BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085132.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 = 1,502,412 number of mapped reads = 1,327,105 (88.33%) number of supplementary alignments = 10,363 (0.69%) number of secondary alignments = 0 number of mapped bases = 88,406,744 bp number of sequenced bases = 88,373,204 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,727 duplication rate = 2.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.667 >>>>>>> ACTG content number of A's = 24,779,249 bp (28.04%) number of C's = 16,409,341 bp (18.57%) number of T's = 27,562,717 bp (31.19%) number of G's = 19,604,079 bp (22.18%) number of N's = 17,818 bp (0.02%) GC percentage = 40.75% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 780,718 number of insertions = 7,052 mapped reads with insertion percentage = 0.53% number of deletions = 20,756 mapped reads with deletion percentage = 1.55% homopolymer indels = 46.58% >>>>>>> Coverage mean coverageData = 0.0286X std coverageData = 0.2712X There is a 2.6% of reference with a coverageData >= 1X There is a 0.18% 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 6811225 0.02732681255787122 0.4305981973904504 chr2 243199373 7605764 0.03127378128561211 0.3453852630623278 chr3 198022430 6141466 0.031013991697809183 0.18843280201099022 chr4 191154276 6126676 0.032050949255249726 0.19665691428144444 chr5 180915260 5155553 0.028497059894228932 0.1810675305964256 chr6 171115067 5243286 0.030641872115212392 0.2092980270263421 chr7 159138663 4885758 0.030701263337872833 0.3691266089417933 chr8 146364022 4611094 0.031504285937154694 0.3933323554254968 chr9 141213431 3525070 0.02496271052291053 0.25307363870532235 chr10 135534747 4113817 0.03035248960917749 0.25072042416517665 chr11 135006516 4129566 0.030587901401736787 0.24531754066682812 chr12 133851895 3958190 0.02957141548126756 0.18710780767486856 chr13 115169878 2901048 0.025189294721663247 0.1691689667974802 chr14 107349540 2708341 0.025229181233566534 0.1750455730837161 chr15 102531392 2513164 0.024511166297244848 0.16990352895793837 chr16 90354753 2499996 0.02766867172997529 0.192887763949663 chr17 81195210 2203418 0.027137290487948735 0.1890785488290647 chr18 78077248 2392542 0.030643267549593962 0.42667196034011823 chr19 59128983 1651107 0.027923818679580537 0.3559567337763208 chr20 63025520 1693528 0.026870512135401658 0.17945350329395232 chr21 48129895 1158110 0.024062175909588 0.17364682652806473 chr22 51304566 919424 0.01792090006179957 0.14238222941558948 chrMT 16571 15617 0.9424295455916963 1.091240613780265 chrX 155270560 5221469 0.03362819712893417 0.2152003725317977 chrY 59373566 221515 0.003730869053746915 0.09296227865709268