BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549147.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 = 13,254,199 number of mapped reads = 11,542,880 (87.09%) number of secondary alignments = 0 number of mapped bases = 458,408,785 bp number of sequenced bases = 458,365,891 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 597,115 duplication rate = 4.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8014 >>>>>>> ACTG content number of A's = 134,240,262 bp (29.29%) number of C's = 93,959,113 bp (20.5%) number of T's = 135,834,971 bp (29.63%) number of G's = 94,239,202 bp (20.56%) number of N's = 92,343 bp (0.02%) GC percentage = 41.06% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 1,382,538 number of insertions = 11,131 mapped reads with insertion percentage = 0.1% number of deletions = 33,900 mapped reads with deletion percentage = 0.29% homopolymer indels = 45.79% >>>>>>> Coverage mean coverageData = 0.1481X std coverageData = 1.0088X There is a 10.67% of reference with a coverageData >= 1X There is a 2.78% of reference with a coverageData >= 2X There is a 0.78% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 36160176 0.1450755703433132 1.7862649436227536 chr2 243199373 38818558 0.15961619276049696 0.749392093283411 chr3 198022430 31213149 0.15762431053896267 0.5137492295724454 chr4 191154276 30955178 0.1619381927925065 0.5580837622161553 chr5 180915260 28755007 0.15894185487725027 0.5270914453090778 chr6 171115067 27559172 0.1610563726688077 0.5932213795307254 chr7 159138663 32605678 0.20488847515326933 1.255453046485401 chr8 146364022 23726715 0.1621075635650406 2.5784510458825514 chr9 141213431 18974051 0.13436435093769517 0.6957312183228148 chr10 135534747 21284419 0.15704031232669804 0.7670489919595407 chr11 135006516 21040062 0.15584478900262858 0.6961051193466845 chr12 133851895 21062040 0.15735331950287293 0.5418737755089621 chr13 115169878 15077814 0.13091803396718021 0.4615230844882652 chr14 107349540 13928476 0.12974881867216198 0.6051507715325254 chr15 102531392 13272711 0.12945021754898245 0.46321842856891626 chr16 90354753 12401627 0.13725483815998035 0.5440236932098322 chr17 81195210 11630427 0.14324030937292975 0.5459815222978843 chr18 78077248 11997038 0.1536560048837787 1.447094218786304 chr19 59128983 8298714 0.1403493444154113 1.408516497503555 chr20 63025520 9269796 0.14708003995841684 0.5329712174974713 chr21 48129895 6060203 0.1259134889033105 0.5486643338242991 chr22 51304566 4920939 0.09591619973941501 0.4345049208002173 chrMT 16571 61379 3.704000965542212 4.436703504266539 chrX 155270560 15565648 0.10024854679470467 0.5150899323253614 chrY 59373566 3769808 0.06349303661498115 0.5213151597401751