BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081695.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 = 2,080,847 number of mapped reads = 1,863,045 (89.53%) number of supplementary alignments = 20,437 (0.98%) number of secondary alignments = 0 number of mapped bases = 125,924,794 bp number of sequenced bases = 125,878,428 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,341 duplication rate = 4.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5407 >>>>>>> ACTG content number of A's = 35,468,107 bp (28.18%) number of C's = 22,479,911 bp (17.86%) number of T's = 40,863,116 bp (32.46%) number of G's = 26,974,577 bp (21.43%) number of N's = 92,717 bp (0.07%) GC percentage = 39.29% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,088,739 number of insertions = 10,630 mapped reads with insertion percentage = 0.57% number of deletions = 28,481 mapped reads with deletion percentage = 1.51% homopolymer indels = 49.87% >>>>>>> Coverage mean coverageData = 0.0407X std coverageData = 0.3147X There is a 3.26% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 9710196 0.038957559909148634 0.3917904168045623 chr2 243199373 10863600 0.04466952305835098 0.3397552881408968 chr3 198022430 9394043 0.047439287559495155 0.262190978904307 chr4 191154276 8237575 0.04309385681751634 0.25890045642802506 chr5 180915260 7253462 0.04009314637140062 0.2417035444588044 chr6 171115067 7969416 0.046573432367589235 0.29189949342032595 chr7 159138663 7349202 0.04618112193138131 0.3656149352321869 chr8 146364022 6515795 0.044517736742708536 0.5932257531593114 chr9 141213431 5513650 0.039044798791129154 0.29479860739245894 chr10 135534747 5498560 0.04056937517284774 0.29625440622863425 chr11 135006516 5168440 0.038282892953107536 0.2686016306787367 chr12 133851895 6013818 0.04492889697228418 0.25709866099233086 chr13 115169878 4956897 0.043039873672523994 0.2510675081046813 chr14 107349540 3634564 0.03385728527574501 0.22764208587942356 chr15 102531392 3426355 0.03341761906441298 0.22033700792383373 chr16 90354753 3476502 0.03847613860446279 0.24487527062762982 chr17 81195210 2892086 0.035618923825678876 0.2365125652690554 chr18 78077248 3079197 0.03943782700947656 0.48177673596653814 chr19 59128983 1868343 0.03159775300041944 0.32662696037882716 chr20 63025520 2427231 0.03851187582426928 0.23949840412019863 chr21 48129895 1566204 0.032541188797523865 0.2252930067685654 chr22 51304566 1181235 0.023023974123472752 0.1818581346963815 chrMT 16571 2638 0.15919377225273068 0.41924925243092465 chrX 155270560 7624032 0.04910159401756521 0.28050829536107674 chrY 59373566 301753 0.005082278534524943 0.1154898037365619