08854229652968719 0.9726851576156572 chr3 198022430 18915575 0.09552238602465388 0.3903192731659727 chr4 191154276 10169379 0.05319985099365499 0.29414392817239077 chr5 180915260 15403493 0.08514203279480127 0.36059631553326177 chr6 171115067 17675141 0.10329389053741246 0.4563461511236213 chr7 159138663 10801834 0.06787686786082901 0.7824237349352583 chr8 146364022 14807682 0.10117023157507929 0.8030573788444839 chr9 141213431 10456627 0.07404838849924976 0.5877218281043669 chr10 135534747 11740220 0.08662147722163085 0.58453331161386 chr11 135006516 9567586 0.07086758686521472 0.48687156899845613 chr12 133851895 9198937 0.06872474237290402 0.3174428554750083 chr13 115169878 10727137 0.09314186301386895 0.3647658980901399 chr14 107349540 5819590 0.05421159699426751 0.3326206703746673 chr15 102531392 5200736 0.0507233530975567 0.271424633442746 chr16 90354753 5576212 0.06171465047334035 0.3583253265648121 chr17 81195210 6132279 0.07552513257863364 0.37440336305868743 chr18 78077248 5935696 0.07602337623375251 1.2199612030246645 chr19 59128983 3714061 0.06281286792975958 0.7185011336664359 chr20 63025520 4408893 0.0699540916124135 0.3812717645179114 chr21 48129895 5185332 0.10773620013091656 0.4151938093308169 chr22 51304566 3188182 0.06214226624585422 0.30248119677112756 chrMT 16571 10427 0.6292317904773399 1.5569955416802155 chrX 155270560 8204081 0.05283732473174567 0.38830054486380616 chrY 59373566 489534 0.008244982287235367 0.22288263646718678