BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124971.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,735,672 number of mapped reads = 4,534,117 (95.74%) number of supplementary alignments = 13,712 (0.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,307,340 number of mapped paired reads (second in pair) = 2,226,777 number of mapped paired reads (both in pair) = 4,429,176 number of mapped paired reads (singletons) = 104,941 number of mapped bases = 275,861,836 bp number of sequenced bases = 275,725,037 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 376,404 duplication rate = 5.7% >>>>>>> Insert size mean insert size = 73,487.5074 std insert size = 2,619,448.4443 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 51.6407 >>>>>>> ACTG content number of A's = 76,818,673 bp (27.86%) number of C's = 48,441,478 bp (17.57%) number of T's = 83,243,162 bp (30.19%) number of G's = 67,221,724 bp (24.38%) number of N's = 0 bp (0%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 2,082,929 number of insertions = 33,703 mapped reads with insertion percentage = 0.74% number of deletions = 86,617 mapped reads with deletion percentage = 1.89% homopolymer indels = 47.16% >>>>>>> Coverage mean coverageData = 0.0891X std coverageData = 1.0191X There is a 6.69% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 28689273 0.11510211242362361 0.7551276766018346 chr2 243199373 22557418 0.09275278024668263 0.9090020361185661 chr3 198022430 19547766 0.09871490820509575 0.4537714142085114 chr4 191154276 13832135 0.07236110689985298 0.8189293284944027 chr5 180915260 15176172 0.08388552740106059 0.36545713456566886 chr6 171115067 16726933 0.09775254332220785 0.5718475585734312 chr7 159138663 20345907 0.12785018182539337 0.7632588060090185 chr8 146364022 18494459 0.12635932483462364 0.5179081833701767 chr9 141213431 10085173 0.07141794465711976 0.5228600074781092 chr10 135534747 14193468 0.10472198690126304 3.7556580813718266 chr11 135006516 9468267 0.07013192607681247 0.387947878711038 chr12 133851895 13260254 0.09906661388693824 0.3884373605242405 chr13 115169878 6111531 0.05306535967677243 0.2748081008569456 chr14 107349540 8592293 0.08004033366142044 0.3705002886971727 chr15 102531392 7156402 0.06979717977495127 0.3287612944070618 chr16 90354753 7866296 0.08706012399812547 1.0577086193424634 chr17 81195210 5792361 0.07133870335454517 0.637119689075116 chr18 78077248 3786693 0.04849931442255752 0.684219518115075 chr19 59128983 4480631 0.07577723770422366 0.5616876591507235 chr20 63025520 6203100 0.09842203602604152 0.45428734804256354 chr21 48129895 2592623 0.0538672066498379 0.48939824405007365 chr22 51304566 2159123 0.04208442188167034 0.2608221575156517 chrMT 16571 566992 34.215919377225276 18.391742151955935 chrX 155270560 13035926 0.08395619877973004 0.4422483969606952 chrY 59373566 5140640 0.08658129107488675 1.7963360906084693