BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094115.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 407,974 number of mapped reads = 390,325 (95.67%) number of supplementary alignments = 31,533 (7.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 196,277 number of mapped paired reads (second in pair) = 194,048 number of mapped paired reads (both in pair) = 386,984 number of mapped paired reads (singletons) = 3,341 number of mapped bases = 47,857,645 bp number of sequenced bases = 46,997,293 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 376,943 duplication rate = 53.48% >>>>>>> Insert size mean insert size = 1,992,791.0633 std insert size = 12,371,070.4337 median insert size = 141 >>>>>>> Mapping quality mean mapping quality = 39.6397 >>>>>>> ACTG content number of A's = 13,561,419 bp (28.86%) number of C's = 10,159,499 bp (21.62%) number of T's = 12,634,451 bp (26.88%) number of G's = 10,641,419 bp (22.64%) number of N's = 505 bp (0%) GC percentage = 44.26% >>>>>>> Mismatches and indels general error rate = 0.0345 number of mismatches = 1,554,050 number of insertions = 30,262 mapped reads with insertion percentage = 7.63% number of deletions = 123,297 mapped reads with deletion percentage = 30.66% homopolymer indels = 28.84% >>>>>>> Coverage mean coverageData = 0.0155X std coverageData = 3.382X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 1275587 0.005117688352720293 1.840651102143415 chr2 243199373 1928354 0.007929107613283196 2.6807985102472016 chr3 198022430 1050001 0.005302434678738161 1.7036633249893791 chr4 191154276 1531634 0.008012554215632612 2.6038851870249538 chr5 180915260 1154651 0.006382275326028329 2.879561679917433 chr6 171115067 1442381 0.008429304474982323 3.120361684672775 chr7 159138663 923449 0.0058027947614465005 2.0031828762082355 chr8 146364022 1080500 0.007382278685946469 2.104495940509779 chr9 141213431 912430 0.006461354231949793 2.5272816156947844 chr10 135534747 950148 0.007010364655788231 2.0971031273426703 chr11 135006516 1713129 0.01268923197751433 3.9986675297300525 chr12 133851895 1407556 0.010515771928369038 2.9239783657670384 chr13 115169878 609070 0.005288448773037686 1.6582125607806508 chr14 107349540 131549 0.0012254267694114013 0.4679374981393364 chr15 102531392 462862 0.004514344250783214 1.295864476251567 chr16 90354753 142215 0.0015739625783714997 0.4392289462173485 chr17 81195210 345026 0.004249339339106334 1.144042699153517 chr18 78077248 323936 0.004148916724114046 1.2744727066105332 chr19 59128983 111608 0.0018875345784316975 0.5498719543052597 chr20 63025520 352089 0.005586451329556662 2.063208339807755 chr21 48129895 84569 0.0017570991999878661 0.3818953816223156 chr22 51304566 64994 0.0012668268161551157 0.3015923909664411 chrMT 16571 76476 4.615050389234204 29.72784327627393 chrX 155270560 29044120 0.1870549059654322 11.401878412063892 chrY 59373566 739311 0.012451854416155499 2.673944928874121