BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013205.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,171,146 number of mapped reads = 1,946,425 (89.65%) number of supplementary alignments = 17,698 (0.82%) number of secondary alignments = 0 number of mapped bases = 132,473,615 bp number of sequenced bases = 132,421,630 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,966 duplication rate = 4.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4833 >>>>>>> ACTG content number of A's = 37,776,221 bp (28.53%) number of C's = 24,391,780 bp (18.42%) number of T's = 42,176,719 bp (31.85%) number of G's = 28,047,264 bp (21.18%) number of N's = 29,646 bp (0.02%) GC percentage = 39.6% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,064,819 number of insertions = 10,197 mapped reads with insertion percentage = 0.52% number of deletions = 29,686 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.37% >>>>>>> Coverage mean coverageData = 0.0428X std coverageData = 0.481X There is a 3.36% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.13% 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 0.01% 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 7150268 0.02868706192711953 0.8163044739062947 chr2 243199373 14121467 0.05806539229852373 0.6148710303343612 chr3 198022430 11951087 0.060352188385931836 0.2957869383658717 chr4 191154276 8960169 0.04687401813601073 0.31230021585805096 chr5 180915260 6405052 0.03540360276960606 0.2303668848208444 chr6 171115067 6204826 0.03626113181488571 0.3249183648741176 chr7 159138663 6097898 0.03831814271306276 0.58794495259367 chr8 146364022 9276103 0.06337693425779185 0.6436607830370523 chr9 141213431 5707796 0.04041963968710597 0.4898639225870324 chr10 135534747 3155279 0.023280222008309058 0.4899436197066449 chr11 135006516 8374835 0.06203282069733582 0.4211787822087119 chr12 133851895 6196785 0.046295833166949185 0.27307261988337955 chr13 115169878 1823094 0.0158296078076943 0.15104533288432356 chr14 107349540 5765047 0.053703509116107995 0.30218471345863623 chr15 102531392 3403653 0.03319620394893302 0.21760563527738377 chr16 90354753 1778248 0.01968073555577093 0.2266902454288598 chr17 81195210 5416048 0.06670403340295566 0.3558155582702305 chr18 78077248 5484491 0.07024441998775367 1.0224838741021989 chr19 59128983 2149119 0.036346287234468415 0.57164234561215 chr20 63025520 2532052 0.04017502751266471 0.2629522142645019 chr21 48129895 2108158 0.043801425288794 0.2891602471359592 chr22 51304566 1357925 0.026467917105077936 0.19020380466460535 chrMT 16571 506593 30.57105787218635 17.270961235688038 chrX 155270560 6266556 0.04035894505693803 0.27835125613090134 chrY 59373566 281066 0.004733857488027585 0.1792070615339727