BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240222.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,252,048 number of mapped reads = 1,762,737 (78.27%) number of supplementary alignments = 21,092 (0.94%) number of secondary alignments = 0 number of mapped bases = 115,542,070 bp number of sequenced bases = 115,478,726 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 288,223 duplication rate = 11.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3722 >>>>>>> ACTG content number of A's = 32,703,754 bp (28.32%) number of C's = 21,271,740 bp (18.42%) number of T's = 36,936,391 bp (31.99%) number of G's = 24,556,886 bp (21.27%) number of N's = 9,955 bp (0.01%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 976,637 number of insertions = 8,567 mapped reads with insertion percentage = 0.48% number of deletions = 36,246 mapped reads with deletion percentage = 2.03% homopolymer indels = 45.02% >>>>>>> Coverage mean coverageData = 0.0373X std coverageData = 0.5191X There is a 1.49% of reference with a coverageData >= 1X There is a 0.82% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5558688 0.022301601407043233 0.685744741389374 chr2 243199373 11371940 0.04675974226298684 0.5445279879906564 chr3 198022430 8881227 0.04484960112851862 0.4363139916567767 chr4 191154276 7017520 0.03671128968101137 0.4000280054485505 chr5 180915260 5588576 0.030890572746599707 0.370804186291159 chr6 171115067 5099600 0.029802168151563183 0.38203115730191844 chr7 159138663 6874037 0.04319526675927898 0.5621247164109648 chr8 146364022 5502544 0.03759492206356559 0.9961216425370132 chr9 141213431 4827842 0.034188263579545776 0.5076957393658355 chr10 135534747 5817464 0.04292230685316438 0.46423948544012283 chr11 135006516 5786779 0.04286296077738944 0.47917830732597183 chr12 133851895 3736769 0.027917191609427718 0.3603078272649169 chr13 115169878 2672781 0.023207292101151657 0.32518322124538 chr14 107349540 3219935 0.029994865371570294 0.39401618541517247 chr15 102531392 3774966 0.03681766068288627 0.3929296470457533 chr16 90354753 5006630 0.055410809434673566 0.5053095130201066 chr17 81195210 4162797 0.051268997272129725 0.45751512737863587 chr18 78077248 3629418 0.046484963199522604 0.8057224785262374 chr19 59128983 2989303 0.05055563022282998 0.5808076260728754 chr20 63025520 2552841 0.04050487802401313 0.4066671429194817 chr21 48129895 1557278 0.032355732336420015 0.373530636328552 chr22 51304566 1193148 0.02325617567839868 0.30627587165653647 chrMT 16571 22607 1.3642507995896445 2.0827911104641026 chrX 155270560 8346345 0.053753557660898496 0.4945500992761388 chrY 59373566 351035 0.005912311212703646 0.1580370758998857