BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504614.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 = 481,467,640 number of mapped reads = 320,458,430 (66.56%) number of supplementary alignments = 2,066,647 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 160,535,647 number of mapped paired reads (second in pair) = 159,922,783 number of mapped paired reads (both in pair) = 318,362,214 number of mapped paired reads (singletons) = 2,096,216 number of mapped bases = 31,828,005,751 bp number of sequenced bases = 31,819,872,564 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,491,680 duplication rate = 23.99% >>>>>>> Insert size mean insert size = 25,519.384 std insert size = 1,546,446.5315 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.7562 >>>>>>> ACTG content number of A's = 8,228,898,595 bp (25.86%) number of C's = 7,612,749,633 bp (23.92%) number of T's = 8,266,730,350 bp (25.98%) number of G's = 7,709,726,776 bp (24.23%) number of N's = 1,767,210 bp (0.01%) GC percentage = 48.15% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 156,726,517 number of insertions = 2,368,802 mapped reads with insertion percentage = 0.72% number of deletions = 3,125,972 mapped reads with deletion percentage = 0.95% homopolymer indels = 40.1% >>>>>>> Coverage mean coverageData = 10.2814X std coverageData = 26.522X There is a 68.99% of reference with a coverageData >= 1X There is a 59.46% of reference with a coverageData >= 2X There is a 52.19% of reference with a coverageData >= 3X There is a 46.55% of reference with a coverageData >= 4X There is a 41.87% of reference with a coverageData >= 5X There is a 37.94% of reference with a coverageData >= 6X There is a 34.58% of reference with a coverageData >= 7X There is a 31.67% of reference with a coverageData >= 8X There is a 29.12% of reference with a coverageData >= 9X There is a 26.88% of reference with a coverageData >= 10X There is a 24.9% of reference with a coverageData >= 11X There is a 23.13% of reference with a coverageData >= 12X There is a 21.55% of reference with a coverageData >= 13X There is a 20.12% of reference with a coverageData >= 14X There is a 18.83% of reference with a coverageData >= 15X There is a 17.66% of reference with a coverageData >= 16X There is a 16.59% of reference with a coverageData >= 17X There is a 15.62% of reference with a coverageData >= 18X There is a 14.73% of reference with a coverageData >= 19X There is a 13.91% of reference with a coverageData >= 20X There is a 13.16% of reference with a coverageData >= 21X There is a 12.47% of reference with a coverageData >= 22X There is a 11.82% of reference with a coverageData >= 23X There is a 11.23% of reference with a coverageData >= 24X There is a 10.68% of reference with a coverageData >= 25X There is a 10.16% of reference with a coverageData >= 26X There is a 9.68% of reference with a coverageData >= 27X There is a 9.24% of reference with a coverageData >= 28X There is a 8.82% of reference with a coverageData >= 29X There is a 8.43% of reference with a coverageData >= 30X There is a 8.06% of reference with a coverageData >= 31X There is a 7.72% of reference with a coverageData >= 32X There is a 7.4% of reference with a coverageData >= 33X There is a 7.09% of reference with a coverageData >= 34X There is a 6.81% of reference with a coverageData >= 35X There is a 6.54% of reference with a coverageData >= 36X There is a 6.28% of reference with a coverageData >= 37X There is a 6.04% of reference with a coverageData >= 38X There is a 5.82% of reference with a coverageData >= 39X There is a 5.6% of reference with a coverageData >= 40X There is a 5.4% of reference with a coverageData >= 41X There is a 5.2% of reference with a coverageData >= 42X There is a 5.02% of reference with a coverageData >= 43X There is a 4.84% of reference with a coverageData >= 44X There is a 4.68% of reference with a coverageData >= 45X There is a 4.52% of reference with a coverageData >= 46X There is a 4.37% of reference with a coverageData >= 47X There is a 4.22% of reference with a coverageData >= 48X There is a 4.09% of reference with a coverageData >= 49X There is a 3.96% of reference with a coverageData >= 50X There is a 3.83% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3227768870 12.94989299144013 25.864006011813373 chr2 243199373 1421382596 5.84451587381354 15.532279394806524 chr3 198022430 1797907105 9.079310384182236 24.703728545736386 chr4 191154276 1073289942 5.614783851343194 10.652922753190804 chr5 180915260 1551884064 8.57796110731621 24.630883490841725 chr6 171115067 1348824059 7.882555771666793 15.326247031959271 chr7 159138663 2545680138 15.996616347090963 29.634926043693714 chr8 146364022 2867541690 19.591848125080904 46.972761641061965 chr9 141213431 970729557 6.874201342788704 19.163771547173393 chr10 135534747 1563960979 11.539188389823018 23.922125824068274 chr11 135006516 1794396150 13.291181812291194 30.600715632399258 chr12 133851895 959345532 7.16721666137039 17.8437465462249 chr13 115169878 870115992 7.555065674377114 16.868938881391003 chr14 107349540 1127610154 10.50409861094887 21.02045362143582 chr15 102531392 970628586 9.466647892579084 19.76589845543352 chr16 90354753 1187933912 13.147442415121205 29.70638997886128 chr17 81195210 1546319873 19.044471625850836 61.47030160389275 chr18 78077248 726926994 9.310356251285906 26.560406953601696 chr19 59128983 670133896 11.333425031172952 24.284441127961504 chr20 63025520 1807367607 28.67675835122027 51.18982368889478 chr21 48129895 265178961 5.50965176632943 14.186857994808506 chr22 51304566 350137159 6.824678314206966 17.591115986294483 chrMT 16571 543455 32.79554643654577 16.318142393886134 chrX 155270560 1151824527 7.418177193410006 13.914505050386275 chrY 59373566 30573953 0.5149421714033481 11.737669632574832