BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084817.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 = 2,150,558 number of mapped reads = 1,986,686 (92.38%) number of supplementary alignments = 15,653 (0.73%) number of secondary alignments = 0 number of mapped bases = 134,401,860 bp number of sequenced bases = 134,350,419 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,818 duplication rate = 3.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3004 >>>>>>> ACTG content number of A's = 37,358,267 bp (27.81%) number of C's = 24,785,610 bp (18.45%) number of T's = 42,608,590 bp (31.71%) number of G's = 29,578,628 bp (22.02%) number of N's = 19,324 bp (0.01%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,024,537 number of insertions = 10,573 mapped reads with insertion percentage = 0.53% number of deletions = 31,334 mapped reads with deletion percentage = 1.56% homopolymer indels = 49.01% >>>>>>> Coverage mean coverageData = 0.0434X std coverageData = 0.2953X There is a 3.64% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.1% 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 10847931 0.043522182438213465 0.3616177538663903 chr2 243199373 11554171 0.04750904929347824 0.44756516457034073 chr3 198022430 11733096 0.0592513484457291 0.28284085623241617 chr4 191154276 8742085 0.045733138608942236 0.24955764549837017 chr5 180915260 7740941 0.042787662024751254 0.24160630217102289 chr6 171115067 7466252 0.04363293151736311 0.2603144133607945 chr7 159138663 8550328 0.05372879122404089 0.3593343617698875 chr8 146364022 6120274 0.04181542647140429 0.3147408500247566 chr9 141213431 9888944 0.07002835303959154 0.35687765176992875 chr10 135534747 3928839 0.02898768830106718 0.20679385230937128 chr11 135006516 5903761 0.04372945228806586 0.27688257568068114 chr12 133851895 5827411 0.043536260730563436 0.24282811382256983 chr13 115169878 3471241 0.030140181272051012 0.20049014740986454 chr14 107349540 2632561 0.024523262978118025 0.18258660666558538 chr15 102531392 2831379 0.02761475236774314 0.1980630510580179 chr16 90354753 2590428 0.028669526660097228 0.20215057600331282 chr17 81195210 3717825 0.04578872325103907 0.2517052679201398 chr18 78077248 5774737 0.07396184097062437 0.46424446199254915 chr19 59128983 2756803 0.04662354838742956 0.3034766861629949 chr20 63025520 2729645 0.043310154362867614 0.24596056249774706 chr21 48129895 1116698 0.023201754335844697 0.18111835570205104 chr22 51304566 867421 0.0169072865756237 0.14723434010237202 chrMT 16571 39622 2.3910445959809303 2.14335857179625 chrX 155270560 7329049 0.0472017940812476 0.2620951812384183 chrY 59373566 240418 0.004049243058771306 0.08923614455485444