BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081222.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,144,599 number of mapped reads = 1,898,793 (88.54%) number of supplementary alignments = 25,705 (1.2%) number of secondary alignments = 0 number of mapped bases = 124,305,718 bp number of sequenced bases = 124,260,178 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,829 duplication rate = 3.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2234 >>>>>>> ACTG content number of A's = 35,370,704 bp (28.47%) number of C's = 23,833,461 bp (19.18%) number of T's = 38,265,698 bp (30.79%) number of G's = 26,774,832 bp (21.55%) number of N's = 15,483 bp (0.01%) GC percentage = 40.73% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,088,319 number of insertions = 9,022 mapped reads with insertion percentage = 0.47% number of deletions = 28,225 mapped reads with deletion percentage = 1.47% homopolymer indels = 48.36% >>>>>>> Coverage mean coverageData = 0.0402X std coverageData = 0.2998X There is a 3.3% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 13878965 0.05568276999398128 0.4502172472641227 chr2 243199373 8161876 0.03356043191772538 0.3186764942388619 chr3 198022430 7726071 0.03901614074728807 0.23521326096875547 chr4 191154276 5895580 0.030841999056301517 0.20993879397270254 chr5 180915260 7290488 0.04029780572407214 0.2361621182366954 chr6 171115067 9535410 0.055725133777962406 0.31819109800538725 chr7 159138663 8501578 0.053422454604887565 0.43077673535437777 chr8 146364022 7028927 0.04802359831297885 0.35185925158298426 chr9 141213431 3517031 0.024905782510163642 0.22582101183836126 chr10 135534747 3930075 0.028996807733739305 0.3153784989363158 chr11 135006516 6670971 0.049412215037087544 0.33253006593004714 chr12 133851895 4452561 0.033264833493765626 0.21518216799455211 chr13 115169878 3231720 0.028060462128821566 0.19914978962426613 chr14 107349540 3944715 0.03674645461918141 0.22961200418407995 chr15 102531392 3050483 0.029751697899507695 0.20765396712027043 chr16 90354753 3748387 0.041485222144318185 0.24578615797537093 chr17 81195210 1858708 0.022891843004039278 0.20309214009022108 chr18 78077248 3469462 0.04443627418835254 0.35717915764721675 chr19 59128983 2735116 0.046256773941131375 0.3709925097214916 chr20 63025520 3137488 0.049781231475757755 0.26569620388147136 chr21 48129895 1842818 0.03828842759785784 0.23724823687415617 chr22 51304566 634642 0.012370088073642413 0.1275277166634901 chrMT 16571 26423 1.594532617222859 1.617541634122648 chrX 155270560 9727457 0.06264843122868881 0.32063317031025934 chrY 59373566 308766 0.005200395071436336 0.1019229896094449