BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251067.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 3,918,213 number of mapped reads = 3,695,212 (94.31%) number of supplementary alignments = 31,340 (0.8%) number of secondary alignments = 0 number of mapped bases = 286,573,369 bp number of sequenced bases = 286,381,234 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 790,435 duplication rate = 19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0538 >>>>>>> ACTG content number of A's = 83,644,675 bp (29.21%) number of C's = 57,413,497 bp (20.05%) number of T's = 84,499,797 bp (29.51%) number of G's = 60,820,776 bp (21.24%) number of N's = 2,489 bp (0%) GC percentage = 41.29% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,670,116 number of insertions = 36,561 mapped reads with insertion percentage = 0.97% number of deletions = 107,399 mapped reads with deletion percentage = 2.86% homopolymer indels = 45.15% >>>>>>> Coverage mean coverageData = 0.0926X std coverageData = 0.9135X There is a 6.17% of reference with a coverageData >= 1X There is a 1.88% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% 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 23993655 0.09626317039346514 1.792862498188023 chr2 243199373 25297058 0.10401777639451398 1.3830593639128506 chr3 198022430 19744420 0.0997079977253082 0.4396649303247894 chr4 191154276 17091582 0.08941250155450355 0.49195186258343737 chr5 180915260 17442054 0.09641007618705022 0.4571491187002837 chr6 171115067 16666638 0.09740017809185675 0.5365248428433913 chr7 159138663 15721231 0.09878951289165977 1.2395226302900473 chr8 146364022 13563231 0.09266779372870745 0.6047717038139808 chr9 141213431 12196154 0.0863668130830983 0.9400753578591636 chr10 135534747 17165316 0.12664882164866548 0.9795094195428162 chr11 135006516 13133121 0.09727768250830204 0.5596237162060952 chr12 133851895 12823828 0.09580609971939508 0.4451568930394547 chr13 115169878 8187428 0.07109001192134631 0.3682947830877285 chr14 107349540 8630189 0.08039334868132644 0.5554484713336895 chr15 102531392 8758635 0.08542393533484847 0.4074873263031491 chr16 90354753 7771043 0.08600591271606929 0.8243610097946368 chr17 81195210 8118994 0.09999350946933938 0.49760525141814077 chr18 78077248 6984332 0.08945412625199085 1.0206909435943887 chr19 59128983 5985954 0.10123553114383854 1.663490215036125 chr20 63025520 5876501 0.09324002404105512 0.452344785996346 chr21 48129895 3454738 0.0717794626395923 0.39678260781068536 chr22 51304566 3594783 0.07006750627224875 0.3983922449372598 chrMT 16571 307677 18.567195703337156 10.882945863775197 chrX 155270560 13297901 0.08564341495258342 0.4698178909966014 chrY 59373566 766906 0.012916623535800427 1.006809155794526