BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153353.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 64,343,454 number of mapped reads = 63,756,015 (99.09%) number of supplementary alignments = 574,195 (0.89%) number of secondary alignments = 0 number of mapped bases = 6,203,013,522 bp number of sequenced bases = 6,201,916,711 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,303,506 duplication rate = 34.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.4343 >>>>>>> ACTG content number of A's = 1,600,063,429 bp (25.8%) number of C's = 1,493,442,712 bp (24.08%) number of T's = 1,631,442,870 bp (26.31%) number of G's = 1,475,209,747 bp (23.79%) number of N's = 1,757,953 bp (0.03%) GC percentage = 47.87% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 20,981,845 number of insertions = 737,834 mapped reads with insertion percentage = 1.14% number of deletions = 525,642 mapped reads with deletion percentage = 0.81% homopolymer indels = 49.01% >>>>>>> Coverage mean coverageData = 2.0038X std coverageData = 20.0299X There is a 24.03% of reference with a coverageData >= 1X There is a 12.58% of reference with a coverageData >= 2X There is a 7.16% of reference with a coverageData >= 3X There is a 5.3% of reference with a coverageData >= 4X There is a 4.22% of reference with a coverageData >= 5X There is a 3.66% of reference with a coverageData >= 6X There is a 3.28% of reference with a coverageData >= 7X There is a 3.01% of reference with a coverageData >= 8X There is a 2.81% of reference with a coverageData >= 9X There is a 2.64% of reference with a coverageData >= 10X There is a 2.5% of reference with a coverageData >= 11X There is a 2.38% of reference with a coverageData >= 12X There is a 2.27% of reference with a coverageData >= 13X There is a 2.18% of reference with a coverageData >= 14X There is a 2.09% of reference with a coverageData >= 15X There is a 2.01% of reference with a coverageData >= 16X There is a 1.93% of reference with a coverageData >= 17X There is a 1.86% of reference with a coverageData >= 18X There is a 1.8% of reference with a coverageData >= 19X There is a 1.74% of reference with a coverageData >= 20X There is a 1.69% of reference with a coverageData >= 21X There is a 1.63% of reference with a coverageData >= 22X There is a 1.58% of reference with a coverageData >= 23X There is a 1.54% of reference with a coverageData >= 24X There is a 1.49% of reference with a coverageData >= 25X There is a 1.45% of reference with a coverageData >= 26X There is a 1.41% of reference with a coverageData >= 27X There is a 1.37% of reference with a coverageData >= 28X There is a 1.34% of reference with a coverageData >= 29X There is a 1.3% of reference with a coverageData >= 30X There is a 1.27% of reference with a coverageData >= 31X There is a 1.24% of reference with a coverageData >= 32X There is a 1.21% of reference with a coverageData >= 33X There is a 1.18% of reference with a coverageData >= 34X There is a 1.15% of reference with a coverageData >= 35X There is a 1.12% of reference with a coverageData >= 36X There is a 1.1% of reference with a coverageData >= 37X There is a 1.07% of reference with a coverageData >= 38X There is a 1.05% of reference with a coverageData >= 39X There is a 1.03% of reference with a coverageData >= 40X There is a 1% of reference with a coverageData >= 41X There is a 0.98% of reference with a coverageData >= 42X There is a 0.96% of reference with a coverageData >= 43X There is a 0.94% of reference with a coverageData >= 44X There is a 0.92% of reference with a coverageData >= 45X There is a 0.9% of reference with a coverageData >= 46X There is a 0.89% of reference with a coverageData >= 47X There is a 0.87% of reference with a coverageData >= 48X There is a 0.85% of reference with a coverageData >= 49X There is a 0.84% of reference with a coverageData >= 50X There is a 0.82% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 770102146 3.089669919016972 37.77923547599065 chr2 243199373 400571587 1.6470913640061071 13.382606155714216 chr3 198022430 286099780 1.444784714539661 11.49426756530315 chr4 191154276 218018972 1.1405393411131437 11.089846672623276 chr5 180915260 346531599 1.915435983675451 17.1971674526355 chr6 171115067 198992070 1.1629137836237413 12.894834272475745 chr7 159138663 282530960 1.7753759813854915 15.07678444373541 chr8 146364022 323470887 2.2100437155245705 20.70220033263551 chr9 141213431 147134430 1.0419294323356536 9.770101363130333 chr10 135534747 290258658 2.141581140074729 17.883815899678407 chr11 135006516 281854138 2.0877076629397653 16.165284799654177 chr12 133851895 310328125 2.3184440160522195 18.493542046979247 chr13 115169878 60587525 0.5260709314982517 5.081538700452915 chr14 107349540 166213096 1.5483354283586124 12.835671851511798 chr15 102531392 277537789 2.7068567351548296 20.456553610025164 chr16 90354753 349734157 3.870678026201898 31.78207254209798 chr17 81195210 286332213 3.5264668075863095 23.401610380220237 chr18 78077248 61747334 0.7908492625149903 7.995863007856388 chr19 59128983 411692685 6.962620767551507 42.12986023006296 chr20 63025520 150288467 2.384565284030977 19.33273565400875 chr21 48129895 60555356 1.2581651383199568 13.032155541578685 chr22 51304566 109814942 2.140451631537045 17.76677347802573 chrMT 16571 2615 0.15780580532255145 0.6111005128192413 chrX 155270560 407813365 2.6264693384244895 26.954380811716547 chrY 59373566 4800626 0.08085460118733646 3.5882095289258045