BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237606.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 = 1,302,131 number of mapped reads = 1,154,375 (88.65%) number of supplementary alignments = 5,358 (0.41%) number of secondary alignments = 0 number of mapped bases = 73,899,948 bp number of sequenced bases = 73,859,888 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,088 duplication rate = 2.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5653 >>>>>>> ACTG content number of A's = 19,616,823 bp (26.56%) number of C's = 12,836,471 bp (17.38%) number of T's = 24,006,471 bp (32.5%) number of G's = 17,271,780 bp (23.38%) number of N's = 128,343 bp (0.17%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 641,743 number of insertions = 6,279 mapped reads with insertion percentage = 0.54% number of deletions = 24,426 mapped reads with deletion percentage = 2.09% homopolymer indels = 45.46% >>>>>>> Coverage mean coverageData = 0.0239X std coverageData = 0.2277X There is a 2.15% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 5388625 0.02161930421027918 0.2912767491032024 chr2 243199373 6637314 0.027291657532357207 0.3537251608316569 chr3 198022430 6210028 0.03136022520277122 0.19290579999930077 chr4 191154276 3702340 0.019368334716195416 0.16457301087235018 chr5 180915260 5633956 0.031141408414082923 0.19265568010683798 chr6 171115067 4016810 0.02347432093750108 0.19512741649633153 chr7 159138663 3925315 0.02466600464024258 0.2729458426751296 chr8 146364022 3395145 0.023196581739192708 0.29507093971269294 chr9 141213431 3103195 0.02197521140889212 0.19654830277586754 chr10 135534747 4924496 0.03633382663118853 0.2569355025924108 chr11 135006516 5040003 0.03733155368589765 0.24742601641447554 chr12 133851895 2481522 0.018539311677283312 0.15078257638589404 chr13 115169878 2932317 0.025460798004839424 0.17663674841106108 chr14 107349540 2053783 0.019131735450380133 0.15517697234483563 chr15 102531392 1863430 0.018174238773623595 0.1487318344308348 chr16 90354753 1419742 0.015712975276463873 0.17424685515448174 chr17 81195210 1165450 0.014353679237974752 0.14279264297548605 chr18 78077248 1460073 0.01870036454153712 0.28415782025012776 chr19 59128983 1046495 0.017698511743386488 0.2374702739650186 chr20 63025520 1262804 0.020036391607717002 0.15802903768489263 chr21 48129895 933575 0.019396988088172643 0.15981000326995684 chr22 51304566 439866 0.008573622862339387 0.09950047412120766 chrMT 16571 12869 0.7765976706294129 1.0814006723167187 chrX 155270560 4636715 0.029862164469555592 0.20061273494108917 chrY 59373566 214080 0.0036056449767561546 0.09852098696018506