BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548995.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,704,856 number of mapped reads = 6,641,406 (86.2%) number of secondary alignments = 0 number of mapped bases = 263,633,310 bp number of sequenced bases = 263,604,065 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 475,203 duplication rate = 6.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3764 >>>>>>> ACTG content number of A's = 80,072,627 bp (30.38%) number of C's = 51,664,319 bp (19.6%) number of T's = 79,467,895 bp (30.15%) number of G's = 52,396,924 bp (19.88%) number of N's = 2,300 bp (0%) GC percentage = 39.48% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 798,648 number of insertions = 7,739 mapped reads with insertion percentage = 0.12% number of deletions = 22,544 mapped reads with deletion percentage = 0.34% homopolymer indels = 43.01% >>>>>>> Coverage mean coverageData = 0.0852X std coverageData = 0.7704X There is a 6.78% of reference with a coverageData >= 1X There is a 1.27% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 21130231 0.0847750385344075 1.109037929951937 chr2 243199373 23181906 0.09532058291943048 0.4815328771712805 chr3 198022430 18900521 0.09544636433357574 0.37010649102889775 chr4 191154276 18484642 0.09670012299384817 0.3985255035576157 chr5 180915260 17028157 0.09412228133768262 0.3726098494232347 chr6 171115067 16071591 0.09392271108423199 0.43540955580832436 chr7 159138663 14617582 0.09185437230926088 0.7031565053996582 chr8 146364022 14231831 0.09723585622701732 2.5432743060441783 chr9 141213431 11196886 0.0792905173446285 0.4486088131607579 chr10 135534747 12536060 0.09249332940430398 0.5332417128297468 chr11 135006516 12244272 0.09069393361724852 0.45765824774935 chr12 133851895 12087303 0.09030356275493896 0.3736440866666516 chr13 115169878 9353558 0.08121531569218125 0.33717898504779814 chr14 107349540 8373768 0.07800469382542301 0.39884141046635146 chr15 102531392 7379422 0.07197231848759061 0.31760353937352415 chr16 90354753 6764434 0.07486528129848355 0.36462027307066575 chr17 81195210 6096113 0.07507971221455059 0.35963688296707447 chr18 78077248 7380294 0.09452553962967547 0.9015453833519697 chr19 59128983 4139911 0.0700149197560188 0.8505981894297113 chr20 63025520 5160875 0.0818854806751297 0.35947583126065746 chr21 48129895 3498612 0.07269103745187892 0.38795075132198026 chr22 51304566 2495181 0.048634677077280024 0.2881880853590569 chrMT 16571 19380 1.169513004646672 1.619626643863924 chrX 155270560 8945386 0.057611603899670356 0.3629139193525989 chrY 59373566 2315394 0.03899705131404774 0.4117580141868896