BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046488.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 8,591,848 number of mapped reads = 8,557,733 (99.6%) number of supplementary alignments = 49,880 (0.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,285,260 number of mapped paired reads (second in pair) = 4,272,473 number of mapped paired reads (both in pair) = 8,534,238 number of mapped paired reads (singletons) = 23,495 number of mapped bases = 814,356,682 bp number of sequenced bases = 814,107,985 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,165,812 duplication rate = 43.21% >>>>>>> Insert size mean insert size = 17,326.0994 std insert size = 1,262,395.7753 median insert size = 121 >>>>>>> Mapping quality mean mapping quality = 53.0414 >>>>>>> ACTG content number of A's = 238,512,174 bp (29.3%) number of C's = 169,071,909 bp (20.77%) number of T's = 235,240,621 bp (28.9%) number of G's = 171,205,718 bp (21.03%) number of N's = 77,563 bp (0.01%) GC percentage = 41.8% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 3,312,373 number of insertions = 67,810 mapped reads with insertion percentage = 0.77% number of deletions = 89,952 mapped reads with deletion percentage = 1.02% homopolymer indels = 48.02% >>>>>>> Coverage mean coverageData = 0.2631X std coverageData = 18.659X There is a 2.47% of reference with a coverageData >= 1X There is a 1.54% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.06% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 77007057 0.30895432352804447 19.591789460007206 chr2 243199373 88996546 0.36594068850662703 21.556023900126856 chr3 198022430 49280409 0.24886276266784527 15.627900706784628 chr4 191154276 24916380 0.13034696644714347 8.796895269698478 chr5 180915260 57716009 0.31902233675589337 19.502583590460798 chr6 171115067 84120230 0.491600368540311 28.468788062571278 chr7 159138663 50905763 0.31988306323775006 22.728466492230442 chr8 146364022 71924487 0.49140824375542236 27.416337773758926 chr9 141213431 18458881 0.13071618520479117 9.895093107973498 chr10 135534747 16481939 0.12160674192279268 8.830813242754001 chr11 135006516 19443231 0.14401698211366332 7.776168976318346 chr12 133851895 29745271 0.22222525127492593 13.527960955697653 chr13 115169878 18787359 0.1631273673833361 9.99360453765878 chr14 107349540 41651769 0.3880013738298273 23.149132728051207 chr15 102531392 17603863 0.1716924217706905 11.105327997741957 chr16 90354753 42175762 0.4667796723433022 28.437743234679218 chr17 81195210 27351840 0.336865191924499 15.251243664809008 chr18 78077248 6167971 0.07899831459223562 3.229176814405645 chr19 59128983 5597222 0.09466122561248855 4.671707971002741 chr20 63025520 14071537 0.2232672891869833 14.326706857525455 chr21 48129895 8271517 0.17185819748827627 21.0532166878206 chr22 51304566 12155605 0.23693027634226552 13.86933650255285 chrMT 16571 38108 2.2996801641421762 2.4707593663424903 chrX 155270560 31299257 0.20157882473019997 28.851483324446562 chrY 59373566 188669 0.003177659903398762 0.44946068636069875