BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013208.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,326,035 number of mapped reads = 2,054,150 (88.31%) number of supplementary alignments = 16,188 (0.7%) number of secondary alignments = 0 number of mapped bases = 139,289,919 bp number of sequenced bases = 139,232,256 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,283 duplication rate = 4.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3648 >>>>>>> ACTG content number of A's = 39,813,265 bp (28.59%) number of C's = 25,249,237 bp (18.13%) number of T's = 44,847,341 bp (32.21%) number of G's = 29,291,746 bp (21.04%) number of N's = 30,667 bp (0.02%) GC percentage = 39.17% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,088,529 number of insertions = 10,542 mapped reads with insertion percentage = 0.51% number of deletions = 33,154 mapped reads with deletion percentage = 1.6% homopolymer indels = 47.11% >>>>>>> Coverage mean coverageData = 0.045X std coverageData = 0.4752X There is a 3.55% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 4162178 0.016698766820725394 0.6384300641492887 chr2 243199373 31842162 0.13093027998883863 0.614778836252062 chr3 198022430 6330439 0.03196829268280366 0.2198347683908452 chr4 191154276 5392172 0.0282084822418516 0.26015205727821367 chr5 180915260 6289502 0.03476490595652351 0.22978969345887307 chr6 171115067 16287086 0.09518206833300075 0.46847353947805154 chr7 159138663 10549172 0.06628918328916714 1.249955368679667 chr8 146364022 6929043 0.047341162843967215 0.3716407522536317 chr9 141213431 7260036 0.05141179524205456 0.40889454290411936 chr10 135534747 5752394 0.042442208565158575 0.48375514397584685 chr11 135006516 1828297 0.013542287099683395 0.1928827316379156 chr12 133851895 9786269 0.07311266680236392 0.33527922104877816 chr13 115169878 444550 0.0038599502553957727 0.07907466417472997 chr14 107349540 5664680 0.052768554015229126 0.29905261485695933 chr15 102531392 1241486 0.012108350191910006 0.13278066950318446 chr16 90354753 2886430 0.031945524769460665 0.24843707913037733 chr17 81195210 2592784 0.031932721154363665 0.2216454750676533 chr18 78077248 2710463 0.03471514518544506 0.6590774678792063 chr19 59128983 1007220 0.01703428587635272 0.46105277260580035 chr20 63025520 2876719 0.0456437170212955 0.2661400340132038 chr21 48129895 1966755 0.04086347996396003 0.2892324655163376 chr22 51304566 1046685 0.02040140053031537 0.16409209008168693 chrMT 16571 37067 2.236859573954499 2.0510457461855887 chrX 155270560 4196935 0.027029818144534288 0.22917854891598202 chrY 59373566 209395 0.003526737807865541 0.17232660216248472