BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618656.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 52,608,431 number of mapped reads = 43,847,013 (83.35%) number of supplementary alignments = 96,031 (0.18%) number of secondary alignments = 0 number of mapped bases = 4,252,921,779 bp number of sequenced bases = 4,250,228,529 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,230,430 duplication rate = 32.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.1048 >>>>>>> ACTG content number of A's = 1,107,943,809 bp (26.07%) number of C's = 1,007,481,707 bp (23.7%) number of T's = 1,155,399,388 bp (27.18%) number of G's = 978,531,328 bp (23.02%) number of N's = 872,297 bp (0.02%) GC percentage = 46.73% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 34,857,606 number of insertions = 677,877 mapped reads with insertion percentage = 1.52% number of deletions = 1,868,309 mapped reads with deletion percentage = 4.17% homopolymer indels = 53.48% >>>>>>> Coverage mean coverageData = 1.3738X std coverageData = 19.9868X There is a 19.53% of reference with a coverageData >= 1X There is a 13.22% of reference with a coverageData >= 2X There is a 10.01% of reference with a coverageData >= 3X There is a 7.97% of reference with a coverageData >= 4X There is a 6.55% of reference with a coverageData >= 5X There is a 5.5% of reference with a coverageData >= 6X There is a 4.7% of reference with a coverageData >= 7X There is a 4.06% of reference with a coverageData >= 8X There is a 3.55% of reference with a coverageData >= 9X There is a 3.13% of reference with a coverageData >= 10X There is a 2.78% of reference with a coverageData >= 11X There is a 2.49% of reference with a coverageData >= 12X There is a 2.25% of reference with a coverageData >= 13X There is a 2.04% of reference with a coverageData >= 14X There is a 1.85% of reference with a coverageData >= 15X There is a 1.7% of reference with a coverageData >= 16X There is a 1.56% of reference with a coverageData >= 17X There is a 1.43% of reference with a coverageData >= 18X There is a 1.33% of reference with a coverageData >= 19X There is a 1.23% of reference with a coverageData >= 20X There is a 1.14% of reference with a coverageData >= 21X There is a 1.07% of reference with a coverageData >= 22X There is a 1% of reference with a coverageData >= 23X There is a 0.93% of reference with a coverageData >= 24X There is a 0.88% of reference with a coverageData >= 25X There is a 0.82% of reference with a coverageData >= 26X There is a 0.78% of reference with a coverageData >= 27X There is a 0.73% of reference with a coverageData >= 28X There is a 0.69% of reference with a coverageData >= 29X There is a 0.65% of reference with a coverageData >= 30X There is a 0.62% of reference with a coverageData >= 31X There is a 0.59% of reference with a coverageData >= 32X There is a 0.56% of reference with a coverageData >= 33X There is a 0.53% of reference with a coverageData >= 34X There is a 0.51% of reference with a coverageData >= 35X There is a 0.48% of reference with a coverageData >= 36X There is a 0.46% of reference with a coverageData >= 37X There is a 0.44% of reference with a coverageData >= 38X There is a 0.42% of reference with a coverageData >= 39X There is a 0.4% of reference with a coverageData >= 40X There is a 0.38% of reference with a coverageData >= 41X There is a 0.37% of reference with a coverageData >= 42X There is a 0.35% of reference with a coverageData >= 43X There is a 0.34% of reference with a coverageData >= 44X There is a 0.33% of reference with a coverageData >= 45X There is a 0.31% of reference with a coverageData >= 46X There is a 0.3% of reference with a coverageData >= 47X There is a 0.29% of reference with a coverageData >= 48X There is a 0.28% of reference with a coverageData >= 49X There is a 0.27% of reference with a coverageData >= 50X There is a 0.26% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 393947115 1.5805261123100671 19.857813144633248 chr2 243199373 360403665 1.481926785230651 25.37434553430634 chr3 198022430 267988873 1.3533258479860084 26.208355736973633 chr4 191154276 195751282 1.0240486694631932 14.742556051746115 chr5 180915260 241362450 1.3341188023608401 20.430471503493113 chr6 171115067 222151162 1.2982559975270909 16.974181143588428 chr7 159138663 218225221 1.371289772617984 22.769315297301894 chr8 146364022 208726644 1.4260789034616717 20.31583832692998 chr9 141213431 201050021 1.4237315783369076 20.335564193934022 chr10 135534747 221892992 1.6371668292559693 20.06189804730561 chr11 135006516 233133102 1.7268285184101781 19.606230982826844 chr12 133851895 207028723 1.5466999776133166 28.351284166592826 chr13 115169878 108061208 0.938276655984649 16.407490802870278 chr14 107349540 128935946 1.2010852212315022 17.03808285382396 chr15 102531392 142912984 1.3938461305587269 13.166105840356117 chr16 90354753 170884324 1.891259931837786 18.042405935447093 chr17 81195210 168218577 2.0717795667995684 21.554531536693524 chr18 78077248 104826374 1.3425982176011122 15.792255877114094 chr19 59128983 127579372 2.1576452955397523 17.732882943966953 chr20 63025520 134720872 2.137560657968391 19.951754811051973 chr21 48129895 57640932 1.1976118377154157 25.93522956913332 chr22 51304566 96587552 1.882630719456822 15.806446131393953 chrMT 16571 3661 0.22092812745157203 1.1652487831596252 chrX 155270560 10159541 0.06543121245907789 5.803952520421423 chrY 59373566 30729186 0.5175566850742972 6.914364240775778