BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504626.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 = 303,496,300 number of mapped reads = 284,879,741 (93.87%) number of supplementary alignments = 2,847,326 (0.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 143,598,716 number of mapped paired reads (second in pair) = 141,281,025 number of mapped paired reads (both in pair) = 278,728,384 number of mapped paired reads (singletons) = 6,151,357 number of mapped bases = 27,279,403,262 bp number of sequenced bases = 27,253,534,393 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,205,104 duplication rate = 16.18% >>>>>>> Insert size mean insert size = 114,029.464 std insert size = 3,155,648.0029 median insert size = 367 >>>>>>> Mapping quality mean mapping quality = 52.1079 >>>>>>> ACTG content number of A's = 7,299,494,645 bp (26.78%) number of C's = 6,275,299,829 bp (23.03%) number of T's = 7,360,760,657 bp (27.01%) number of G's = 6,314,370,573 bp (23.17%) number of N's = 3,608,689 bp (0.01%) GC percentage = 46.19% >>>>>>> Mismatches and indels general error rate = 0.013 number of mismatches = 324,364,460 number of insertions = 8,035,606 mapped reads with insertion percentage = 2.61% number of deletions = 7,776,506 mapped reads with deletion percentage = 2.54% homopolymer indels = 33.6% >>>>>>> Coverage mean coverageData = 8.812X std coverageData = 206.8254X There is a 82.3% of reference with a coverageData >= 1X There is a 73.12% of reference with a coverageData >= 2X There is a 64.51% of reference with a coverageData >= 3X There is a 56.97% of reference with a coverageData >= 4X There is a 50.38% of reference with a coverageData >= 5X There is a 44.65% of reference with a coverageData >= 6X There is a 39.63% of reference with a coverageData >= 7X There is a 35.24% of reference with a coverageData >= 8X There is a 31.37% of reference with a coverageData >= 9X There is a 27.96% of reference with a coverageData >= 10X There is a 24.94% of reference with a coverageData >= 11X There is a 22.26% of reference with a coverageData >= 12X There is a 19.88% of reference with a coverageData >= 13X There is a 17.78% of reference with a coverageData >= 14X There is a 15.9% of reference with a coverageData >= 15X There is a 14.24% of reference with a coverageData >= 16X There is a 12.75% of reference with a coverageData >= 17X There is a 11.44% of reference with a coverageData >= 18X There is a 10.27% of reference with a coverageData >= 19X There is a 9.22% of reference with a coverageData >= 20X There is a 8.29% of reference with a coverageData >= 21X There is a 7.46% of reference with a coverageData >= 22X There is a 6.72% of reference with a coverageData >= 23X There is a 6.07% of reference with a coverageData >= 24X There is a 5.48% of reference with a coverageData >= 25X There is a 4.96% of reference with a coverageData >= 26X There is a 4.49% of reference with a coverageData >= 27X There is a 4.07% of reference with a coverageData >= 28X There is a 3.7% of reference with a coverageData >= 29X There is a 3.37% of reference with a coverageData >= 30X There is a 3.07% of reference with a coverageData >= 31X There is a 2.8% of reference with a coverageData >= 32X There is a 2.56% of reference with a coverageData >= 33X There is a 2.35% of reference with a coverageData >= 34X There is a 2.16% of reference with a coverageData >= 35X There is a 1.99% of reference with a coverageData >= 36X There is a 1.83% of reference with a coverageData >= 37X There is a 1.69% of reference with a coverageData >= 38X There is a 1.57% of reference with a coverageData >= 39X There is a 1.46% of reference with a coverageData >= 40X There is a 1.35% of reference with a coverageData >= 41X There is a 1.26% of reference with a coverageData >= 42X There is a 1.18% of reference with a coverageData >= 43X There is a 1.1% of reference with a coverageData >= 44X There is a 1.04% of reference with a coverageData >= 45X There is a 0.98% of reference with a coverageData >= 46X There is a 0.92% of reference with a coverageData >= 47X There is a 0.87% of reference with a coverageData >= 48X There is a 0.82% of reference with a coverageData >= 49X There is a 0.78% of reference with a coverageData >= 50X There is a 0.74% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1920928169 7.706813974196678 60.63846076241444 chr2 243199373 2078515407 8.54654920101295 240.29748120582602 chr3 198022430 1380081924 6.969321222853391 23.49974101479055 chr4 191154276 1960723856 10.257284833115635 530.4047311672712 chr5 180915260 1664991163 9.203154907993941 34.24949019334138 chr6 171115067 797346819 4.659711344998041 26.430016244463303 chr7 159138663 1278044333 8.031010873831459 34.43941593940705 chr8 146364022 1502991564 10.268859405899628 140.2141423038236 chr9 141213431 711844279 5.040910584489658 74.82882945934084 chr10 135534747 2035566868 15.018782364348237 476.0250036264844 chr11 135006516 1105880739 8.19131381036453 25.28969851105162 chr12 133851895 1026024531 7.665371722977848 20.061545735160376 chr13 115169878 413399938 3.589479690166903 11.638862296063175 chr14 107349540 698903122 6.510536719579795 30.461682785299907 chr15 102531392 935258176 9.121676374002607 16.934154078480127 chr16 90354753 1465132136 16.21532998933659 203.60253623044898 chr17 81195210 893407344 11.003202578083116 72.21595814264386 chr18 78077248 461646525 5.912689507191647 281.77417871580593 chr19 59128983 1080781589 18.27837270598752 41.20187815918103 chr20 63025520 807913424 12.818829959673478 129.75385756169786 chr21 48129895 521854344 10.842623778838496 169.68208053598752 chr22 51304566 489299077 9.537144842039986 30.565456168417956 chrMT 16571 9355805 564.5890410958904 254.5666770539354 chrX 155270560 1551798270 9.994156458249394 21.453985267473435 chrY 59373566 487713860 8.214326557377403 508.0013530928597