BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504607.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 441,345,966 number of mapped reads = 294,225,897 (66.67%) number of supplementary alignments = 1,863,768 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 147,297,612 number of mapped paired reads (second in pair) = 146,928,285 number of mapped paired reads (both in pair) = 292,576,654 number of mapped paired reads (singletons) = 1,649,243 number of mapped bases = 29,225,074,733 bp number of sequenced bases = 29,217,647,242 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,681,841 duplication rate = 22.69% >>>>>>> Insert size mean insert size = 24,081.5544 std insert size = 1,497,161.9172 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.7816 >>>>>>> ACTG content number of A's = 7,544,234,770 bp (25.82%) number of C's = 7,000,935,272 bp (23.96%) number of T's = 7,593,958,999 bp (25.99%) number of G's = 7,073,464,428 bp (24.21%) number of N's = 5,053,773 bp (0.02%) GC percentage = 48.17% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 141,905,609 number of insertions = 2,173,290 mapped reads with insertion percentage = 0.72% number of deletions = 2,866,659 mapped reads with deletion percentage = 0.94% homopolymer indels = 39.99% >>>>>>> Coverage mean coverageData = 9.4406X std coverageData = 24.2585X There is a 68.14% of reference with a coverageData >= 1X There is a 58.27% of reference with a coverageData >= 2X There is a 50.79% of reference with a coverageData >= 3X There is a 45.02% of reference with a coverageData >= 4X There is a 40.26% of reference with a coverageData >= 5X There is a 36.29% of reference with a coverageData >= 6X There is a 32.91% of reference with a coverageData >= 7X There is a 30.01% of reference with a coverageData >= 8X There is a 27.48% of reference with a coverageData >= 9X There is a 25.26% of reference with a coverageData >= 10X There is a 23.31% of reference with a coverageData >= 11X There is a 21.58% of reference with a coverageData >= 12X There is a 20.03% of reference with a coverageData >= 13X There is a 18.64% of reference with a coverageData >= 14X There is a 17.39% of reference with a coverageData >= 15X There is a 16.26% of reference with a coverageData >= 16X There is a 15.24% of reference with a coverageData >= 17X There is a 14.31% of reference with a coverageData >= 18X There is a 13.45% of reference with a coverageData >= 19X There is a 12.68% of reference with a coverageData >= 20X There is a 11.96% of reference with a coverageData >= 21X There is a 11.31% of reference with a coverageData >= 22X There is a 10.7% of reference with a coverageData >= 23X There is a 10.14% of reference with a coverageData >= 24X There is a 9.62% of reference with a coverageData >= 25X There is a 9.14% of reference with a coverageData >= 26X There is a 8.7% of reference with a coverageData >= 27X There is a 8.28% of reference with a coverageData >= 28X There is a 7.89% of reference with a coverageData >= 29X There is a 7.53% of reference with a coverageData >= 30X There is a 7.19% of reference with a coverageData >= 31X There is a 6.88% of reference with a coverageData >= 32X There is a 6.58% of reference with a coverageData >= 33X There is a 6.3% of reference with a coverageData >= 34X There is a 6.04% of reference with a coverageData >= 35X There is a 5.79% of reference with a coverageData >= 36X There is a 5.56% of reference with a coverageData >= 37X There is a 5.34% of reference with a coverageData >= 38X There is a 5.13% of reference with a coverageData >= 39X There is a 4.93% of reference with a coverageData >= 40X There is a 4.75% of reference with a coverageData >= 41X There is a 4.57% of reference with a coverageData >= 42X There is a 4.4% of reference with a coverageData >= 43X There is a 4.24% of reference with a coverageData >= 44X There is a 4.09% of reference with a coverageData >= 45X There is a 3.95% of reference with a coverageData >= 46X There is a 3.82% of reference with a coverageData >= 47X There is a 3.69% of reference with a coverageData >= 48X There is a 3.56% of reference with a coverageData >= 49X There is a 3.45% of reference with a coverageData >= 50X There is a 3.33% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2962180633 11.884346049432711 23.66387493025078 chr2 243199373 1304353755 5.363310517252033 13.426280014116637 chr3 198022430 1650878106 8.33682379314303 22.613205858269477 chr4 191154276 986748068 5.162050719702446 9.801843165448226 chr5 180915260 1424840108 7.875732030565028 22.512457560060103 chr6 171115067 1238353817 7.2369653865723 14.050861732479461 chr7 159138663 2337911408 14.691033366291384 27.128330479305312 chr8 146364022 2635201510 18.004434928687598 42.998064227841965 chr9 141213431 892993944 6.323718202130504 17.645823288662605 chr10 135534747 1436946211 10.602050343591964 21.92157647737646 chr11 135006516 1646949929 12.19904029669205 27.979286883540645 chr12 133851895 880757003 6.580086169119982 16.23810493074783 chr13 115169878 799100481 6.9384503559168484 15.447816230964015 chr14 107349540 1036240367 9.652955820770169 19.288560427299537 chr15 102531392 891202556 8.691997042232686 18.110205179062987 chr16 90354753 1091184296 12.076667355839044 27.254477969154323 chr17 81195210 1417669993 17.460020030738267 56.22743957279105 chr18 78077248 668426099 8.561086822629814 24.59590298423668 chr19 59128983 614058495 10.385067759409967 22.208644738316934 chr20 63025520 1658202288 26.310013594493153 46.98276093875943 chr21 48129895 243440418 5.057987722599436 13.029376214020948 chr22 51304566 320794105 6.252739863348615 16.187540706069836 chrMT 16571 498912 30.107537263894756 14.91600326051798 chrX 155270560 1058249531 6.815519509944448 12.741237788517157 chrY 59373566 27892700 0.46978313547816886 10.788905153105699