BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549057.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 3,159,665 number of mapped reads = 2,749,864 (87.03%) number of secondary alignments = 0 number of mapped bases = 108,946,936 bp number of sequenced bases = 108,936,217 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,165 duplication rate = 2.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1854 >>>>>>> ACTG content number of A's = 31,833,051 bp (29.22%) number of C's = 22,217,882 bp (20.4%) number of T's = 32,610,144 bp (29.94%) number of G's = 22,274,229 bp (20.45%) number of N's = 911 bp (0%) GC percentage = 40.84% >>>>>>> Mismatches and indels general error rate = 0.0025 number of mismatches = 268,017 number of insertions = 2,800 mapped reads with insertion percentage = 0.1% number of deletions = 8,036 mapped reads with deletion percentage = 0.29% homopolymer indels = 42.5% >>>>>>> Coverage mean coverageData = 0.0352X std coverageData = 0.358X There is a 3.17% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% 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 8826920 0.035413833532635414 0.6435523346966264 chr2 243199373 9469416 0.038936843805103066 0.3061783562044292 chr3 198022430 7500514 0.03787709301416006 0.2117898487793486 chr4 191154276 7708521 0.04032617611964903 0.22580275891065182 chr5 180915260 6894449 0.0381087200714854 0.21410546551894166 chr6 171115067 6640340 0.03880628466223842 0.2273565340042599 chr7 159138663 6263603 0.039359404445920225 0.41605110943482493 chr8 146364022 5732929 0.03916897692248441 0.7864667490672546 chr9 141213431 4634840 0.03282152389598125 0.29223651414558593 chr10 135534747 5222837 0.03853504075969537 0.2916948397182551 chr11 135006516 5124659 0.03795860490170711 0.2624714798920742 chr12 133851895 5023573 0.03753083211858898 0.2170264891752551 chr13 115169878 3625376 0.0314785086426852 0.18984878473469427 chr14 107349540 3309591 0.030830043612669417 0.2159968613095616 chr15 102531392 2973179 0.028997743442320572 0.18296501187962189 chr16 90354753 2853673 0.0315829871174569 0.20916753553175102 chr17 81195210 2655051 0.03269960136811026 0.20322892062330755 chr18 78077248 2991752 0.038317846448686306 0.5346855213657389 chr19 59128983 1989046 0.03363910385538003 0.5652556763772985 chr20 63025520 2160612 0.03428154182623166 0.2062364090205349 chr21 48129895 1392113 0.028924081384345424 0.2190209977606632 chr22 51304566 1110532 0.02164587066188222 0.18506683102545646 chrMT 16571 3981 0.2402389716975439 0.5189434598350641 chrX 155270560 3797908 0.024459936255784742 0.2119544023618684 chrY 59373566 1041521 0.017541829978681086 0.21491637343492226