BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083761.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 = 1,901,726 number of mapped reads = 1,247,615 (65.6%) number of supplementary alignments = 5,390 (0.28%) number of secondary alignments = 0 number of mapped bases = 79,494,478 bp number of sequenced bases = 79,468,246 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,239 duplication rate = 2.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0729 >>>>>>> ACTG content number of A's = 22,690,710 bp (28.55%) number of C's = 15,123,541 bp (19.03%) number of T's = 23,600,016 bp (29.7%) number of G's = 18,053,057 bp (22.72%) number of N's = 922 bp (0%) GC percentage = 41.75% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 689,804 number of insertions = 5,805 mapped reads with insertion percentage = 0.46% number of deletions = 16,519 mapped reads with deletion percentage = 1.31% homopolymer indels = 45.38% >>>>>>> Coverage mean coverageData = 0.0257X std coverageData = 0.2124X There is a 2.33% of reference with a coverageData >= 1X There is a 0.18% 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% 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 6357510 0.025506496130254377 0.2692060317102591 chr2 243199373 6627737 0.027252278318990568 0.2686657993066306 chr3 198022430 5244397 0.026483853369540008 0.1748716247191293 chr4 191154276 5206988 0.027239715003811896 0.1798828504705199 chr5 180915260 4582910 0.02533180451444505 0.17170152158274368 chr6 171115067 4447128 0.02598910825310316 0.1935733323067416 chr7 159138663 4082734 0.025655198573586106 0.2329971072003518 chr8 146364022 3834898 0.026201097425431506 0.22050073007289928 chr9 141213431 3064716 0.021702723163776114 0.20527875204335347 chr10 135534747 3967348 0.029271814702985354 0.21682325882509204 chr11 135006516 3519275 0.02606744551500018 0.19955835471488653 chr12 133851895 3838768 0.02867922041746215 0.18361082099051074 chr13 115169878 2479584 0.021529796185075407 0.15914684457828687 chr14 107349540 2504081 0.023326425059669562 0.17190395145703558 chr15 102531392 2347053 0.022891067352328542 0.16922268617364628 chr16 90354753 2510570 0.027785699331168555 0.1936474797647685 chr17 81195210 2198496 0.02707667114845814 0.1891666159253177 chr18 78077248 2321271 0.02973044080652023 0.3924094432524128 chr19 59128983 1553532 0.026273612722207653 0.23700880507698302 chr20 63025520 1605958 0.02548107496772736 0.17326095047497522 chr21 48129895 1142491 0.023737658268317436 0.17123520497109485 chr22 51304566 939182 0.018306011983416838 0.14595863320023358 chrMT 16571 20483 1.2360750709070063 1.4290359268103094 chrX 155270560 4899997 0.031557798207206826 0.20587723121817586 chrY 59373566 197371 0.0033242234431396624 0.07018962389045998