BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472757.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,068,244 number of mapped reads = 16,887,781 (98.94%) number of supplementary alignments = 125,526 (0.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,487,530 number of mapped paired reads (second in pair) = 8,400,251 number of mapped paired reads (both in pair) = 16,766,954 number of mapped paired reads (singletons) = 120,827 number of mapped bases = 1,666,390,993 bp number of sequenced bases = 1,666,149,191 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,511,166 duplication rate = 47.51% >>>>>>> Insert size mean insert size = 56,016.2901 std insert size = 2,316,313.9017 median insert size = 254 >>>>>>> Mapping quality mean mapping quality = 55.391 >>>>>>> ACTG content number of A's = 465,101,761 bp (27.91%) number of C's = 370,394,802 bp (22.23%) number of T's = 462,973,651 bp (27.79%) number of G's = 367,358,764 bp (22.05%) number of N's = 320,213 bp (0.02%) GC percentage = 44.28% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 10,983,249 number of insertions = 97,818 mapped reads with insertion percentage = 0.57% number of deletions = 93,213 mapped reads with deletion percentage = 0.55% homopolymer indels = 45.29% >>>>>>> Coverage mean coverageData = 0.5383X std coverageData = 16.5579X There is a 4.75% of reference with a coverageData >= 1X There is a 2.03% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 148251600 0.5947892904146466 19.342713250239644 chr2 243199373 115964442 0.4768287046529516 16.386522588556836 chr3 198022430 182315272 0.9206799047966435 20.37674345062611 chr4 191154276 74506265 0.3897703287579086 16.161593183804964 chr5 180915260 104195708 0.5759365351491079 17.726742988116776 chr6 171115067 89275164 0.5217259097353478 14.195616543487892 chr7 159138663 75177315 0.47240132336665414 15.48806309947881 chr8 146364022 74038694 0.5058530982429548 15.884868875668419 chr9 141213431 90489711 0.6408010226732611 14.965135316802494 chr10 135534747 41145459 0.30357867565872243 11.240614419747601 chr11 135006516 69408387 0.5141113855571238 14.027845074820045 chr12 133851895 97374828 0.7274818783850613 19.69440798506982 chr13 115169878 48436883 0.4205690223966374 15.363975063176683 chr14 107349540 46260751 0.43093571709762335 14.303117398932518 chr15 102531392 40793905 0.39786746482482166 14.921118656809881 chr16 90354753 52821938 0.5846060804349716 17.561421150870625 chr17 81195210 80316064 0.9891724400983752 22.454162121895777 chr18 78077248 47516926 0.6085886377552652 21.678632039345256 chr19 59128983 46957019 0.7941455546428052 24.42474064196321 chr20 63025520 29766472 0.47229236664766905 11.541389292824688 chr21 48129895 8001376 0.16624544890446988 7.943420782063895 chr22 51304566 16891768 0.32924492529573296 9.171570086717884 chrMT 16571 5045 0.3044475288154004 0.7661393290371089 chrX 155270560 81271424 0.523418116093611 14.899502389404956 chrY 59373566 5208577 0.08772552081510482 4.660329047727748