BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089817.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 18,400,750 number of mapped reads = 14,765,760 (80.25%) number of supplementary alignments = 736 (0%) number of secondary alignments = 0 number of mapped bases = 692,288,323 bp number of sequenced bases = 692,158,376 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,548,620 duplication rate = 12.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8807 >>>>>>> ACTG content number of A's = 204,623,682 bp (29.56%) number of C's = 140,920,923 bp (20.36%) number of T's = 198,828,689 bp (28.73%) number of G's = 147,604,266 bp (21.33%) number of N's = 180,816 bp (0.03%) GC percentage = 41.68% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 3,656,163 number of insertions = 28,192 mapped reads with insertion percentage = 0.19% number of deletions = 86,694 mapped reads with deletion percentage = 0.59% homopolymer indels = 46.04% >>>>>>> Coverage mean coverageData = 0.2236X std coverageData = 1.4211X There is a 11.51% of reference with a coverageData >= 1X There is a 4.7% of reference with a coverageData >= 2X There is a 2.34% of reference with a coverageData >= 3X There is a 1.28% of reference with a coverageData >= 4X There is a 0.75% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 55784483 0.22380880246633367 2.1130672009124534 chr2 243199373 71024912 0.29204397661008774 1.9670258350628236 chr3 198022430 60235123 0.3041833341808804 1.032317229501716 chr4 191154276 33839909 0.1770293069457677 0.7824336833164913 chr5 180915260 32588898 0.18013349454324637 0.774519098485839 chr6 171115067 36591927 0.21384398020309925 0.9635492781187519 chr7 159138663 48947250 0.30757610424312787 2.7739301675681634 chr8 146364022 61983367 0.4234877270590446 2.1373582882743998 chr9 141213431 21681758 0.15353892222900525 1.0962391411035501 chr10 135534747 20852314 0.15385216309143218 1.0679735312342866 chr11 135006516 27781993 0.2057826083001801 1.1715482134534132 chr12 133851895 26974403 0.20152425186061057 0.8453973270143849 chr13 115169878 21854873 0.18976205740184945 0.7759527863108433 chr14 107349540 24920871 0.23214697519896219 0.8976353266249896 chr15 102531392 18876305 0.1841026892524779 0.766679776368463 chr16 90354753 15411221 0.17056347882440673 0.8062421530035412 chr17 81195210 14059480 0.17315651994742054 0.8418523451070756 chr18 78077248 25847807 0.33105427844997815 1.7479816005463469 chr19 59128983 12114385 0.2048806589485904 1.4103923496621373 chr20 63025520 16811034 0.266733761181185 0.9991440298364931 chr21 48129895 9817534 0.20397995881769532 0.9414543748216574 chr22 51304566 5624550 0.10963059311329132 0.5955515019570903 chrMT 16571 690191 41.65053406553618 28.19172196731563 chrX 155270560 26058213 0.16782455734042565 0.9896973545010119 chrY 59373566 1915522 0.03226220234102159 1.1685412170111533