BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618604.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 56,233,946 number of mapped reads = 49,505,881 (88.04%) number of supplementary alignments = 248,980 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 25,056,668 number of mapped paired reads (second in pair) = 24,449,213 number of mapped paired reads (both in pair) = 48,476,068 number of mapped paired reads (singletons) = 1,029,813 number of mapped bases = 4,684,550,785 bp number of sequenced bases = 4,680,786,736 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,651,133 duplication rate = 32.66% >>>>>>> Insert size mean insert size = 89,314.5513 std insert size = 2,963,687.214 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 53.4399 >>>>>>> ACTG content number of A's = 1,270,527,767 bp (27.14%) number of C's = 1,025,865,185 bp (21.92%) number of T's = 1,282,893,630 bp (27.41%) number of G's = 1,101,272,332 bp (23.53%) number of N's = 227,822 bp (0%) GC percentage = 45.44% >>>>>>> Mismatches and indels general error rate = 0.0136 number of mismatches = 62,016,693 number of insertions = 922,398 mapped reads with insertion percentage = 1.83% number of deletions = 2,784,145 mapped reads with deletion percentage = 5.46% homopolymer indels = 52.77% >>>>>>> Coverage mean coverageData = 1.5132X std coverageData = 6.442X There is a 26.23% of reference with a coverageData >= 1X There is a 18.46% of reference with a coverageData >= 2X There is a 14.12% of reference with a coverageData >= 3X There is a 11.33% of reference with a coverageData >= 4X There is a 9.28% of reference with a coverageData >= 5X There is a 7.76% of reference with a coverageData >= 6X There is a 6.56% of reference with a coverageData >= 7X There is a 5.62% of reference with a coverageData >= 8X There is a 4.84% of reference with a coverageData >= 9X There is a 4.21% of reference with a coverageData >= 10X There is a 3.68% of reference with a coverageData >= 11X There is a 3.24% of reference with a coverageData >= 12X There is a 2.87% of reference with a coverageData >= 13X There is a 2.55% of reference with a coverageData >= 14X There is a 2.27% of reference with a coverageData >= 15X There is a 2.04% of reference with a coverageData >= 16X There is a 1.83% of reference with a coverageData >= 17X There is a 1.65% of reference with a coverageData >= 18X There is a 1.5% of reference with a coverageData >= 19X There is a 1.36% of reference with a coverageData >= 20X There is a 1.24% of reference with a coverageData >= 21X There is a 1.13% of reference with a coverageData >= 22X There is a 1.03% of reference with a coverageData >= 23X There is a 0.95% of reference with a coverageData >= 24X There is a 0.87% of reference with a coverageData >= 25X There is a 0.8% of reference with a coverageData >= 26X There is a 0.74% of reference with a coverageData >= 27X There is a 0.69% of reference with a coverageData >= 28X There is a 0.63% of reference with a coverageData >= 29X There is a 0.59% of reference with a coverageData >= 30X There is a 0.55% of reference with a coverageData >= 31X There is a 0.51% of reference with a coverageData >= 32X There is a 0.47% of reference with a coverageData >= 33X There is a 0.44% of reference with a coverageData >= 34X There is a 0.41% of reference with a coverageData >= 35X There is a 0.39% of reference with a coverageData >= 36X There is a 0.36% of reference with a coverageData >= 37X There is a 0.34% of reference with a coverageData >= 38X There is a 0.32% of reference with a coverageData >= 39X There is a 0.3% of reference with a coverageData >= 40X There is a 0.28% of reference with a coverageData >= 41X There is a 0.26% of reference with a coverageData >= 42X There is a 0.25% of reference with a coverageData >= 43X There is a 0.23% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 436883299 1.752787203687649 7.636881049001201 chr2 243199373 406689262 1.6722463425101017 7.649247778921404 chr3 198022430 297359056 1.5016433037408945 4.813836024034582 chr4 191154276 209179731 1.0942979428825332 4.981498868868171 chr5 180915260 312454672 1.7270774836793756 5.613259467150987 chr6 171115067 290002736 1.6947820030365883 7.154886899493971 chr7 159138663 213699772 1.3428526290936602 4.548211067423035 chr8 146364022 242763664 1.658629359064757 5.360339259000935 chr9 141213431 226562166 1.6043953071291073 6.986724702403143 chr10 135534747 237115043 1.74947788850043 6.462193544687049 chr11 135006516 245258091 1.8166389168949446 7.200061848509349 chr12 133851895 247151775 1.8464570486656167 6.312307220817292 chr13 115169878 111861302 0.97127221060354 3.616509629571015 chr14 107349540 129719561 1.2083848798979484 4.6181024127251975 chr15 102531392 141604598 1.3810852972716883 4.823608990960721 chr16 90354753 145520720 1.6105485895136031 12.703334700178024 chr17 81195210 184814589 2.276176008412319 7.5292202051671415 chr18 78077248 134385946 1.7211921455018497 7.035490428303152 chr19 59128983 102177811 1.7280495252218357 6.143180711183494 chr20 63025520 108813096 1.7264926334602237 5.440963740247477 chr21 48129895 65252016 1.355748147798785 9.051918536341004 chr22 51304566 91899723 1.7912581698868675 6.774196538007986 chrMT 16571 180523 10.893911049423693 37.291521808326664 chrX 155270560 60339135 0.38860641064217194 2.648499477872137 chrY 59373566 42862498 0.7219121384759002 6.274897453348368