BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549104.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 = 11,770,868 number of mapped reads = 10,193,919 (86.6%) number of secondary alignments = 0 number of mapped bases = 404,532,024 bp number of sequenced bases = 404,493,542 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 440,659 duplication rate = 3.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3203 >>>>>>> ACTG content number of A's = 122,519,103 bp (30.29%) number of C's = 79,507,194 bp (19.66%) number of T's = 123,253,507 bp (30.47%) number of G's = 79,212,047 bp (19.58%) number of N's = 1,691 bp (0%) GC percentage = 39.24% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 1,208,586 number of insertions = 10,507 mapped reads with insertion percentage = 0.1% number of deletions = 31,066 mapped reads with deletion percentage = 0.3% homopolymer indels = 46.49% >>>>>>> Coverage mean coverageData = 0.1307X std coverageData = 0.8654X There is a 10.46% of reference with a coverageData >= 1X There is a 1.88% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 31977441 0.12829432830179388 1.8143404962013625 chr2 243199373 35852289 0.1474193315457273 0.7872118834177214 chr3 198022430 29215359 0.14753560493121914 0.464850000475755 chr4 191154276 29167563 0.1525865055720752 0.47528874746126004 chr5 180915260 26677004 0.14745579781384943 0.4781006719078524 chr6 171115067 24930212 0.14569267591146723 0.5549100294392321 chr7 159138663 23058661 0.14489666159882214 1.3216033738485684 chr8 146364022 21648000 0.14790520036406216 0.6947098117027439 chr9 141213431 17149790 0.12144588427994502 0.7469379493000314 chr10 135534747 18849650 0.13907614406805954 0.7114206339742166 chr11 135006516 18748427 0.13887053421925205 0.7725045948742707 chr12 133851895 18776545 0.1402785145477395 0.4907442144477346 chr13 115169878 14276770 0.12396270837414623 0.4106296912981306 chr14 107349540 12621291 0.11757191507294767 0.5961478798786809 chr15 102531392 11346130 0.1106600600916449 0.39333627970622004 chr16 90354753 10090907 0.11168097598584548 0.4863250509677503 chr17 81195210 8850802 0.10900645493742796 0.45927794747469874 chr18 78077248 11484393 0.14709013565642068 1.7333295719535489 chr19 59128983 6025896 0.10191103743489044 1.4500914934555795 chr20 63025520 7713903 0.1223933257512195 0.47451003063088976 chr21 48129895 5331316 0.11076932538498162 0.4930827348257941 chr22 51304566 3537277 0.06894663137779979 0.3400974935215584 chrMT 16571 53008 3.198841349345242 4.289392763354477 chrX 155270560 14006708 0.09020839494621517 0.5333481370312633 chrY 59373566 3142682 0.052930659411631095 0.40136686134470617