BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472617.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,640,148 number of mapped reads = 16,536,934 (99.38%) number of supplementary alignments = 90,567 (0.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,288,414 number of mapped paired reads (second in pair) = 8,248,520 number of mapped paired reads (both in pair) = 16,466,988 number of mapped paired reads (singletons) = 69,946 number of mapped bases = 1,626,983,282 bp number of sequenced bases = 1,626,750,212 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,602,664 duplication rate = 50.35% >>>>>>> Insert size mean insert size = 21,351.3024 std insert size = 1,480,597.3729 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 54.5293 >>>>>>> ACTG content number of A's = 438,140,227 bp (26.93%) number of C's = 377,342,725 bp (23.2%) number of T's = 439,290,631 bp (27%) number of G's = 371,680,085 bp (22.85%) number of N's = 296,544 bp (0.02%) GC percentage = 46.04% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 9,381,186 number of insertions = 97,497 mapped reads with insertion percentage = 0.58% number of deletions = 88,099 mapped reads with deletion percentage = 0.53% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 0.5256X std coverageData = 23.4896X There is a 3.24% of reference with a coverageData >= 1X There is a 1.52% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 191394864 0.7678811921595975 26.743431129129156 chr2 243199373 143650967 0.5906716173976321 23.690352021701663 chr3 198022430 138127027 0.6975322290510222 25.00841204697426 chr4 191154276 30727844 0.16074892303220045 7.612344167311848 chr5 180915260 42108950 0.23275510313502576 10.506390295529535 chr6 171115067 98921102 0.5780969714373545 15.404109848655537 chr7 159138663 85787269 0.5390724502944957 24.061292787083218 chr8 146364022 100735927 0.6882560729302725 28.8648248819784 chr9 141213431 73815498 0.5227229271130732 20.25392629134276 chr10 135534747 28582821 0.21088924893924066 13.567326219758785 chr11 135006516 56476735 0.41832599398387554 17.27120290347862 chr12 133851895 56332132 0.42085419859016565 15.349835787662798 chr13 115169878 88030631 0.7643546431472299 33.51106438349295 chr14 107349540 22436638 0.2090054414765075 9.123815758652192 chr15 102531392 54886597 0.5353150477075352 22.433463787093693 chr16 90354753 103037539 1.140366561568709 51.513191028110185 chr17 81195210 92843482 1.143460088347576 48.08479537447589 chr18 78077248 16094510 0.20613572343123568 8.626093602266819 chr19 59128983 25031462 0.42333658943533664 11.312035482173474 chr20 63025520 64342683 1.0208988834998902 33.51800920466063 chr21 48129895 12482131 0.25934257699918106 20.5876107751614 chr22 51304566 21029120 0.409887884053049 17.4534026698716 chrMT 16571 1034 0.06239816546979663 0.2587530265975902 chrX 155270560 77876174 0.5015514467134015 24.110607035125906 chrY 59373566 2230145 0.03756124400545522 4.11870462741148