BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818987.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,728,964 number of mapped reads = 2,671,390 (97.89%) number of supplementary alignments = 43,070 (1.58%) number of secondary alignments = 0 number of mapped bases = 247,132,844 bp number of sequenced bases = 246,989,864 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,584,824 duplication rate = 48.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3678 >>>>>>> ACTG content number of A's = 72,733,732 bp (29.45%) number of C's = 53,707,392 bp (21.74%) number of T's = 70,035,299 bp (28.36%) number of G's = 50,500,952 bp (20.45%) number of N's = 12,489 bp (0.01%) GC percentage = 42.19% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,547,003 number of insertions = 36,650 mapped reads with insertion percentage = 1.34% number of deletions = 81,699 mapped reads with deletion percentage = 2.99% homopolymer indels = 43.1% >>>>>>> Coverage mean coverageData = 0.0798X std coverageData = 0.8842X There is a 2.58% of reference with a coverageData >= 1X There is a 1.58% of reference with a coverageData >= 2X There is a 1.08% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.27% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 25069570 0.10057976946825742 1.394687356565006 chr2 243199373 19500563 0.08018344274267517 1.2640702677807805 chr3 198022430 12850767 0.06489551208921131 0.5835671449570954 chr4 191154276 14080592 0.0736608790273674 0.6818249738509506 chr5 180915260 13536641 0.0748231022634575 0.644090729539237 chr6 171115067 10716435 0.06262706836914601 0.6578046915327225 chr7 159138663 12147369 0.07633197848344371 0.9046816685573417 chr8 146364022 23273488 0.15901098973626182 1.0088425274646107 chr9 141213431 10138447 0.07179520338968323 0.8173331253341936 chr10 135534747 12713570 0.09380303045092932 0.9995469340806814 chr11 135006516 8407466 0.06227452014242039 0.654661613077763 chr12 133851895 11221355 0.08383411381661798 0.677701319417027 chr13 115169878 5445860 0.0472854542747714 0.498558873711617 chr14 107349540 5850961 0.054503829266525035 0.549642470227881 chr15 102531392 6400202 0.06242187758457429 0.5809762208623034 chr16 90354753 7643127 0.08459020412573094 1.0095356337193333 chr17 81195210 8699187 0.10713916498276191 0.8299280316418416 chr18 78077248 5671532 0.07264000903310526 0.9020717861760917 chr19 59128983 4706146 0.0795911879627627 1.2129952082350528 chr20 63025520 7145868 0.11338054807005163 0.8433189348247635 chr21 48129895 3418985 0.0710366187169118 0.6823660973417005 chr22 51304566 1999693 0.038976901198228636 0.4876008709385349 chrMT 16571 37853 2.284291835133667 3.9072021997399666 chrX 155270560 15607719 0.10051949963985446 0.7911792756847985 chrY 59373566 849448 0.01430683816431036 0.8198583146201993