BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472641.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 = 16,043,086 number of mapped reads = 15,947,778 (99.41%) number of supplementary alignments = 79,331 (0.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,992,831 number of mapped paired reads (second in pair) = 7,954,947 number of mapped paired reads (both in pair) = 15,883,826 number of mapped paired reads (singletons) = 63,952 number of mapped bases = 1,565,973,492 bp number of sequenced bases = 1,565,798,358 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,267,787 duplication rate = 49.48% >>>>>>> Insert size mean insert size = 18,805.6557 std insert size = 1,389,765.0628 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 54.9365 >>>>>>> ACTG content number of A's = 423,376,414 bp (27.04%) number of C's = 361,449,139 bp (23.08%) number of T's = 424,028,820 bp (27.08%) number of G's = 356,651,843 bp (22.78%) number of N's = 292,142 bp (0.02%) GC percentage = 45.86% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 8,538,708 number of insertions = 90,577 mapped reads with insertion percentage = 0.56% number of deletions = 74,443 mapped reads with deletion percentage = 0.46% homopolymer indels = 46.96% >>>>>>> Coverage mean coverageData = 0.5059X std coverageData = 23.5799X There is a 3.23% of reference with a coverageData >= 1X There is a 1.55% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.36% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.3% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.22% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.21% of reference with a coverageData >= 18X There is a 0.21% of reference with a coverageData >= 19X There is a 0.2% of reference with a coverageData >= 20X There is a 0.2% of reference with a coverageData >= 21X There is a 0.19% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.18% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.16% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.15% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 158596258 0.6362923284351617 27.54761090315275 chr2 243199373 68650804 0.2822819942056347 12.003902618137944 chr3 198022430 110070159 0.5558469260275212 19.221797490323993 chr4 191154276 55052453 0.2880001125373727 14.393799304252441 chr5 180915260 107691526 0.5952594933119517 28.816740442739583 chr6 171115067 77505954 0.45294640243456763 15.477768999027504 chr7 159138663 95612070 0.600809810749761 29.852877509126813 chr8 146364022 71033074 0.48531786042337643 22.01882848650228 chr9 141213431 68160379 0.4826763185153401 16.76930010505756 chr10 135534747 34877098 0.25732956877840335 11.406762974215642 chr11 135006516 84060187 0.6226379991910909 25.74177605468276 chr12 133851895 81739757 0.610673139890922 21.559761388177048 chr13 115169878 54924816 0.4769026151091347 24.279530588144667 chr14 107349540 40263377 0.3750679974967755 15.338716260466592 chr15 102531392 31310481 0.3053745822547693 12.469043316518722 chr16 90354753 115087315 1.2737272935713742 46.801880084291305 chr17 81195210 73347955 0.903353227364028 29.0864981190053 chr18 78077248 45353169 0.5808756092427848 36.696878394015165 chr19 59128983 44448860 0.7517271183236823 26.572486856242673 chr20 63025520 42114179 0.6682083543301189 35.27870473420048 chr21 48129895 11857646 0.24636758505290735 17.669497542048028 chr22 51304566 26549502 0.5174880925802978 23.229801789781593 chrMT 16571 395 0.023836823366121536 0.15254058220006197 chrX 155270560 65667236 0.42292135740348974 28.612983798769623 chrY 59373566 1998842 0.033665520443895855 2.041410717068964