BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617417.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,023,822 (93.82%) number of supplementary alignments = 493,588 (1.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,154,886 number of mapped paired reads (second in pair) = 14,868,936 number of mapped paired reads (both in pair) = 29,450,286 number of mapped paired reads (singletons) = 573,536 number of mapped bases = 2,955,850,600 bp number of sequenced bases = 2,955,192,085 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,421,997 duplication rate = 4.22% >>>>>>> Insert size mean insert size = 61,225.4302 std insert size = 2,367,692.3336 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 53.8967 >>>>>>> ACTG content number of A's = 881,835,552 bp (29.84%) number of C's = 594,090,271 bp (20.1%) number of T's = 873,733,011 bp (29.57%) number of G's = 604,835,513 bp (20.47%) number of N's = 697,738 bp (0.02%) GC percentage = 40.57% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 25,848,968 number of insertions = 243,627 mapped reads with insertion percentage = 0.8% number of deletions = 290,826 mapped reads with deletion percentage = 0.95% homopolymer indels = 45.01% >>>>>>> Coverage mean coverageData = 0.9548X std coverageData = 2.9433X There is a 29.58% of reference with a coverageData >= 1X There is a 16.99% of reference with a coverageData >= 2X There is a 10.88% of reference with a coverageData >= 3X There is a 7.53% of reference with a coverageData >= 4X There is a 5.47% of reference with a coverageData >= 5X There is a 4.12% of reference with a coverageData >= 6X There is a 3.19% of reference with a coverageData >= 7X There is a 2.52% of reference with a coverageData >= 8X There is a 2.03% of reference with a coverageData >= 9X There is a 1.66% of reference with a coverageData >= 10X There is a 1.38% of reference with a coverageData >= 11X There is a 1.15% of reference with a coverageData >= 12X There is a 0.98% of reference with a coverageData >= 13X There is a 0.83% of reference with a coverageData >= 14X There is a 0.72% of reference with a coverageData >= 15X There is a 0.62% of reference with a coverageData >= 16X There is a 0.54% of reference with a coverageData >= 17X There is a 0.47% of reference with a coverageData >= 18X There is a 0.42% of reference with a coverageData >= 19X There is a 0.37% of reference with a coverageData >= 20X There is a 0.33% of reference with a coverageData >= 21X There is a 0.29% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 190350788 0.7636923319842 2.753893331754201 chr2 243199373 295005137 1.213017670896709 3.14238216801373 chr3 198022430 249387867 1.259392014328882 3.4218484499298287 chr4 191154276 141502322 0.7402519313771458 2.2870928424092836 chr5 180915260 188981910 1.0445880021397864 2.864589806375549 chr6 171115067 135221878 0.7902394591587893 2.605138240208609 chr7 159138663 221020093 1.388852267786113 3.2431856596658717 chr8 146364022 130840120 0.8939363527465787 3.2693409052996767 chr9 141213431 118218837 0.8371642567058654 2.624831814214086 chr10 135534747 94801333 0.6994614672501658 2.4260227699990407 chr11 135006516 219464946 1.6255878049619472 3.842984917828255 chr12 133851895 140777282 1.051739177842794 2.842313770019598 chr13 115169878 128041939 1.111765864682083 2.7764599784849864 chr14 107349540 85542806 0.7968623433318858 2.895377963361535 chr15 102531392 67749380 0.6607671921590609 2.3902825804339893 chr16 90354753 74807495 0.8279309335282008 3.343031578463912 chr17 81195210 91566623 1.1277342961487506 3.7581210010311863 chr18 78077248 42375366 0.5427364191934634 2.019354503572939 chr19 59128983 42485196 0.7185172794194684 2.347906839890887 chr20 63025520 101235711 1.6062653826576916 4.751369576650911 chr21 48129895 40378216 0.8389425324946169 2.5199401194501196 chr22 51304566 24042571 0.4686243910532252 2.108696428670759 chrMT 16571 180687 10.903807857099753 5.391755184867619 chrX 155270560 129483381 0.8339210021526295 2.5780273602223627 chrY 59373566 2388716 0.0402319779815819 0.6367718135175442