BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080775.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,376,849 number of mapped reads = 2,095,618 (88.17%) number of supplementary alignments = 20,418 (0.86%) number of secondary alignments = 0 number of mapped bases = 140,075,788 bp number of sequenced bases = 140,025,714 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,460 duplication rate = 3.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0899 >>>>>>> ACTG content number of A's = 39,183,746 bp (27.98%) number of C's = 27,274,799 bp (19.48%) number of T's = 42,501,693 bp (30.35%) number of G's = 31,062,654 bp (22.18%) number of N's = 2,822 bp (0%) GC percentage = 41.66% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,074,608 number of insertions = 10,867 mapped reads with insertion percentage = 0.51% number of deletions = 31,195 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.62% >>>>>>> Coverage mean coverageData = 0.0452X std coverageData = 0.3685X There is a 3.62% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% 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 17236574 0.0691535849774272 0.6820582479565158 chr2 243199373 11484782 0.047223731946052346 0.41078628410981494 chr3 198022430 9022813 0.04556460093939863 0.2558250064993408 chr4 191154276 8031858 0.042017673724442345 0.26374778706671026 chr5 180915260 12077512 0.06675784010702027 0.3130896112207616 chr6 171115067 9403057 0.05495166010132819 0.33450513351538136 chr7 159138663 8189550 0.05146172429511991 0.5212541786461051 chr8 146364022 6010051 0.04106235205807613 0.40169892860595424 chr9 141213431 4601203 0.03258332417402988 0.294574795505493 chr10 135534747 5703891 0.0420843446145954 0.30334949636366687 chr11 135006516 5683564 0.04209844212260096 0.28920957201680353 chr12 133851895 4947626 0.036963436341338314 0.2344408894918883 chr13 115169878 5582678 0.04847342114923487 0.26674778456100695 chr14 107349540 3689272 0.03436691018890253 0.24089315558963265 chr15 102531392 3650486 0.0356035934828623 0.23548608495578943 chr16 90354753 3622594 0.04009300982760697 0.2593638209914297 chr17 81195210 3520235 0.04335520531321983 0.2668522037038561 chr18 78077248 1713112 0.021941244650426205 0.5299543725036427 chr19 59128983 2345558 0.039668498949153246 0.4760273931342876 chr20 63025520 2777167 0.04406416638847248 0.2587756982738711 chr21 48129895 2186768 0.04543471370548388 0.2700732548872566 chr22 51304566 915151 0.01783761312784519 0.1556441068165488 chrMT 16571 14427 0.8706173435519884 1.1502733897294415 chrX 155270560 7329716 0.047206089808654005 0.27905597804494153 chrY 59373566 336143 0.005661492523457324 0.13287175873058