BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504611.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 = 483,831,634 number of mapped reads = 321,606,140 (66.47%) number of supplementary alignments = 2,061,529 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 161,080,532 number of mapped paired reads (second in pair) = 160,525,608 number of mapped paired reads (both in pair) = 319,527,030 number of mapped paired reads (singletons) = 2,079,110 number of mapped bases = 31,944,772,094 bp number of sequenced bases = 31,936,627,787 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,055,408 duplication rate = 24.05% >>>>>>> Insert size mean insert size = 25,183.8068 std insert size = 1,531,329.4853 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.7611 >>>>>>> ACTG content number of A's = 8,254,040,512 bp (25.85%) number of C's = 7,643,098,691 bp (23.93%) number of T's = 8,294,048,264 bp (25.97%) number of G's = 7,740,153,499 bp (24.24%) number of N's = 5,286,821 bp (0.02%) GC percentage = 48.17% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 161,267,906 number of insertions = 2,376,366 mapped reads with insertion percentage = 0.72% number of deletions = 3,124,361 mapped reads with deletion percentage = 0.94% homopolymer indels = 40.05% >>>>>>> Coverage mean coverageData = 10.3191X std coverageData = 26.6484X There is a 69% of reference with a coverageData >= 1X There is a 59.49% of reference with a coverageData >= 2X There is a 52.23% of reference with a coverageData >= 3X There is a 46.59% of reference with a coverageData >= 4X There is a 41.91% of reference with a coverageData >= 5X There is a 37.99% of reference with a coverageData >= 6X There is a 34.63% of reference with a coverageData >= 7X There is a 31.73% of reference with a coverageData >= 8X There is a 29.18% of reference with a coverageData >= 9X There is a 26.94% of reference with a coverageData >= 10X There is a 24.96% of reference with a coverageData >= 11X There is a 23.18% of reference with a coverageData >= 12X There is a 21.6% of reference with a coverageData >= 13X There is a 20.17% of reference with a coverageData >= 14X There is a 18.88% of reference with a coverageData >= 15X There is a 17.71% of reference with a coverageData >= 16X There is a 16.64% of reference with a coverageData >= 17X There is a 15.67% of reference with a coverageData >= 18X There is a 14.78% of reference with a coverageData >= 19X There is a 13.96% of reference with a coverageData >= 20X There is a 13.2% of reference with a coverageData >= 21X There is a 12.51% of reference with a coverageData >= 22X There is a 11.87% of reference with a coverageData >= 23X There is a 11.27% of reference with a coverageData >= 24X There is a 10.72% of reference with a coverageData >= 25X There is a 10.2% of reference with a coverageData >= 26X There is a 9.73% of reference with a coverageData >= 27X There is a 9.28% of reference with a coverageData >= 28X There is a 8.86% of reference with a coverageData >= 29X There is a 8.47% of reference with a coverageData >= 30X There is a 8.1% of reference with a coverageData >= 31X There is a 7.76% of reference with a coverageData >= 32X There is a 7.44% of reference with a coverageData >= 33X There is a 7.13% of reference with a coverageData >= 34X There is a 6.84% of reference with a coverageData >= 35X There is a 6.57% of reference with a coverageData >= 36X There is a 6.32% of reference with a coverageData >= 37X There is a 6.08% of reference with a coverageData >= 38X There is a 5.85% of reference with a coverageData >= 39X There is a 5.63% of reference with a coverageData >= 40X There is a 5.43% of reference with a coverageData >= 41X There is a 5.23% of reference with a coverageData >= 42X There is a 5.05% of reference with a coverageData >= 43X There is a 4.87% of reference with a coverageData >= 44X There is a 4.71% of reference with a coverageData >= 45X There is a 4.55% of reference with a coverageData >= 46X There is a 4.4% of reference with a coverageData >= 47X There is a 4.25% of reference with a coverageData >= 48X There is a 4.11% of reference with a coverageData >= 49X There is a 3.98% of reference with a coverageData >= 50X There is a 3.86% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3240238669 12.999922150645313 25.980118752165346 chr2 243199373 1426600168 5.865969761361185 15.441887089182675 chr3 198022430 1803061962 9.105342066552764 24.783156730431347 chr4 191154276 1075350186 5.625561763525499 10.677192109905246 chr5 180915260 1557287543 8.607828565705292 24.756271492776 chr6 171115067 1353426560 7.909452882953901 15.382981267146901 chr7 159138663 2554607733 16.052715819285222 29.756180784643828 chr8 146364022 2875459310 19.64594352292396 47.196455945035 chr9 141213431 975112335 6.905237894828857 19.24558663515245 chr10 135534747 1569862305 11.582729445756076 24.006839720449246 chr11 135006516 1801087570 13.340745494091559 30.727122477678822 chr12 133851895 963893680 7.2011956199798295 17.974046676698283 chr13 115169878 872710117 7.577590010124001 16.948765609328817 chr14 107349540 1132370955 10.54844720340674 21.11685897636644 chr15 102531392 974195520 9.501436594170105 19.829860069379848 chr16 90354753 1194169974 13.216459946495565 29.89920447079303 chr17 81195210 1553988700 19.138920879692286 61.868675652377355 chr18 78077248 729471493 9.342945758026717 26.77997263351345 chr19 59128983 672763080 11.377890264068975 24.374186358044945 chr20 63025520 1814982679 28.79758356614908 51.55611877064034 chr21 48129895 266006991 5.526855834611731 14.274068255591253 chr22 51304566 352199650 6.864879239013542 17.705240170888658 chrMT 16571 506253 30.550540100175006 14.267674521779938 chrX 155270560 1154704049 7.4367223831742475 13.960535039115323 chrY 59373566 30714612 0.5173112223038785 11.818518636338277