BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472607.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 = 15,405,820 number of mapped reads = 15,267,478 (99.1%) number of supplementary alignments = 69,993 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,657,062 number of mapped paired reads (second in pair) = 7,610,416 number of mapped paired reads (both in pair) = 15,179,648 number of mapped paired reads (singletons) = 87,830 number of mapped bases = 1,504,478,617 bp number of sequenced bases = 1,504,266,320 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,145,862 duplication rate = 49.12% >>>>>>> Insert size mean insert size = 20,154.0716 std insert size = 1,388,408.4453 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 54.9162 >>>>>>> ACTG content number of A's = 397,208,255 bp (26.41%) number of C's = 356,570,935 bp (23.7%) number of T's = 398,885,246 bp (26.52%) number of G's = 351,322,080 bp (23.36%) number of N's = 279,804 bp (0.02%) GC percentage = 47.06% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 9,469,972 number of insertions = 88,664 mapped reads with insertion percentage = 0.57% number of deletions = 82,023 mapped reads with deletion percentage = 0.52% homopolymer indels = 45.24% >>>>>>> Coverage mean coverageData = 0.486X std coverageData = 21.066X There is a 3.08% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 208337660 0.8358561321297571 27.20490505108004 chr2 243199373 88961313 0.36579581560023183 12.985213599898254 chr3 198022430 110765567 0.559358689821148 16.365876242162507 chr4 191154276 38288081 0.20029936970910345 10.03147805268737 chr5 180915260 63138645 0.34899568449891955 11.691411326437265 chr6 171115067 129363122 0.7560007676004358 31.718751908068164 chr7 159138663 73308278 0.460656616173783 14.368679835606459 chr8 146364022 62101859 0.4242972975968097 20.456378040113893 chr9 141213431 77495157 0.5487803564520715 24.122660407171892 chr10 135534747 40041895 0.2954363798679611 11.848591500154365 chr11 135006516 23203565 0.17186996366901283 6.4349766838838045 chr12 133851895 50620295 0.37818138473123597 12.191781353758639 chr13 115169878 53463046 0.46421032068819246 21.15658080198496 chr14 107349540 24331059 0.22665266194899392 11.607859817417847 chr15 102531392 14835422 0.14469151067411629 5.7319865143251505 chr16 90354753 114794978 1.2704918577996667 56.603304457630884 chr17 81195210 47402338 0.5838070743335722 14.298282993156555 chr18 78077248 12908588 0.16533098092801632 9.319680139276453 chr19 59128983 49414096 0.8357000829863758 20.485576459276437 chr20 63025520 75779030 1.2023546969545036 39.346069832257236 chr21 48129895 11102037 0.23066821566928414 13.148755968585299 chr22 51304566 34817764 0.678648446222116 21.976514170742266 chrMT 16571 2906 0.17536660430873213 0.46469623339932004 chrX 155270560 98165503 0.6322222512754511 27.821482868776332 chrY 59373566 1836413 0.030929808056332678 1.864838335807658