BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630501.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017516/SRP017516.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 = 108,566,022 number of mapped reads = 108,212,483 (99.67%) number of supplementary alignments = 628,382 (0.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 54,230,706 number of mapped paired reads (second in pair) = 53,981,777 number of mapped paired reads (both in pair) = 107,928,992 number of mapped paired reads (singletons) = 283,491 number of mapped bases = 10,749,428,039 bp number of sequenced bases = 10,747,178,473 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,014,680 duplication rate = 14.69% >>>>>>> Insert size mean insert size = 45,885.6067 std insert size = 2,032,090.5954 median insert size = 317 >>>>>>> Mapping quality mean mapping quality = 53.9297 >>>>>>> ACTG content number of A's = 3,344,106,390 bp (31.12%) number of C's = 2,011,671,790 bp (18.72%) number of T's = 3,325,718,107 bp (30.95%) number of G's = 2,031,524,645 bp (18.9%) number of N's = 34,157,541 bp (0.32%) GC percentage = 37.62% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 131,168,582 number of insertions = 950,051 mapped reads with insertion percentage = 0.86% number of deletions = 1,009,672 mapped reads with deletion percentage = 0.91% homopolymer indels = 43.94% >>>>>>> Coverage mean coverageData = 3.4724X std coverageData = 11.6276X There is a 39.2% of reference with a coverageData >= 1X There is a 28.07% of reference with a coverageData >= 2X There is a 22.34% of reference with a coverageData >= 3X There is a 18.64% of reference with a coverageData >= 4X There is a 16% of reference with a coverageData >= 5X There is a 13.99% of reference with a coverageData >= 6X There is a 12.41% of reference with a coverageData >= 7X There is a 11.12% of reference with a coverageData >= 8X There is a 10.04% of reference with a coverageData >= 9X There is a 9.13% of reference with a coverageData >= 10X There is a 8.35% of reference with a coverageData >= 11X There is a 7.68% of reference with a coverageData >= 12X There is a 7.09% of reference with a coverageData >= 13X There is a 6.57% of reference with a coverageData >= 14X There is a 6.1% of reference with a coverageData >= 15X There is a 5.69% of reference with a coverageData >= 16X There is a 5.32% of reference with a coverageData >= 17X There is a 4.98% of reference with a coverageData >= 18X There is a 4.67% of reference with a coverageData >= 19X There is a 4.39% of reference with a coverageData >= 20X There is a 4.14% of reference with a coverageData >= 21X There is a 3.9% of reference with a coverageData >= 22X There is a 3.69% of reference with a coverageData >= 23X There is a 3.49% of reference with a coverageData >= 24X There is a 3.3% of reference with a coverageData >= 25X There is a 3.13% of reference with a coverageData >= 26X There is a 2.98% of reference with a coverageData >= 27X There is a 2.83% of reference with a coverageData >= 28X There is a 2.69% of reference with a coverageData >= 29X There is a 2.56% of reference with a coverageData >= 30X There is a 2.44% of reference with a coverageData >= 31X There is a 2.33% of reference with a coverageData >= 32X There is a 2.22% of reference with a coverageData >= 33X There is a 2.13% of reference with a coverageData >= 34X There is a 2.03% of reference with a coverageData >= 35X There is a 1.94% of reference with a coverageData >= 36X There is a 1.86% of reference with a coverageData >= 37X There is a 1.78% of reference with a coverageData >= 38X There is a 1.71% of reference with a coverageData >= 39X There is a 1.64% of reference with a coverageData >= 40X There is a 1.57% of reference with a coverageData >= 41X There is a 1.51% of reference with a coverageData >= 42X There is a 1.45% of reference with a coverageData >= 43X There is a 1.4% of reference with a coverageData >= 44X There is a 1.34% of reference with a coverageData >= 45X There is a 1.29% of reference with a coverageData >= 46X There is a 1.25% of reference with a coverageData >= 47X There is a 1.2% of reference with a coverageData >= 48X There is a 1.16% of reference with a coverageData >= 49X There is a 1.11% of reference with a coverageData >= 50X There is a 1.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 842784325 3.381272719075793 11.206719870348012 chr2 243199373 955859073 3.9303517159972285 12.044581790475565 chr3 198022430 776085788 3.919181215986492 11.427481935924183 chr4 191154276 854817764 4.471873618981979 14.431414490477271 chr5 180915260 774140390 4.279022068121837 13.589904678405066 chr6 171115067 695972263 4.067276337506854 12.37260911241777 chr7 159138663 581737525 3.655538597807624 11.460107919658768 chr8 146364022 574867728 3.9276573583089975 12.546193090093782 chr9 141213431 473084729 3.3501397540578135 11.251758602556986 chr10 135534747 427648298 3.1552668777992405 10.56245909063812 chr11 135006516 514829857 3.8133704376165074 12.983193339767066 chr12 133851895 486460368 3.634318124521136 10.517425966244646 chr13 115169878 435571341 3.7819901224519836 13.081360892173754 chr14 107349540 351977892 3.2788020516902074 12.27638166165251 chr15 102531392 286430623 2.7935895281710406 9.671958293161131 chr16 90354753 200081215 2.2143961259016445 8.053981978560994 chr17 81195210 151406199 1.8647183620807188 6.03238319444507 chr18 78077248 297295311 3.8077073490090223 11.25156996397301 chr19 59128983 64904360 1.0976742150292016 4.241058508942248 chr20 63025520 156303983 2.4800110018925667 8.461501842235776 chr21 48129895 132022459 2.7430448165324277 11.392329834626862 chr22 51304566 42619984 0.8307249690017844 3.935812494896681 chrMT 16571 2221 0.13402932834469858 0.7075257264128865 chrX 155270560 666650928 4.29347925324672 14.521479557682415 chrY 59373566 5873415 0.09892306283237223 1.436941432816812