BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094028.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 = 439,730 number of mapped reads = 405,957 (92.32%) number of supplementary alignments = 20,359 (4.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 204,011 number of mapped paired reads (second in pair) = 201,946 number of mapped paired reads (both in pair) = 401,370 number of mapped paired reads (singletons) = 4,587 number of mapped bases = 51,782,856 bp number of sequenced bases = 50,864,207 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 377,853 duplication rate = 47.08% >>>>>>> Insert size mean insert size = 675,749.9632 std insert size = 7,483,986.5286 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 45.4819 >>>>>>> ACTG content number of A's = 14,252,677 bp (28.02%) number of C's = 11,178,485 bp (21.98%) number of T's = 13,579,483 bp (26.7%) number of G's = 11,853,037 bp (23.3%) number of N's = 525 bp (0%) GC percentage = 45.28% >>>>>>> Mismatches and indels general error rate = 0.0349 number of mismatches = 1,716,457 number of insertions = 32,252 mapped reads with insertion percentage = 7.81% number of deletions = 139,964 mapped reads with deletion percentage = 33.22% homopolymer indels = 28.11% >>>>>>> Coverage mean coverageData = 0.0167X std coverageData = 4.9213X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% 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 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 769709 0.0030880926069989613 0.8714070449444017 chr2 243199373 2078631 0.008547024502402809 2.482768139794178 chr3 198022430 924593 0.004669132683605589 1.5916850689476134 chr4 191154276 1075145 0.0056244883582933815 1.990542955632052 chr5 180915260 829580 0.004585461723903224 1.635510680484273 chr6 171115067 657018 0.0038396268167314573 1.0858919282789978 chr7 159138663 1400451 0.008800193325741338 2.6592065434395846 chr8 146364022 962269 0.006574491373296643 2.2589684896320854 chr9 141213431 1063026 0.007527796700867639 2.894161726925658 chr10 135534747 1351076 0.009968484317899675 2.870191990501944 chr11 135006516 1180486 0.008743918700931443 2.5876270201881724 chr12 133851895 1036946 0.007746965405308606 1.7152628890368893 chr13 115169878 1595742 0.013855549972884403 3.6100647806517947 chr14 107349540 332111 0.0030937347286257586 0.5763305526747793 chr15 102531392 514631 0.005019253030330457 1.3464861771201362 chr16 90354753 393571 0.004355841689921946 1.4905615194906974 chr17 81195210 970315 0.01195039707391606 2.685531246569352 chr18 78077248 219616 0.0028128040578479403 0.6884497108710042 chr19 59128983 173154 0.0029284116048469834 0.39028274539990765 chr20 63025520 412780 0.006549410461032293 2.3792643444986674 chr21 48129895 210999 0.004383948894964346 0.7111560468402239 chr22 51304566 157039 0.003060916644339219 0.4685339170476525 chrMT 16571 6027685 363.7490193711906 1546.3736402950128 chrX 155270560 26581292 0.17119338012305746 11.514778055422903 chrY 59373566 864991 0.01456862132889239 2.956057118555551