BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549054.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 3,912,838 number of mapped reads = 3,396,363 (86.8%) number of secondary alignments = 0 number of mapped bases = 134,250,377 bp number of sequenced bases = 134,237,583 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,700 duplication rate = 2.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.2195 >>>>>>> ACTG content number of A's = 37,725,252 bp (28.1%) number of C's = 28,966,497 bp (21.58%) number of T's = 38,567,710 bp (28.73%) number of G's = 28,977,059 bp (21.59%) number of N's = 1,065 bp (0%) GC percentage = 43.16% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 401,679 number of insertions = 4,377 mapped reads with insertion percentage = 0.13% number of deletions = 9,892 mapped reads with deletion percentage = 0.29% homopolymer indels = 39.41% >>>>>>> Coverage mean coverageData = 0.0434X std coverageData = 0.4467X There is a 3.85% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 10452086 0.04193404196172494 0.739298905808973 chr2 243199373 11522971 0.047380759489046874 0.4279252335405119 chr3 198022430 9222734 0.04657418859065612 0.2359467694445814 chr4 191154276 9244206 0.04835992264175142 0.2676012367185255 chr5 180915260 8318157 0.045978194432023035 0.2397868738291805 chr6 171115067 7806734 0.04562271538601566 0.2453447707823591 chr7 159138663 7754479 0.04872781292626544 0.6193054713893786 chr8 146364022 7023244 0.04798477046497123 0.9532496113627357 chr9 141213431 5834004 0.04131337903687079 0.41448674542103064 chr10 135534747 6509016 0.04802470321503607 0.3882925300715487 chr11 135006516 6206480 0.04597170702486686 0.316643003146005 chr12 133851895 6252579 0.04671266701155034 0.2487025929980728 chr13 115169878 4139454 0.03594215841749871 0.2037677079439244 chr14 107349540 4120620 0.03838507365751171 0.2711913864959152 chr15 102531392 3832064 0.03737454378850138 0.21149028360581176 chr16 90354753 3662040 0.04052957789614012 0.25863354891391827 chr17 81195210 3664693 0.0451343496740756 0.2425873748736988 chr18 78077248 3582688 0.04588645337499601 0.744407140144608 chr19 59128983 2891527 0.04890202491728972 0.7618974024710548 chr20 63025520 2740340 0.04347984752842975 0.24343578516073586 chr21 48129895 1719097 0.03571786308696497 0.2705811653804398 chr22 51304566 1478964 0.02882714181813759 0.2497601112546371 chrMT 16571 9144 0.5518073743286465 0.9545925621420859 chrX 155270560 4960921 0.03195017136538955 0.2674662769586683 chrY 59373566 1302135 0.02193122441053987 0.24655516015008244