BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094135.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 = 530,136 number of mapped reads = 507,967 (95.82%) number of supplementary alignments = 3,789 (0.71%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 254,879 number of mapped paired reads (second in pair) = 253,088 number of mapped paired reads (both in pair) = 505,426 number of mapped paired reads (singletons) = 2,541 number of mapped bases = 73,258,709 bp number of sequenced bases = 73,073,556 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 503,860 duplication rate = 41.44% >>>>>>> Insert size mean insert size = 21,554.5855 std insert size = 1,047,992.7379 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 33.5711 >>>>>>> ACTG content number of A's = 20,298,830 bp (27.78%) number of C's = 15,760,283 bp (21.57%) number of T's = 20,710,221 bp (28.34%) number of G's = 16,303,248 bp (22.31%) number of N's = 974 bp (0%) GC percentage = 43.88% >>>>>>> Mismatches and indels general error rate = 0.0191 number of mismatches = 1,266,270 number of insertions = 42,039 mapped reads with insertion percentage = 8.18% number of deletions = 66,636 mapped reads with deletion percentage = 12.79% homopolymer indels = 55.96% >>>>>>> Coverage mean coverageData = 0.0237X std coverageData = 34.9781X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 171786 6.892099177558318E-4 0.4505946106578844 chr2 243199373 255608 0.00105102244650935 0.8779075475938426 chr3 198022430 148100 7.478950743105213E-4 0.33413159013218496 chr4 191154276 3083124 0.01612898264436418 18.697304461575005 chr5 180915260 193827 0.001071368993417139 0.6792512888090434 chr6 171115067 2817620 0.016466229709625746 16.524116030762553 chr7 159138663 67678 4.2527691714991974E-4 0.16511934210718215 chr8 146364022 24313 1.661132269240319E-4 0.04710664644514975 chr9 141213431 71408 5.056742796653669E-4 0.2081824481156019 chr10 135534747 1126855 0.008314141022449394 6.59675341764756 chr11 135006516 88347 6.543906369674779E-4 0.346883837667733 chr12 133851895 287020 0.0021443103214937673 1.0868671359920514 chr13 115169878 31926 2.77207899794771E-4 0.0836430179481343 chr14 107349540 100313 9.344520712431558E-4 0.6469535568373085 chr15 102531392 433672 0.004229650954119496 3.1333123234975613 chr16 90354753 565167 0.006254978086210916 4.037615377186825 chr17 81195210 108466 0.00133586698033049 0.7532168280434807 chr18 78077248 7049 9.028238290365972E-5 0.016821655731793127 chr19 59128983 51348 8.684066154156584E-4 0.2951995449137711 chr20 63025520 5070 8.044360443198247E-5 0.016884442505212382 chr21 48129895 48561 0.001008957114907481 0.30771704284898166 chr22 51304566 4550 8.868606353672303E-5 0.015505453741966303 chrMT 16571 57629142 3477.7105787218634 14321.071324120068 chrX 155270560 5916230 0.03810271567256536 20.65315410028679 chrY 59373566 21529 3.626024416320219E-4 0.12997344465498253