BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006383.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 4,920,688 number of mapped reads = 4,343,620 (88.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,205,283 number of mapped paired reads (second in pair) = 2,138,337 number of mapped paired reads (both in pair) = 3,984,328 number of mapped paired reads (singletons) = 359,292 number of mapped bases = 168,237,920 bp number of sequenced bases = 168,217,494 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 144,870 duplication rate = 2.89% >>>>>>> Insert size mean insert size = 72,612.4557 std insert size = 2,570,802.3651 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 48.3715 >>>>>>> ACTG content number of A's = 46,874,607 bp (27.87%) number of C's = 36,295,728 bp (21.58%) number of T's = 47,513,213 bp (28.25%) number of G's = 37,526,776 bp (22.31%) number of N's = 7,170 bp (0%) GC percentage = 43.89% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 621,532 number of insertions = 4,585 mapped reads with insertion percentage = 0.11% number of deletions = 15,225 mapped reads with deletion percentage = 0.35% homopolymer indels = 44.28% >>>>>>> Coverage mean coverageData = 0.0543X std coverageData = 0.3314X There is a 4.69% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.09% 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 13993537 0.05614243584973856 0.4204302633537107 chr2 243199373 14639522 0.06019555815219968 0.31879698032781756 chr3 198022430 11106390 0.056086525147681504 0.2643383134343171 chr4 191154276 10757798 0.05627809236137621 0.2927919706091845 chr5 180915260 9725577 0.05375763769181218 0.25914561333307573 chr6 171115067 9596386 0.05608147878643556 0.2818119079520652 chr7 159138663 9170245 0.05762424307913156 0.3484797853198261 chr8 146364022 8062178 0.05508305859482326 0.6780747091162974 chr9 141213431 6916118 0.04897634701617015 0.27220131678274206 chr10 135534747 7817551 0.05767931230210656 0.33826754911222945 chr11 135006516 7746311 0.057377312069885576 0.30092895106035167 chr12 133851895 7320672 0.05469232990687207 0.2640831158712065 chr13 115169878 5335224 0.04632482114811305 0.2427794901448738 chr14 107349540 5183000 0.048281529664682306 0.2553072929004093 chr15 102531392 4887010 0.047663548740272635 0.24487851496550642 chr16 90354753 5296586 0.058619893521262796 0.30191548237668087 chr17 81195210 4747267 0.05846732830668213 0.28350834538456826 chr18 78077248 4212868 0.0539576907218861 0.39324187492940654 chr19 59128983 3499944 0.059191682698144836 0.3445204775058342 chr20 63025520 3737340 0.059298836407855104 0.2796622214619947 chr21 48129895 2239149 0.046523039370852566 0.2742671512155554 chr22 51304566 2295056 0.04473395213985437 0.24422761766037904 chrMT 16571 4605 0.2778951179771891 0.6305870540143893 chrX 155270560 9489691 0.06111712999553811 0.29247385370597584 chrY 59373566 457895 0.007712102048915169 0.18990917052147036