BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240190.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,182,496 number of mapped reads = 1,725,392 (79.06%) number of supplementary alignments = 7,808 (0.36%) number of secondary alignments = 0 number of mapped bases = 105,827,254 bp number of sequenced bases = 105,768,165 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 169,472 duplication rate = 8.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5374 >>>>>>> ACTG content number of A's = 28,507,101 bp (26.95%) number of C's = 18,155,742 bp (17.17%) number of T's = 34,820,676 bp (32.92%) number of G's = 24,260,012 bp (22.94%) number of N's = 24,634 bp (0.02%) GC percentage = 40.1% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 1,009,524 number of insertions = 7,533 mapped reads with insertion percentage = 0.43% number of deletions = 35,507 mapped reads with deletion percentage = 2.04% homopolymer indels = 49.76% >>>>>>> Coverage mean coverageData = 0.0342X std coverageData = 0.3378X There is a 2.47% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 8452763 0.03391270587847402 0.5006007017414049 chr2 243199373 10317682 0.04242478865272403 0.399651972587444 chr3 198022430 7261818 0.03667169421161027 0.2540500588293036 chr4 191154276 7058197 0.03692408638559568 0.2622605733053409 chr5 180915260 6125246 0.03385698917824843 0.2453863165968511 chr6 171115067 6176280 0.036094308398920825 0.2969671163721148 chr7 159138663 6360952 0.039971128826186 0.5414504162312206 chr8 146364022 6093225 0.0416306201260307 0.4794963712219476 chr9 141213431 3998529 0.02831550066933789 0.30399917068411636 chr10 135534747 4614972 0.03405010229590793 0.28637077449728626 chr11 135006516 4739690 0.03510712031114113 0.31488328426544165 chr12 133851895 4739496 0.03540850878502692 0.25143346684118995 chr13 115169878 2986239 0.025928993343207328 0.21299708500352227 chr14 107349540 3579173 0.033341297969232096 0.2502864257352239 chr15 102531392 2623591 0.02558817303484966 0.21940479248100464 chr16 90354753 2873943 0.031807325066784256 0.2430772521076769 chr17 81195210 2643320 0.032555122401924944 0.25320820052935267 chr18 78077248 2512955 0.03218549659947031 0.47672431742122556 chr19 59128983 1696073 0.028684291762636947 0.3344062065017359 chr20 63025520 2177713 0.03455287635865598 0.25116226989276724 chr21 48129895 1679435 0.03489380145126018 0.25576124355181945 chr22 51304566 933492 0.018195105675389595 0.17096348550124107 chrMT 16571 72540 4.3775270050087505 4.448908782168402 chrX 155270560 5861830 0.03775235949429177 0.27777637487596113 chrY 59373566 248100 0.004178627236235061 0.09389159731165464