BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081239.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 = 2,681,005 number of mapped reads = 2,321,581 (86.59%) number of supplementary alignments = 29,571 (1.1%) number of secondary alignments = 0 number of mapped bases = 149,045,548 bp number of sequenced bases = 148,989,754 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 147,755 duplication rate = 5.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.706 >>>>>>> ACTG content number of A's = 42,965,386 bp (28.84%) number of C's = 29,111,929 bp (19.54%) number of T's = 45,186,831 bp (30.33%) number of G's = 31,707,222 bp (21.28%) number of N's = 18,386 bp (0.01%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,369,517 number of insertions = 11,573 mapped reads with insertion percentage = 0.49% number of deletions = 34,143 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.62% >>>>>>> Coverage mean coverageData = 0.0481X std coverageData = 0.3541X There is a 3.55% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 16169145 0.0648710319562253 0.5629065270905347 chr2 243199373 9638820 0.03963340810093289 0.3821126621810083 chr3 198022430 9611684 0.04853836002315495 0.2879011697798288 chr4 191154276 6095845 0.031889660684336456 0.2355246098836411 chr5 180915260 9472343 0.05235789949393987 0.2981579469633291 chr6 171115067 11158743 0.06521192549338745 0.3639224719777307 chr7 159138663 6974906 0.04382911021440465 0.34352411216770296 chr8 146364022 9476424 0.06474558344672983 0.49807611620428055 chr9 141213431 4507169 0.031917424341881474 0.27849850201513315 chr10 135534747 4144127 0.03057612229873421 0.2918755450059526 chr11 135006516 8615759 0.0638173567859495 0.3855330265565467 chr12 133851895 4448220 0.03323240212624558 0.23766724588418042 chr13 115169878 4392572 0.03813993794453789 0.25614936552388806 chr14 107349540 5981666 0.05572139386903754 0.3154358855859053 chr15 102531392 3221572 0.03142034782869231 0.24010554327790976 chr16 90354753 5802643 0.06422067248637157 0.3355466367104738 chr17 81195210 2655560 0.032705870210816626 0.24841765964462015 chr18 78077248 3859917 0.04943715485463832 0.4280223393733865 chr19 59128983 4458422 0.07540163509999825 0.48857684855020794 chr20 63025520 3804262 0.06036066025317998 0.32152482935202026 chr21 48129895 2396110 0.049784234933402616 0.2980153103241428 chr22 51304566 1209255 0.023570124343318684 0.19263108921941738 chrMT 16571 111719 6.741838150986664 5.64233958602854 chrX 155270560 10465087 0.06739904203346726 0.3536327906965332 chrY 59373566 373578 0.006291991961540596 0.11239944203813655