BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063564.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 = 2,898,381 number of mapped reads = 2,629,559 (90.73%) number of supplementary alignments = 20,742 (0.72%) number of secondary alignments = 0 number of mapped bases = 174,114,890 bp number of sequenced bases = 174,037,692 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,643 duplication rate = 3.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7957 >>>>>>> ACTG content number of A's = 48,494,824 bp (27.86%) number of C's = 31,784,495 bp (18.26%) number of T's = 55,303,955 bp (31.78%) number of G's = 38,450,721 bp (22.09%) number of N's = 3,697 bp (0%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,362,443 number of insertions = 13,251 mapped reads with insertion percentage = 0.5% number of deletions = 47,147 mapped reads with deletion percentage = 1.78% homopolymer indels = 46.47% >>>>>>> Coverage mean coverageData = 0.0562X std coverageData = 0.5207X There is a 4.67% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 18589864 0.07458301979516432 1.0741782074153687 chr2 243199373 17322365 0.07122701340188077 0.6408320674350386 chr3 198022430 11069511 0.055900288669318926 0.2766978212785052 chr4 191154276 9630420 0.05038035351089923 0.2665002621848754 chr5 180915260 6355065 0.03512730214134507 0.21735211147614855 chr6 171115067 12817986 0.0749085759934863 0.38007017589525866 chr7 159138663 13018566 0.08180643065978253 0.6920144028113191 chr8 146364022 6070408 0.04147472799018874 0.7227580234371758 chr9 141213431 5897236 0.04176115514111402 0.4314269021009328 chr10 135534747 7303232 0.05388457323050893 0.4457372044147164 chr11 135006516 8384959 0.062107809670460645 0.384950480197671 chr12 133851895 6588169 0.04921984107882821 0.2730507917550255 chr13 115169878 4251781 0.036917474202759856 0.22232035098525738 chr14 107349540 3760903 0.035034179000673876 0.2672659605943451 chr15 102531392 3243430 0.031633531318876466 0.21470588677532093 chr16 90354753 3601496 0.03985950799954043 0.2688218238244047 chr17 81195210 4798049 0.05909275928961819 0.30738468491364657 chr18 78077248 5036520 0.06450688425903536 0.7290841740234948 chr19 59128983 3069842 0.051917720282792616 0.7726760319541255 chr20 63025520 2730866 0.0433295274676036 0.2584219568364254 chr21 48129895 3075341 0.06389669040416564 0.3067014809227207 chr22 51304566 1829008 0.035650004329049384 0.21553932257784028 chrMT 16571 8238 0.49713354655723857 0.7881121033558826 chrX 155270560 15177668 0.09774981168355418 0.44413753925687477 chrY 59373566 483967 0.008151220022728634 0.1794107860377025