BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124923.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 3,623,998 number of mapped reads = 3,582,793 (98.86%) number of supplementary alignments = 38,753 (1.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,795,481 number of mapped paired reads (second in pair) = 1,787,312 number of mapped paired reads (both in pair) = 3,568,656 number of mapped paired reads (singletons) = 14,137 number of mapped bases = 484,251,774 bp number of sequenced bases = 483,933,479 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 492,059 duplication rate = 13.33% >>>>>>> Insert size mean insert size = 66,865.5619 std insert size = 2,451,935.7628 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 53.8077 >>>>>>> ACTG content number of A's = 139,689,869 bp (28.87%) number of C's = 99,687,446 bp (20.6%) number of T's = 139,131,690 bp (28.75%) number of G's = 105,403,537 bp (21.78%) number of N's = 20,937 bp (0%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0136 number of mismatches = 6,423,298 number of insertions = 83,408 mapped reads with insertion percentage = 2.23% number of deletions = 171,539 mapped reads with deletion percentage = 4.63% homopolymer indels = 46.54% >>>>>>> Coverage mean coverageData = 0.1564X std coverageData = 1.5785X There is a 8.21% of reference with a coverageData >= 1X There is a 4.74% of reference with a coverageData >= 2X There is a 1.06% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 30217218 0.12123226766203322 2.897052105974194 chr2 243199373 37407866 0.1538156350427762 1.4969924996405626 chr3 198022430 40879704 0.20643976543465303 0.728731318651169 chr4 191154276 22810521 0.11933042502277061 0.7439874672460823 chr5 180915260 24145624 0.1334637221868404 0.5289300115152834 chr6 171115067 30377237 0.17752520296766153 1.1147027038233321 chr7 159138663 49710735 0.312373712728754 2.661086969339718 chr8 146364022 29418918 0.20099828904674402 0.8561214393300655 chr9 141213431 18041919 0.12776347739897348 1.5811465785111993 chr10 135534747 19706891 0.14540102398981125 3.5913648336175177 chr11 135006516 26054062 0.19298373717013778 1.097860412562068 chr12 133851895 23921189 0.17871386131664405 0.608571084047719 chr13 115169878 17335220 0.15051869725867037 0.5797052169563153 chr14 107349540 11889143 0.1107516902261528 0.5078063302942937 chr15 102531392 13222761 0.12896304967750755 0.5273943366560965 chr16 90354753 11604929 0.12843739388009837 1.725210578399804 chr17 81195210 13811834 0.1701065124408201 1.1762079403347099 chr18 78077248 14113238 0.18075993149758557 1.7514663595786617 chr19 59128983 12418938 0.21003131408500633 1.6109283108083323 chr20 63025520 12930226 0.2051585770335572 0.7048209638202029 chr21 48129895 6553651 0.13616591102058295 0.6226751278163447 chr22 51304566 4590820 0.08948170422102392 0.4299572199696014 chrMT 16571 20879 1.2599722406613965 1.6769290257319367 chrX 155270560 8835009 0.0569007350781758 0.43498716196389153 chrY 59373566 4233242 0.07129842933806603 1.2169435363978427