BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046485.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 7,887,352 number of mapped reads = 7,855,708 (99.6%) number of supplementary alignments = 35,107 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,933,835 number of mapped paired reads (second in pair) = 3,921,873 number of mapped paired reads (both in pair) = 7,833,046 number of mapped paired reads (singletons) = 22,662 number of mapped bases = 770,849,238 bp number of sequenced bases = 770,619,999 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,273,613 duplication rate = 39.48% >>>>>>> Insert size mean insert size = 17,003.6682 std insert size = 1,317,105.6183 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 53.6345 >>>>>>> ACTG content number of A's = 223,361,330 bp (28.98%) number of C's = 162,635,921 bp (21.1%) number of T's = 224,986,797 bp (29.2%) number of G's = 159,567,606 bp (20.71%) number of N's = 68,345 bp (0.01%) GC percentage = 41.81% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 2,799,522 number of insertions = 62,902 mapped reads with insertion percentage = 0.78% number of deletions = 80,751 mapped reads with deletion percentage = 0.99% homopolymer indels = 49.02% >>>>>>> Coverage mean coverageData = 0.249X std coverageData = 14.3363X There is a 2.94% of reference with a coverageData >= 1X There is a 1.23% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.07% of reference with a coverageData >= 28X There is a 0.07% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.06% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% 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 0.06% of reference with a coverageData >= 41X There is a 0.06% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 133309956 0.5348430245234975 24.42797803265536 chr2 243199373 75862191 0.31193415535656005 15.215982392147145 chr3 198022430 33144365 0.16737682190850803 8.002140964593249 chr4 191154276 22448672 0.11743745664365886 6.764264291329221 chr5 180915260 39455298 0.21808717517803639 13.043610609731282 chr6 171115067 54102489 0.3161760676515996 14.582754462927497 chr7 159138663 42440378 0.26668803922275003 11.652703274137343 chr8 146364022 67892295 0.4638591784530217 20.2967628933153 chr9 141213431 17692547 0.12528940678454303 7.365402368844346 chr10 135534747 23791192 0.17553573918576024 9.212510241247598 chr11 135006516 20432897 0.15134748755386 7.39645488375825 chr12 133851895 22326061 0.1667967494968973 11.556278765173445 chr13 115169878 17068105 0.14819938421746007 9.306760852517202 chr14 107349540 32901150 0.30648617590722793 20.39179296344004 chr15 102531392 21512690 0.20981564358357682 11.697257830813005 chr16 90354753 54469761 0.6028433390770267 31.2946881488266 chr17 81195210 41605612 0.5124146116501207 19.65028601508525 chr18 78077248 3931298 0.05035139045884404 1.6095588800055387 chr19 59128983 7566820 0.1279714213924498 4.70912319814739 chr20 63025520 16406466 0.2603146471461084 15.448259120783264 chr21 48129895 4039495 0.08392902166106948 6.670246664257085 chr22 51304566 5213164 0.10161208653436421 4.6962983968331855 chrMT 16571 36396 2.1963671474262267 2.030935898489822 chrX 155270560 13071649 0.08418626815025333 7.13680218692877 chrY 59373566 128291 0.0021607427116639754 0.1543934617703449