BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514755.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 88,935,803 number of mapped reads = 83,847,319 (94.28%) number of supplementary alignments = 11,936,482 (13.42%) number of secondary alignments = 0 number of mapped bases = 8,008,364,558 bp number of sequenced bases = 8,003,574,867 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,174,779 duplication rate = 48.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.967 >>>>>>> ACTG content number of A's = 2,496,691,909 bp (31.19%) number of C's = 1,498,976,859 bp (18.73%) number of T's = 2,464,920,107 bp (30.8%) number of G's = 1,542,435,924 bp (19.27%) number of N's = 550,068 bp (0.01%) GC percentage = 38% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 39,314,735 number of insertions = 5,242,864 mapped reads with insertion percentage = 6.01% number of deletions = 1,790,235 mapped reads with deletion percentage = 2.01% homopolymer indels = 56.26% >>>>>>> Coverage mean coverageData = 2.5869X std coverageData = 76.8255X There is a 6.3% of reference with a coverageData >= 1X There is a 4.23% of reference with a coverageData >= 2X There is a 3.49% of reference with a coverageData >= 3X There is a 3.07% of reference with a coverageData >= 4X There is a 2.79% of reference with a coverageData >= 5X There is a 2.58% of reference with a coverageData >= 6X There is a 2.42% of reference with a coverageData >= 7X There is a 2.28% of reference with a coverageData >= 8X There is a 2.17% of reference with a coverageData >= 9X There is a 2.07% of reference with a coverageData >= 10X There is a 1.98% of reference with a coverageData >= 11X There is a 1.91% of reference with a coverageData >= 12X There is a 1.84% of reference with a coverageData >= 13X There is a 1.77% of reference with a coverageData >= 14X There is a 1.72% of reference with a coverageData >= 15X There is a 1.66% of reference with a coverageData >= 16X There is a 1.62% of reference with a coverageData >= 17X There is a 1.57% of reference with a coverageData >= 18X There is a 1.53% of reference with a coverageData >= 19X There is a 1.49% of reference with a coverageData >= 20X There is a 1.45% of reference with a coverageData >= 21X There is a 1.42% of reference with a coverageData >= 22X There is a 1.38% of reference with a coverageData >= 23X There is a 1.35% of reference with a coverageData >= 24X There is a 1.32% of reference with a coverageData >= 25X There is a 1.3% of reference with a coverageData >= 26X There is a 1.27% of reference with a coverageData >= 27X There is a 1.24% of reference with a coverageData >= 28X There is a 1.22% of reference with a coverageData >= 29X There is a 1.2% of reference with a coverageData >= 30X There is a 1.17% of reference with a coverageData >= 31X There is a 1.15% of reference with a coverageData >= 32X There is a 1.13% of reference with a coverageData >= 33X There is a 1.11% of reference with a coverageData >= 34X There is a 1.09% of reference with a coverageData >= 35X There is a 1.08% of reference with a coverageData >= 36X There is a 1.06% of reference with a coverageData >= 37X There is a 1.04% of reference with a coverageData >= 38X There is a 1.02% of reference with a coverageData >= 39X There is a 1.01% of reference with a coverageData >= 40X There is a 0.99% of reference with a coverageData >= 41X There is a 0.98% of reference with a coverageData >= 42X There is a 0.96% of reference with a coverageData >= 43X There is a 0.95% of reference with a coverageData >= 44X There is a 0.94% of reference with a coverageData >= 45X There is a 0.92% of reference with a coverageData >= 46X There is a 0.91% of reference with a coverageData >= 47X There is a 0.9% of reference with a coverageData >= 48X There is a 0.89% of reference with a coverageData >= 49X There is a 0.87% of reference with a coverageData >= 50X There is a 0.86% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 687765980 2.7593350710247577 66.12410320688144 chr2 243199373 800528913 3.291656977257092 61.25675795042987 chr3 198022430 532709657 2.690148065549948 42.073648614179454 chr4 191154276 547612078 2.8647649922306733 40.048170136964856 chr5 180915260 368757259 2.0382872014223676 35.053167432778864 chr6 171115067 469957725 2.746442690520058 42.37658730298332 chr7 159138663 399036843 2.5074789210714936 42.11527937177073 chr8 146364022 435941898 2.978477169751457 47.468439664356595 chr9 141213431 444892112 3.1504943180652556 160.06533806075237 chr10 135534747 322869947 2.3821931581869555 75.8321865265537 chr11 135006516 339870640 2.5174387879174662 42.64857286002755 chr12 133851895 314606403 2.3504067910282482 47.7989078887535 chr13 115169878 249481226 2.166202051546846 46.681518671197196 chr14 107349540 188818937 1.7589170573064403 31.571199478647518 chr15 102531392 273834796 2.6707410350968415 57.28061535050223 chr16 90354753 192399002 2.1293733380024844 70.2367364212461 chr17 81195210 167102743 2.0580369580914932 49.90698971637764 chr18 78077248 202076864 2.5881658124015847 33.93978468012466 chr19 59128983 36825501 0.6227994991897629 15.024041198153114 chr20 63025520 163662961 2.596772878668831 41.528126616045505 chr21 48129895 179780795 3.7353248952651983 85.86811836970973 chr22 51304566 28870912 0.562735722196734 13.315531920971667 chrMT 16571 242258290 14619.412829642146 15123.457255542933 chrX 155270560 384744039 2.4778943220144245 40.718126229526895 chrY 59373566 33959037 0.5719554894176307 16.07354824660119