BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472479.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,939,254 number of mapped reads = 16,638,638 (98.23%) number of supplementary alignments = 69,887 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,365,189 number of mapped paired reads (second in pair) = 8,273,449 number of mapped paired reads (both in pair) = 16,487,336 number of mapped paired reads (singletons) = 151,302 number of mapped bases = 1,634,986,297 bp number of sequenced bases = 1,634,775,358 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,472,059 duplication rate = 46.44% >>>>>>> Insert size mean insert size = 32,603.3327 std insert size = 1,792,216.1233 median insert size = 247 >>>>>>> Mapping quality mean mapping quality = 55.0271 >>>>>>> ACTG content number of A's = 450,274,427 bp (27.54%) number of C's = 369,372,670 bp (22.59%) number of T's = 447,853,135 bp (27.4%) number of G's = 367,026,378 bp (22.45%) number of N's = 248,748 bp (0.02%) GC percentage = 45.05% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 10,673,002 number of insertions = 87,190 mapped reads with insertion percentage = 0.52% number of deletions = 85,807 mapped reads with deletion percentage = 0.51% homopolymer indels = 44.58% >>>>>>> Coverage mean coverageData = 0.5281X std coverageData = 19.0175X There is a 5.08% of reference with a coverageData >= 1X There is a 2.23% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 149730745 0.6007236587787679 22.084603562471134 chr2 243199373 137806042 0.5666381467192352 20.22757706168027 chr3 198022430 193904803 0.9792062596141256 21.13240365032147 chr4 191154276 72954243 0.3816511172368438 13.636373856791948 chr5 180915260 85154077 0.470684877549854 15.0454682577325 chr6 171115067 93636458 0.5472134023124918 14.731854574696778 chr7 159138663 65047475 0.4087471502761086 12.310534197986719 chr8 146364022 61219479 0.4182686302512239 12.710696533320563 chr9 141213431 98843277 0.6999566280632329 17.496157591780793 chr10 135534747 33457264 0.24685377543811698 7.735792516031744 chr11 135006516 71804992 0.5318631583678524 17.296162648948588 chr12 133851895 99826024 0.7457946262172829 26.756871728354692 chr13 115169878 35615717 0.30924507013891256 13.852444594979136 chr14 107349540 40427379 0.3765957357618859 20.349467322805996 chr15 102531392 45636797 0.4451007258342889 14.465211894548549 chr16 90354753 47791018 0.5289264417556429 14.418377071338131 chr17 81195210 47201044 0.5813279379411668 16.27282204227355 chr18 78077248 28417803 0.3639703463933565 12.673897036610985 chr19 59128983 28940316 0.48944383163160443 12.689065056961411 chr20 63025520 38233163 0.6066298699320529 24.88009460949482 chr21 48129895 9419948 0.19571927177485013 8.530344913853902 chr22 51304566 18341766 0.357507477989386 11.621449191932351 chrMT 16571 6462 0.38995836099209463 1.236796517202177 chrX 155270560 129603784 0.8346964421330096 41.011505115720844 chrY 59373566 1966221 0.033116100858755895 1.1071454156770955