BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085108.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 = 2,952,359 number of mapped reads = 2,477,057 (83.9%) number of supplementary alignments = 15,962 (0.54%) number of secondary alignments = 0 number of mapped bases = 148,766,713 bp number of sequenced bases = 148,717,558 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,336 duplication rate = 2.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5567 >>>>>>> ACTG content number of A's = 42,843,793 bp (28.81%) number of C's = 30,799,458 bp (20.71%) number of T's = 41,905,510 bp (28.18%) number of G's = 33,165,658 bp (22.3%) number of N's = 3,139 bp (0%) GC percentage = 43.01% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,282,764 number of insertions = 10,955 mapped reads with insertion percentage = 0.44% number of deletions = 30,701 mapped reads with deletion percentage = 1.23% homopolymer indels = 43.7% >>>>>>> Coverage mean coverageData = 0.0481X std coverageData = 0.3697X There is a 4.17% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% 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 0.01% 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 13018676 0.05223126806171528 0.5657727669042539 chr2 243199373 14218842 0.058465783955783474 0.47590642661072347 chr3 198022430 9895728 0.04997276318647337 0.25846006082360484 chr4 191154276 8015789 0.04193361073439968 0.24386055980188961 chr5 180915260 6886904 0.03806701546348274 0.2185946927974429 chr6 171115067 9647704 0.056381382242628585 0.37648819428744323 chr7 159138663 13625706 0.08562159404342866 0.45849649868438436 chr8 146364022 10550667 0.07208511255587115 0.5116726567751091 chr9 141213431 4916454 0.034815767630488346 0.3332215765028035 chr10 135534747 11078734 0.08174091327296314 0.5651705250440355 chr11 135006516 6216820 0.04604829592076874 0.3339306095926863 chr12 133851895 5324997 0.03978275391618475 0.2303450512890765 chr13 115169878 2775325 0.02409766380059897 0.1700955357374589 chr14 107349540 4715812 0.043929503563778664 0.24530226165225275 chr15 102531392 2117884 0.020655956762978503 0.16107309297852038 chr16 90354753 3584163 0.039667675257769784 0.24775897363074958 chr17 81195210 2139544 0.026350618466286373 0.21774764530078874 chr18 78077248 3933598 0.05038084846433112 0.5431167109367016 chr19 59128983 2564200 0.04336621179498386 0.4060495737314186 chr20 63025520 3413901 0.054166962842988046 0.265412199547879 chr21 48129895 1693370 0.035183330443583974 0.22493435665374745 chr22 51304566 1072388 0.020902389077806446 0.15912779873630664 chrMT 16571 12536 0.7565023233359484 1.0309461534507907 chrX 155270560 6981097 0.04496085413744885 0.2921014841174358 chrY 59373566 365874 0.006162237248812039 0.12190635209217522