BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819099.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 = 1,337,884 number of mapped reads = 1,227,321 (91.74%) number of supplementary alignments = 4,865 (0.36%) number of secondary alignments = 0 number of mapped bases = 71,898,206 bp number of sequenced bases = 71,875,122 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,756 duplication rate = 2.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2234 >>>>>>> ACTG content number of A's = 18,450,375 bp (25.67%) number of C's = 14,157,104 bp (19.7%) number of T's = 22,387,791 bp (31.15%) number of G's = 16,878,755 bp (23.48%) number of N's = 1,097 bp (0%) GC percentage = 43.18% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 361,886 number of insertions = 5,099 mapped reads with insertion percentage = 0.41% number of deletions = 13,808 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.79% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.2281X There is a 2.1% of reference with a coverageData >= 1X There is a 0.16% 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 7023972 0.028180359077219712 0.4078426810252166 chr2 243199373 5735901 0.023585180048963365 0.2566193495953192 chr3 198022430 3977357 0.020085386286795896 0.1545043513468235 chr4 191154276 4101212 0.021454984349918493 0.17813591841104556 chr5 180915260 3975081 0.021972060289441587 0.16009707174524349 chr6 171115067 3116970 0.01821563731731467 0.18084031076583226 chr7 159138663 3654398 0.022963608786885435 0.28200179527277086 chr8 146364022 6562805 0.04483892223185832 0.26509322439743543 chr9 141213431 3043926 0.02155549920743729 0.1963398146330594 chr10 135534747 3802887 0.028058391550323254 0.2403736096754313 chr11 135006516 2482150 0.018385408893893684 0.20316103874845667 chr12 133851895 3235534 0.024172493037920757 0.1693763209586817 chr13 115169878 1577819 0.013699927684216181 0.12694512290754673 chr14 107349540 1685951 0.0157052466177312 0.13743064267325142 chr15 102531392 1934653 0.018868884565616743 0.149647142317427 chr16 90354753 2204046 0.024393249129904655 0.1762394603228044 chr17 81195210 2523105 0.031074554767454878 0.19871873777399343 chr18 78077248 1705063 0.021838154439049903 0.33539437517803955 chr19 59128983 1456794 0.02463756225944221 0.27749763130825056 chr20 63025520 2039873 0.03236582577977937 0.19661219495415122 chr21 48129895 989540 0.020559778906644198 0.16876117732276544 chr22 51304566 601940 0.011732678919845068 0.1160288383241418 chrMT 16571 8426 0.508478667551747 0.8618101408073833 chrX 155270560 4211785 0.02712545765275787 0.19172741375789895 chrY 59373566 247018 0.004160403638211658 0.13200770262481226