BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085123.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 = 2,401,855 number of mapped reads = 2,169,633 (90.33%) number of supplementary alignments = 20,804 (0.87%) number of secondary alignments = 0 number of mapped bases = 147,504,380 bp number of sequenced bases = 147,440,895 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,742 duplication rate = 3.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2577 >>>>>>> ACTG content number of A's = 41,531,142 bp (28.17%) number of C's = 27,482,868 bp (18.64%) number of T's = 46,398,976 bp (31.47%) number of G's = 32,004,464 bp (21.71%) number of N's = 23,445 bp (0.02%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,344,283 number of insertions = 11,627 mapped reads with insertion percentage = 0.53% number of deletions = 38,893 mapped reads with deletion percentage = 1.77% homopolymer indels = 46.61% >>>>>>> Coverage mean coverageData = 0.0476X std coverageData = 0.4204X There is a 4.14% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.06% 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 11806109 0.0473664175946025 0.7923077101962391 chr2 243199373 12699999 0.05222052525604168 0.4617021216125056 chr3 198022430 10043505 0.05071902713243141 0.249470429068008 chr4 191154276 9694913 0.05071774067978474 0.2687841448451787 chr5 180915260 9180807 0.050746448917576105 0.25234226602383947 chr6 171115067 8686477 0.050763951721446016 0.3048731984306183 chr7 159138663 8180087 0.0514022604299497 0.5343723744109956 chr8 146364022 7663883 0.05236179557842432 0.6761417939780487 chr9 141213431 6245511 0.044227457372663086 0.36226612040080836 chr10 135534747 6908903 0.05097514218992123 0.3708737867405665 chr11 135006516 6728115 0.0498354834962188 0.37460476459800474 chr12 133851895 6653792 0.04971010683113601 0.252211361702416 chr13 115169878 4868163 0.04226941179880385 0.22924749568759278 chr14 107349540 4449770 0.04145122559444596 0.24212204577717228 chr15 102531392 4164765 0.040619413418282665 0.2250865011420059 chr16 90354753 3929261 0.04348704267942606 0.2559379652912071 chr17 81195210 3680837 0.045333179137045154 0.2707345706447209 chr18 78077248 4023504 0.05153234909099255 0.663407741643188 chr19 59128983 2592902 0.04385162518354155 0.5865233992030648 chr20 63025520 2908431 0.046146878280417206 0.24644258736125596 chr21 48129895 1951133 0.04053889999136711 0.2436109601987978 chr22 51304566 1526682 0.029757234473048656 0.1894455114409734 chrMT 16571 7560 0.4562186953110856 0.7255275128348748 chrX 155270560 8539603 0.05499821086495727 0.3002764257384695 chrY 59373566 369668 0.006226137739478205 0.1537391577170187