BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084900.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,349,216 number of mapped reads = 2,093,399 (89.11%) number of supplementary alignments = 14,822 (0.63%) number of secondary alignments = 0 number of mapped bases = 141,714,893 bp number of sequenced bases = 141,660,286 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,550 duplication rate = 4.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1458 >>>>>>> ACTG content number of A's = 40,184,119 bp (28.37%) number of C's = 25,633,019 bp (18.09%) number of T's = 45,591,699 bp (32.18%) number of G's = 30,229,504 bp (21.34%) number of N's = 21,945 bp (0.02%) GC percentage = 39.43% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,164,528 number of insertions = 10,998 mapped reads with insertion percentage = 0.52% number of deletions = 31,376 mapped reads with deletion percentage = 1.48% homopolymer indels = 48.65% >>>>>>> Coverage mean coverageData = 0.0458X std coverageData = 0.3781X There is a 3.87% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 10079296 0.04043839874725929 0.7881460408929968 chr2 243199373 13101682 0.053872186586599466 0.3796425934409841 chr3 198022430 8920309 0.045046962609235734 0.24100826357149435 chr4 191154276 9348786 0.04890702000304717 0.2570933579028629 chr5 180915260 8175905 0.04519190365699389 0.2490199439068583 chr6 171115067 6878522 0.04019822520947264 0.23571458302099493 chr7 159138663 9029706 0.05674112016386615 0.3345810422505253 chr8 146364022 8715529 0.05954693565335339 0.5328262411856598 chr9 141213431 10489126 0.07427852949766513 0.3941023669616586 chr10 135534747 5994104 0.04422558888164671 0.2913515534375226 chr11 135006516 6424794 0.047588769715381736 0.30361175638826454 chr12 133851895 5359249 0.040038648687043245 0.22760991501707545 chr13 115169878 5711013 0.049587731611559056 0.25282119854007257 chr14 107349540 2995065 0.027900119553376755 0.19835542532714553 chr15 102531392 3314290 0.03232463673174358 0.20518793576041727 chr16 90354753 2842426 0.031458511097916454 0.22231920666878666 chr17 81195210 3659123 0.04506574956823192 0.2570484985991706 chr18 78077248 3986320 0.0510561027970658 0.6569137268570621 chr19 59128983 2852518 0.04824229769011924 0.4503127292188761 chr20 63025520 2758406 0.04376649331889685 0.24802582707051216 chr21 48129895 1663584 0.03456446352106108 0.21960870615330955 chr22 51304566 1426542 0.027805361417539327 0.1877319654371107 chrMT 16571 209469 12.640697604248386 6.487295262825216 chrX 155270560 7452572 0.04799732801891099 0.2719115535024049 chrY 59373566 326557 0.005500040203076231 0.13033742967442008