BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085112.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 = 2,014,447 number of mapped reads = 1,663,736 (82.59%) number of supplementary alignments = 11,724 (0.58%) number of secondary alignments = 0 number of mapped bases = 101,136,337 bp number of sequenced bases = 101,103,036 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,586 duplication rate = 2.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9827 >>>>>>> ACTG content number of A's = 29,727,941 bp (29.4%) number of C's = 19,844,940 bp (19.63%) number of T's = 28,903,354 bp (28.59%) number of G's = 22,624,712 bp (22.38%) number of N's = 2,089 bp (0%) GC percentage = 42.01% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 884,925 number of insertions = 7,698 mapped reads with insertion percentage = 0.46% number of deletions = 20,879 mapped reads with deletion percentage = 1.24% homopolymer indels = 44.15% >>>>>>> Coverage mean coverageData = 0.0327X std coverageData = 0.2866X There is a 2.97% of reference with a coverageData >= 1X There is a 0.22% 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% 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 7972937 0.03198763143703461 0.4784962075426547 chr2 243199373 10173437 0.04183167445912782 0.32753134654477856 chr3 198022430 5535057 0.027951666889452876 0.18478378486043942 chr4 191154276 5737491 0.030014975966323663 0.19033931412722152 chr5 180915260 4154626 0.02296448624621273 0.1630174010112549 chr6 171115067 6890670 0.040269218373388475 0.24526621860204503 chr7 159138663 9317222 0.05854782127960947 0.32951742003658296 chr8 146364022 5963412 0.040743701344856456 0.4388555633908237 chr9 141213431 3313119 0.0234617838865483 0.2391766068717609 chr10 135534747 7427159 0.05479892916316138 0.4213409833940296 chr11 135006516 4278971 0.03169455169111986 0.27524727941700705 chr12 133851895 4180324 0.03123096613611634 0.19241735028814544 chr13 115169878 2151383 0.018680084040724607 0.14421330375658598 chr14 107349540 3546671 0.0330385300207155 0.20338049813054482 chr15 102531392 1810948 0.017662376026261303 0.14118608253277684 chr16 90354753 2824898 0.03126452019629781 0.20428262322212493 chr17 81195210 1882080 0.023179692496638656 0.1878968063204249 chr18 78077248 2614710 0.033488757185704085 0.4313851923938017 chr19 59128983 1772560 0.02997785366949403 0.3300305429660246 chr20 63025520 2431902 0.03858598865983176 0.21115369333067474 chr21 48129895 1240446 0.02577287982863873 0.18243281452641233 chr22 51304566 791333 0.015424221695979262 0.13168259519858813 chrMT 16571 7787 0.4699173254480719 0.8086332375764901 chrX 155270560 4869519 0.03136150858218068 0.21028813858059825 chrY 59373566 247675 0.004171469168619584 0.0897650941900657