BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053668.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 7,985,600 number of mapped reads = 5,773,825 (72.3%) number of supplementary alignments = 185 (0%) number of secondary alignments = 0 number of mapped bases = 273,023,857 bp number of sequenced bases = 272,965,368 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,615,279 duplication rate = 21.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5409 >>>>>>> ACTG content number of A's = 79,421,997 bp (29.1%) number of C's = 52,387,239 bp (19.19%) number of T's = 83,195,175 bp (30.48%) number of G's = 57,836,504 bp (21.19%) number of N's = 124,453 bp (0.05%) GC percentage = 40.38% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,765,988 number of insertions = 12,546 mapped reads with insertion percentage = 0.22% number of deletions = 39,917 mapped reads with deletion percentage = 0.69% homopolymer indels = 48.66% >>>>>>> Coverage mean coverageData = 0.0882X std coverageData = 0.7276X There is a 3.94% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 1.01% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% 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 0.02% 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 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 25177747 0.10101377841702548 0.8443745766190155 chr2 243199373 15386593 0.06326740406522348 0.9789553825232014 chr3 198022430 16231109 0.08196601263806327 0.607696913071355 chr4 191154276 20961892 0.10965955059252769 0.7513857108002322 chr5 180915260 19379009 0.1071164975248633 0.7116469132505566 chr6 171115067 17454976 0.10200724171180087 0.8070821423447242 chr7 159138663 17221895 0.1082194274813029 0.8774759480540406 chr8 146364022 10274370 0.07019737405139086 0.6363564442353942 chr9 141213431 7895882 0.055914525580785586 0.5218227763023551 chr10 135534747 14739431 0.10875020115690333 0.7759326393193599 chr11 135006516 14433317 0.10690829915202019 0.7687096308764596 chr12 133851895 12751287 0.09526414997710717 0.6689686716181003 chr13 115169878 10637286 0.09236170242361462 0.6688166682680433 chr14 107349540 8495037 0.07913435865677673 0.6145809124356046 chr15 102531392 8148033 0.07946866653288 0.5958939308060965 chr16 90354753 6133104 0.06787804510959153 0.5553743045276077 chr17 81195210 7299511 0.0899007589240794 0.6188842172691406 chr18 78077248 8368911 0.10718757659081427 0.8202166314325546 chr19 59128983 5700651 0.09641043547121383 0.7448548670705107 chr20 63025520 6382050 0.10126136206412895 0.6937434985512312 chr21 48129895 3568451 0.07414208985911978 0.6037206861181281 chr22 51304566 3258089 0.06350485451918646 0.5157446313986696 chrMT 16571 19660 1.1864099933618972 2.361424568055063 chrX 155270560 12470533 0.08031485814181388 0.6394245151169341 chrY 59373566 635033 0.010695550946022005 0.23639054456301797