BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548982.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 = 10,082,255 number of mapped reads = 4,479,168 (44.43%) number of secondary alignments = 0 number of mapped bases = 177,444,906 bp number of sequenced bases = 177,423,519 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,301 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6048 >>>>>>> ACTG content number of A's = 52,771,901 bp (29.74%) number of C's = 35,374,694 bp (19.94%) number of T's = 53,432,006 bp (30.12%) number of G's = 35,835,193 bp (20.2%) number of N's = 9,725 bp (0.01%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 495,450 number of insertions = 5,819 mapped reads with insertion percentage = 0.13% number of deletions = 16,991 mapped reads with deletion percentage = 0.38% homopolymer indels = 45.25% >>>>>>> Coverage mean coverageData = 0.0573X std coverageData = 0.3982X There is a 4.99% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 13829230 0.05548323187527786 0.6667944262336285 chr2 243199373 15298527 0.06290528964480513 0.3717564514870954 chr3 198022430 12754166 0.06440768351342825 0.2819053548060279 chr4 191154276 12301465 0.0643535957312302 0.28802451824581343 chr5 180915260 11094393 0.061323699283299817 0.2794708494134435 chr6 171115067 10891616 0.06365082976591419 0.3402543813459327 chr7 159138663 10275269 0.0645680239251476 0.6096902855264869 chr8 146364022 9528170 0.06509912661459932 0.6104716351936607 chr9 141213431 7530928 0.05333011135463453 0.3464022909893951 chr10 135534747 8283987 0.061120761895840627 0.3315647905967239 chr11 135006516 8287113 0.06138305946655197 0.360948355538148 chr12 133851895 8252138 0.061651260148390126 0.2839451260571576 chr13 115169878 6106071 0.05301795144733938 0.25413578796166275 chr14 107349540 5672726 0.05284350543095015 0.29714529706033005 chr15 102531392 5208681 0.050800841560797304 0.2505739255407835 chr16 90354753 4704624 0.052068362136964724 0.27114207418545144 chr17 81195210 4429752 0.05455681437365579 0.2817809035748146 chr18 78077248 4901747 0.06278073479229186 0.5814054187274956 chr19 59128983 3105833 0.052526406550912605 0.5676925947485267 chr20 63025520 3538065 0.0561370219555507 0.27155689294444174 chr21 48129895 2318525 0.048172243051849584 0.2771503712020072 chr22 51304566 1843217 0.03592695823603693 0.24068438028172856 chrMT 16571 1731 0.10445959809305413 0.35173993886623506 chrX 155270560 5925671 0.03816351921446023 0.261749089134376 chrY 59373566 1361261 0.02292705477720506 0.22070535154227727