BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506012.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 8,195,582 number of mapped reads = 5,620,656 (68.58%) number of supplementary alignments = 276 (0%) number of secondary alignments = 0 number of mapped bases = 263,440,100 bp number of sequenced bases = 263,382,482 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 490,121 duplication rate = 6.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7041 >>>>>>> ACTG content number of A's = 78,863,116 bp (29.94%) number of C's = 51,676,920 bp (19.62%) number of T's = 79,367,408 bp (30.13%) number of G's = 52,595,858 bp (19.97%) number of N's = 879,180 bp (0.33%) GC percentage = 39.59% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 2,086,650 number of insertions = 12,353 mapped reads with insertion percentage = 0.22% number of deletions = 41,191 mapped reads with deletion percentage = 0.73% homopolymer indels = 47.11% >>>>>>> Coverage mean coverageData = 0.0851X std coverageData = 0.7787X There is a 5.79% of reference with a coverageData >= 1X There is a 1.66% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 25482983 0.10223839321948971 1.5009757299638848 chr2 243199373 16089626 0.06615817220877457 0.5395445831723206 chr3 198022430 16444513 0.0830436885356876 0.4039391895209795 chr4 191154276 10984677 0.05746498184534465 0.33311564323616943 chr5 180915260 18227917 0.10075389439232489 0.44954821308135184 chr6 171115067 18228764 0.10652927483001833 0.6041972961087675 chr7 159138663 17116033 0.10755420887254784 1.0982321217112958 chr8 146364022 16658145 0.11381311317066704 1.233591891145875 chr9 141213431 12997043 0.09203829202336992 0.5846775736766396 chr10 135534747 8040767 0.05932624052487441 0.7267007430342282 chr11 135006516 13428024 0.09946204374313311 0.6434589470623402 chr12 133851895 7322716 0.054707600516227285 0.37562726114198763 chr13 115169878 8260549 0.07172490883423528 0.36797830151117317 chr14 107349540 9373108 0.08731390930971851 1.3860223287420674 chr15 102531392 8729629 0.08514103661052412 0.399762757462737 chr16 90354753 7869727 0.08709809654396376 0.49240402739575995 chr17 81195210 3667968 0.04517468456575209 0.34332994861236205 chr18 78077248 7878002 0.10090009832313762 1.0312163220709936 chr19 59128983 5903555 0.0998419844291927 0.9399596481565655 chr20 63025520 6142336 0.09745791863359478 0.4573059126466089 chr21 48129895 3995909 0.08302343065572863 0.4323234019827641 chr22 51304566 1345501 0.026225755423016344 0.21811570694139096 chrMT 16571 142266 8.585239273429485 5.933151418191996 chrX 155270560 18306832 0.11790278852604125 0.5537232187025601 chrY 59373566 803510 0.013533126846381435 0.19911756614998907