BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504612.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 = 480,339,368 number of mapped reads = 319,404,949 (66.5%) number of supplementary alignments = 2,028,887 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 159,908,356 number of mapped paired reads (second in pair) = 159,496,593 number of mapped paired reads (both in pair) = 317,171,248 number of mapped paired reads (singletons) = 2,233,701 number of mapped bases = 31,719,634,148 bp number of sequenced bases = 31,711,521,928 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,978,846 duplication rate = 23.93% >>>>>>> Insert size mean insert size = 25,812.8817 std insert size = 1,552,207.6192 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.7495 >>>>>>> ACTG content number of A's = 8,193,551,307 bp (25.84%) number of C's = 7,580,177,588 bp (23.9%) number of T's = 8,235,947,334 bp (25.97%) number of G's = 7,678,282,912 bp (24.21%) number of N's = 23,562,787 bp (0.07%) GC percentage = 48.12% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 186,698,086 number of insertions = 2,356,042 mapped reads with insertion percentage = 0.72% number of deletions = 3,141,382 mapped reads with deletion percentage = 0.95% homopolymer indels = 40.01% >>>>>>> Coverage mean coverageData = 10.2464X std coverageData = 26.4252X There is a 68.97% of reference with a coverageData >= 1X There is a 59.43% of reference with a coverageData >= 2X There is a 52.15% of reference with a coverageData >= 3X There is a 46.5% of reference with a coverageData >= 4X There is a 41.81% of reference with a coverageData >= 5X There is a 37.88% of reference with a coverageData >= 6X There is a 34.52% of reference with a coverageData >= 7X There is a 31.61% of reference with a coverageData >= 8X There is a 29.07% of reference with a coverageData >= 9X There is a 26.83% of reference with a coverageData >= 10X There is a 24.85% of reference with a coverageData >= 11X There is a 23.08% of reference with a coverageData >= 12X There is a 21.49% of reference with a coverageData >= 13X There is a 20.07% of reference with a coverageData >= 14X There is a 18.78% of reference with a coverageData >= 15X There is a 17.61% of reference with a coverageData >= 16X There is a 16.54% of reference with a coverageData >= 17X There is a 15.57% of reference with a coverageData >= 18X There is a 14.68% of reference with a coverageData >= 19X There is a 13.87% of reference with a coverageData >= 20X There is a 13.12% of reference with a coverageData >= 21X There is a 12.42% of reference with a coverageData >= 22X There is a 11.78% of reference with a coverageData >= 23X There is a 11.19% of reference with a coverageData >= 24X There is a 10.63% of reference with a coverageData >= 25X There is a 10.12% of reference with a coverageData >= 26X There is a 9.64% of reference with a coverageData >= 27X There is a 9.2% of reference with a coverageData >= 28X There is a 8.78% of reference with a coverageData >= 29X There is a 8.39% of reference with a coverageData >= 30X There is a 8.03% of reference with a coverageData >= 31X There is a 7.68% of reference with a coverageData >= 32X There is a 7.36% of reference with a coverageData >= 33X There is a 7.06% of reference with a coverageData >= 34X There is a 6.77% of reference with a coverageData >= 35X There is a 6.51% of reference with a coverageData >= 36X There is a 6.25% of reference with a coverageData >= 37X There is a 6.01% of reference with a coverageData >= 38X There is a 5.79% of reference with a coverageData >= 39X There is a 5.57% of reference with a coverageData >= 40X There is a 5.37% of reference with a coverageData >= 41X There is a 5.18% of reference with a coverageData >= 42X There is a 4.99% of reference with a coverageData >= 43X There is a 4.82% of reference with a coverageData >= 44X There is a 4.65% of reference with a coverageData >= 45X There is a 4.5% of reference with a coverageData >= 46X There is a 4.35% of reference with a coverageData >= 47X There is a 4.2% of reference with a coverageData >= 48X There is a 4.07% of reference with a coverageData >= 49X There is a 3.94% of reference with a coverageData >= 50X There is a 3.81% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3217191190 12.907455063070836 25.754515245397457 chr2 243199373 1417243673 5.827497232075512 15.633841434447685 chr3 198022430 1791658182 9.047753741836216 24.558049247285773 chr4 191154276 1069675410 5.595874873340526 10.632224703905653 chr5 180915260 1546597180 8.54873812192515 24.47343555824183 chr6 171115067 1343805484 7.853227115295463 15.258364011086579 chr7 159138663 2538105466 15.949018410441214 29.497154355541955 chr8 146364022 2856507769 19.516461285820636 46.80130213305153 chr9 141213431 967788543 6.853374612787363 19.071366677124793 chr10 135534747 1559929233 11.509441434970178 23.824462393150245 chr11 135006516 1787852272 13.242710981446258 30.423725984789737 chr12 133851895 956579982 7.146555392435796 17.906551251461938 chr13 115169878 866970449 7.527753472136178 16.814561136471053 chr14 107349540 1123987164 10.470349141691711 20.944010187109917 chr15 102531392 966791728 9.429226592378654 19.646773980585472 chr16 90354753 1184284052 13.107047639209418 29.61969552804512 chr17 81195210 1540978445 18.97868661217823 61.315949773691024 chr18 78077248 724453450 9.278675524014371 26.420535246173166 chr19 59128983 667166775 11.28324454692549 24.174829462904672 chr20 63025520 1801164316 28.578333284675796 51.01082258342973 chr21 48129895 264044934 5.486089965498574 14.154023597105017 chr22 51304566 348481180 6.792400894688399 17.520528799016503 chrMT 16571 532298 32.12226178263231 14.664921069788138 chrX 155270560 1147557812 7.390697966182385 13.86044557959227 chrY 59373566 30287161 0.5101118736914 11.716329994642017