BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819074.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 4,148,401 number of mapped reads = 3,723,752 (89.76%) number of supplementary alignments = 15,223 (0.37%) number of secondary alignments = 0 number of mapped bases = 215,347,962 bp number of sequenced bases = 215,292,377 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 237,887 duplication rate = 4.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.392 >>>>>>> ACTG content number of A's = 51,462,044 bp (23.9%) number of C's = 39,380,917 bp (18.29%) number of T's = 69,736,627 bp (32.39%) number of G's = 54,707,848 bp (25.41%) number of N's = 4,941 bp (0%) GC percentage = 43.7% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 1,021,701 number of insertions = 13,733 mapped reads with insertion percentage = 0.37% number of deletions = 33,119 mapped reads with deletion percentage = 0.88% homopolymer indels = 42.2% >>>>>>> Coverage mean coverageData = 0.0696X std coverageData = 0.4748X There is a 5.54% of reference with a coverageData >= 1X There is a 0.99% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 24191385 0.09705646831668276 0.8357220479971853 chr2 243199373 18161317 0.07467666045339681 0.5364487035073593 chr3 198022430 14146533 0.07143904354673357 0.3258637733659177 chr4 191154276 13744881 0.07190464836894363 0.36856740874116245 chr5 180915260 10753725 0.0594406740481704 0.3036973208012567 chr6 171115067 11393769 0.06658542231117497 0.35691895779671085 chr7 159138663 9203368 0.05783238231679752 0.4085152352299604 chr8 146364022 13649011 0.09325386671869403 0.5050411713058603 chr9 141213431 7881784 0.05581469088446693 0.49039806353027343 chr10 135534747 10028725 0.07399375600708503 0.43975568613301846 chr11 135006516 6805633 0.05040966318988633 0.4510586214166636 chr12 133851895 9713841 0.072571561276738 0.3383149507533666 chr13 115169878 6694800 0.05812978285867421 0.2905074269474851 chr14 107349540 7595926 0.07075881275317994 0.3623548672636633 chr15 102531392 6178630 0.06026086137599693 0.2991397861601954 chr16 90354753 6211706 0.06874797167560183 0.3606419015024679 chr17 81195210 4649934 0.057268575326056795 0.31927027326091856 chr18 78077248 5324185 0.06819124823661818 0.9919071421331075 chr19 59128983 3989768 0.06747567432370687 0.5951890375634544 chr20 63025520 6919195 0.10978402082204161 0.42381536231421246 chr21 48129895 2804710 0.058273761037708476 0.3433633583099939 chr22 51304566 2600438 0.05068628784424373 0.27249143377197393 chrMT 16571 13575 0.8192022207470883 1.1155985725787652 chrX 155270560 12095857 0.07790180572543823 0.4129327615207467 chrY 59373566 595266 0.01002577476986981 0.20605002208842607