BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085118.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 = 2,076,111 number of mapped reads = 1,834,775 (88.38%) number of supplementary alignments = 26,652 (1.28%) number of secondary alignments = 0 number of mapped bases = 121,419,875 bp number of sequenced bases = 121,379,483 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,596 duplication rate = 2.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3935 >>>>>>> ACTG content number of A's = 34,579,427 bp (28.49%) number of C's = 22,969,993 bp (18.92%) number of T's = 36,624,834 bp (30.17%) number of G's = 27,184,869 bp (22.4%) number of N's = 20,360 bp (0.02%) GC percentage = 41.32% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,084,436 number of insertions = 10,187 mapped reads with insertion percentage = 0.55% number of deletions = 24,461 mapped reads with deletion percentage = 1.32% homopolymer indels = 44.52% >>>>>>> Coverage mean coverageData = 0.0392X std coverageData = 0.5187X There is a 3.56% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.02% 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 0.01% 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 9666394 0.03878182514137046 1.0853932508578712 chr2 243199373 10421091 0.04284999122921258 0.5640603795272306 chr3 198022430 8154259 0.041178461450048866 0.2167734656908535 chr4 191154276 7905598 0.04135716011919085 0.23304345082708622 chr5 180915260 7458296 0.04122535600368924 0.22172778892763786 chr6 171115067 7074671 0.041344524033058994 0.30422949593926774 chr7 159138663 6883006 0.043251626413375106 0.7335121216728641 chr8 146364022 6290395 0.04297774080026306 0.7966569200435847 chr9 141213431 5097004 0.036094328732795965 0.44374209946766435 chr10 135534747 5697471 0.04203697668760912 0.4388257031298049 chr11 135006516 5513721 0.04084040654748842 0.43403188240931984 chr12 133851895 5477187 0.04091975687008391 0.23017131161876647 chr13 115169878 3781302 0.03283238695451254 0.19114457281552363 chr14 107349540 3637312 0.033882883894984554 0.23819119299366115 chr15 102531392 3393004 0.033092343074792155 0.20860273888579842 chr16 90354753 3298802 0.03650944627118841 0.26411079886331595 chr17 81195210 3070014 0.03781028462146967 0.2627450435167035 chr18 78077248 3291669 0.042159131940715945 0.9179728794173956 chr19 59128983 2411398 0.04078199687621889 0.7998770116975337 chr20 63025520 2324019 0.03687425347700424 0.21760416278908534 chr21 48129895 1570843 0.032637573798987095 0.21143232731737943 chr22 51304566 1224579 0.02386881120873335 0.16203204775482122 chrMT 16571 15428 0.9310240782089192 1.0779234882917783 chrX 155270560 7430921 0.04785788754803229 0.30649697586970864 chrY 59373566 331491 0.005583141157463912 0.1338326806337803