BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089699.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 = 22,819,058 number of mapped reads = 19,049,141 (83.48%) number of supplementary alignments = 807 (0%) number of secondary alignments = 0 number of mapped bases = 890,338,140 bp number of sequenced bases = 890,165,231 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,681,055 duplication rate = 6.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.6394 >>>>>>> ACTG content number of A's = 259,356,199 bp (29.14%) number of C's = 189,528,406 bp (21.29%) number of T's = 249,503,405 bp (28.03%) number of G's = 191,608,512 bp (21.53%) number of N's = 168,709 bp (0.02%) GC percentage = 42.82% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 4,815,234 number of insertions = 38,783 mapped reads with insertion percentage = 0.2% number of deletions = 116,453 mapped reads with deletion percentage = 0.61% homopolymer indels = 44.06% >>>>>>> Coverage mean coverageData = 0.2876X std coverageData = 1.6486X There is a 16.14% of reference with a coverageData >= 1X There is a 5.95% of reference with a coverageData >= 2X There is a 2.63% of reference with a coverageData >= 3X There is a 1.33% of reference with a coverageData >= 4X There is a 0.75% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 68025425 0.2729197814114975 1.8200407447176643 chr2 243199373 89782243 0.3691713588422779 2.979941381155673 chr3 198022430 72016004 0.36367599367404996 1.0924664472716341 chr4 191154276 39660798 0.20748056925496136 0.8003120525233403 chr5 180915260 41394727 0.22880727142641258 0.8127221047238057 chr6 171115067 51653118 0.301861892734437 1.0990039503919713 chr7 159138663 49830514 0.3131263833729708 2.6008120537941015 chr8 146364022 66694364 0.4556745782785335 2.3437456425062217 chr9 141213431 30870010 0.218605339317901 1.676243668107332 chr10 135534747 40101358 0.2958751086907625 1.3086138693951888 chr11 135006516 42436466 0.31432902097851334 1.6573997150210893 chr12 133851895 31862435 0.23804246477048382 0.8815474266312082 chr13 115169878 24076307 0.20905038207993934 0.7517318111319142 chr14 107349540 36514198 0.3401430318192328 1.1194453736527634 chr15 102531392 24524311 0.23918831610127755 0.8269360852674356 chr16 90354753 19015759 0.21045665411757586 0.871727789353909 chr17 81195210 23004805 0.28332711991261555 1.0840698744705328 chr18 78077248 46665700 0.5976862811558112 2.5471145971976323 chr19 59128983 17198265 0.2908601522877537 2.165112426886749 chr20 63025520 22116710 0.3509167397587517 1.1087386142887592 chr21 48129895 15248408 0.3168178114662415 1.1533921614970857 chr22 51304566 8152269 0.15889948274779286 0.6549593640758755 chrMT 16571 886139 53.475288154003984 43.92253298083479 chrX 155270560 26446585 0.17032581707697841 1.2608199729977234 chrY 59373566 2161222 0.036400407548369255 0.6701531547442316