BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472740.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 = 15,245,516 number of mapped reads = 15,088,646 (98.97%) number of supplementary alignments = 56,625 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,574,372 number of mapped paired reads (second in pair) = 7,514,274 number of mapped paired reads (both in pair) = 14,994,196 number of mapped paired reads (singletons) = 94,450 number of mapped bases = 1,488,551,807 bp number of sequenced bases = 1,488,339,915 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,216,507 duplication rate = 46.36% >>>>>>> Insert size mean insert size = 24,400.1228 std insert size = 1,541,783.2475 median insert size = 253 >>>>>>> Mapping quality mean mapping quality = 55.0729 >>>>>>> ACTG content number of A's = 413,037,172 bp (27.75%) number of C's = 333,270,165 bp (22.39%) number of T's = 410,024,577 bp (27.55%) number of G's = 331,720,688 bp (22.29%) number of N's = 287,313 bp (0.02%) GC percentage = 44.68% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 9,196,302 number of insertions = 90,385 mapped reads with insertion percentage = 0.59% number of deletions = 85,757 mapped reads with deletion percentage = 0.56% homopolymer indels = 46.14% >>>>>>> Coverage mean coverageData = 0.4808X std coverageData = 16.2607X There is a 4.57% of reference with a coverageData >= 1X There is a 1.96% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% 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 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 130032561 0.5216940302026369 15.257600412834034 chr2 243199373 93338399 0.38379374851431053 11.715822754959964 chr3 198022430 160861042 0.8123374811631188 18.277075195470992 chr4 191154276 60241543 0.3151461963634023 13.20050733945113 chr5 180915260 78384552 0.43326666860495905 13.670806102734826 chr6 171115067 88321612 0.5161533320733235 13.791643874573593 chr7 159138663 75097697 0.471901017542167 15.593998657907923 chr8 146364022 63987654 0.4371815773141298 12.442560430164537 chr9 141213431 97373066 0.6895453591804592 22.495707835555873 chr10 135534747 28751212 0.21213166834627287 7.091718162900768 chr11 135006516 77691387 0.5754639798274626 17.829057913671114 chr12 133851895 82249633 0.6144823948887687 18.479888513336864 chr13 115169878 24596948 0.21357101724115746 6.973772527550088 chr14 107349540 43261204 0.4029938460844825 15.967154248081046 chr15 102531392 38544767 0.37593137329102094 17.461816540910785 chr16 90354753 49012616 0.5424464610068714 22.018757700921004 chr17 81195210 76675889 0.9443400540499864 28.630849271131478 chr18 78077248 28598543 0.366285233311502 11.105412985938612 chr19 59128983 49376204 0.8350592466641952 25.045243861499532 chr20 63025520 43867286 0.6960241819504226 33.43340058775404 chr21 48129895 4747254 0.09863420645318258 4.106376591433954 chr22 51304566 17056994 0.3324654183801107 7.723167345990641 chrMT 16571 5252 0.31693923118701345 1.1205496271006907 chrX 155270560 73761066 0.4750486248004773 15.473867030858122 chrY 59373566 2717426 0.04576828011307254 1.435812546206742