BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082511.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 = 2,057,101 number of mapped reads = 1,874,003 (91.1%) number of supplementary alignments = 16,162 (0.79%) number of secondary alignments = 0 number of mapped bases = 127,283,080 bp number of sequenced bases = 127,230,419 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,933 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0657 >>>>>>> ACTG content number of A's = 35,984,740 bp (28.28%) number of C's = 23,727,195 bp (18.65%) number of T's = 39,896,738 bp (31.36%) number of G's = 27,619,074 bp (21.71%) number of N's = 2,672 bp (0%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,071,462 number of insertions = 10,193 mapped reads with insertion percentage = 0.54% number of deletions = 32,834 mapped reads with deletion percentage = 1.73% homopolymer indels = 47.28% >>>>>>> Coverage mean coverageData = 0.0411X std coverageData = 0.3688X There is a 3.58% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 9627938 0.038627538665189524 0.613091951696766 chr2 243199373 10439665 0.042926364781376306 0.4270761525534211 chr3 198022430 9331104 0.04712144982767861 0.24107762912978978 chr4 191154276 8465833 0.0442879603697696 0.24446833431849446 chr5 180915260 7484398 0.04136963349581456 0.2275253736461781 chr6 171115067 7368800 0.043063420008478855 0.28372410983869994 chr7 159138663 6507530 0.04089219977925792 0.3757288490481461 chr8 146364022 7028655 0.048021739932782116 0.6433164122751415 chr9 141213431 5811252 0.0411522612179857 0.35595916049514353 chr10 135534747 6202024 0.04575966043600613 0.326055107385142 chr11 135006516 5970938 0.044227035678781605 0.4139406444475396 chr12 133851895 5816790 0.04345691183527883 0.23579776812789807 chr13 115169878 4450882 0.0386462335229703 0.21839228026162577 chr14 107349540 3282790 0.030580382552174885 0.21667231951472474 chr15 102531392 3977920 0.03879709347942921 0.22348786417813538 chr16 90354753 3384916 0.037462511795035285 0.23339085478858693 chr17 81195210 3289008 0.04050741416889001 0.28004909478338885 chr18 78077248 3049696 0.03905998326170512 0.63738632044615 chr19 59128983 1849024 0.03127102659621255 0.41639399101154323 chr20 63025520 2752642 0.04367503830194499 0.24083459034539748 chr21 48129895 1818890 0.03779127297078043 0.2314222409054203 chr22 51304566 1253582 0.02443412151659172 0.17171068977184994 chrMT 16571 5087 0.3069820771226842 0.6169348840630433 chrX 155270560 7834626 0.05045789749196499 0.29403254347301816 chrY 59373566 279090 0.004700576684243624 0.10886515956916694