BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080684.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 = 1,227,567 number of mapped reads = 1,136,947 (92.62%) number of supplementary alignments = 10,614 (0.86%) number of secondary alignments = 0 number of mapped bases = 75,895,260 bp number of sequenced bases = 75,867,154 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,299 duplication rate = 2.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0653 >>>>>>> ACTG content number of A's = 20,942,541 bp (27.6%) number of C's = 13,881,497 bp (18.3%) number of T's = 24,189,882 bp (31.88%) number of G's = 16,849,505 bp (22.21%) number of N's = 3,729 bp (0%) GC percentage = 40.51% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 510,227 number of insertions = 5,769 mapped reads with insertion percentage = 0.5% number of deletions = 17,290 mapped reads with deletion percentage = 1.51% homopolymer indels = 48.67% >>>>>>> Coverage mean coverageData = 0.0245X std coverageData = 0.2039X There is a 2.18% of reference with a coverageData >= 1X There is a 0.22% 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% 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 9265462 0.03717327548804783 0.24192802334352087 chr2 243199373 5074556 0.020865826821025564 0.27041222423766603 chr3 198022430 4821505 0.02434827711184031 0.17080988224624843 chr4 191154276 3308725 0.01730918642908098 0.14625527375654787 chr5 180915260 3524186 0.019479760855994125 0.15246485446576274 chr6 171115067 4728107 0.027631155355828486 0.20997083346353762 chr7 159138663 4657822 0.029268952699445513 0.3492785677671589 chr8 146364022 8887819 0.06072406919782513 0.2955846573674466 chr9 141213431 2465392 0.01745862261501174 0.16304790428774982 chr10 135534747 3378580 0.024927777376527658 0.18205449534001467 chr11 135006516 3170458 0.023483740592194824 0.17630469578588048 chr12 133851895 2373104 0.017729326880280626 0.1455660339369724 chr13 115169878 1629496 0.01414863007843075 0.13120672400660668 chr14 107349540 1543666 0.014379810104449445 0.13351542902145602 chr15 102531392 1396601 0.013621203933328049 0.13175308742422012 chr16 90354753 1822783 0.02017362606259352 0.15828967492065282 chr17 81195210 1203542 0.014822820213162821 0.13557350631453713 chr18 78077248 2366997 0.0303160915712603 0.23115218161832296 chr19 59128983 1200135 0.02029689906893883 0.17418726602473628 chr20 63025520 1904661 0.030220472595862757 0.19274382065823412 chr21 48129895 1087487 0.022594834250105885 0.16719643953960117 chr22 51304566 690389 0.013456677520671357 0.12585721861969681 chrMT 16571 14676 0.8856435942308852 1.128352017068188 chrX 155270560 5234037 0.033709139710708845 0.20760311295662703 chrY 59373566 145074 0.002443410591171162 0.057252858029037235