BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975315.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 78,546,488 number of mapped reads = 78,396,789 (99.81%) number of supplementary alignments = 136,130 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 39,212,017 number of mapped paired reads (second in pair) = 39,184,772 number of mapped paired reads (both in pair) = 78,328,528 number of mapped paired reads (singletons) = 68,261 number of mapped bases = 7,315,592,574 bp number of sequenced bases = 7,313,088,334 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,623,765 duplication rate = 50.67% >>>>>>> Insert size mean insert size = 86,564.5283 std insert size = 2,905,582.9472 median insert size = 186 >>>>>>> Mapping quality mean mapping quality = 56.0439 >>>>>>> ACTG content number of A's = 1,942,115,850 bp (26.56%) number of C's = 1,653,094,543 bp (22.6%) number of T's = 2,000,165,173 bp (27.35%) number of G's = 1,717,390,798 bp (23.48%) number of N's = 321,970 bp (0%) GC percentage = 46.09% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 45,607,631 number of insertions = 638,398 mapped reads with insertion percentage = 0.81% number of deletions = 1,789,339 mapped reads with deletion percentage = 2.25% homopolymer indels = 48.43% >>>>>>> Coverage mean coverageData = 2.3632X std coverageData = 32.6034X There is a 11.38% of reference with a coverageData >= 1X There is a 5.78% of reference with a coverageData >= 2X There is a 3.59% of reference with a coverageData >= 3X There is a 2.81% of reference with a coverageData >= 4X There is a 2.37% of reference with a coverageData >= 5X There is a 2.13% of reference with a coverageData >= 6X There is a 1.97% of reference with a coverageData >= 7X There is a 1.85% of reference with a coverageData >= 8X There is a 1.76% of reference with a coverageData >= 9X There is a 1.69% of reference with a coverageData >= 10X There is a 1.63% of reference with a coverageData >= 11X There is a 1.58% of reference with a coverageData >= 12X There is a 1.53% of reference with a coverageData >= 13X There is a 1.49% of reference with a coverageData >= 14X There is a 1.46% of reference with a coverageData >= 15X There is a 1.42% of reference with a coverageData >= 16X There is a 1.39% of reference with a coverageData >= 17X There is a 1.36% of reference with a coverageData >= 18X There is a 1.33% of reference with a coverageData >= 19X There is a 1.3% of reference with a coverageData >= 20X There is a 1.28% of reference with a coverageData >= 21X There is a 1.26% of reference with a coverageData >= 22X There is a 1.23% of reference with a coverageData >= 23X There is a 1.21% of reference with a coverageData >= 24X There is a 1.19% of reference with a coverageData >= 25X There is a 1.17% of reference with a coverageData >= 26X There is a 1.15% of reference with a coverageData >= 27X There is a 1.14% of reference with a coverageData >= 28X There is a 1.12% of reference with a coverageData >= 29X There is a 1.1% of reference with a coverageData >= 30X There is a 1.09% of reference with a coverageData >= 31X There is a 1.07% of reference with a coverageData >= 32X There is a 1.06% of reference with a coverageData >= 33X There is a 1.04% of reference with a coverageData >= 34X There is a 1.03% of reference with a coverageData >= 35X There is a 1.02% of reference with a coverageData >= 36X There is a 1% of reference with a coverageData >= 37X There is a 0.99% of reference with a coverageData >= 38X There is a 0.98% of reference with a coverageData >= 39X There is a 0.97% of reference with a coverageData >= 40X There is a 0.95% of reference with a coverageData >= 41X There is a 0.94% of reference with a coverageData >= 42X There is a 0.93% of reference with a coverageData >= 43X There is a 0.92% of reference with a coverageData >= 44X There is a 0.91% of reference with a coverageData >= 45X There is a 0.9% of reference with a coverageData >= 46X There is a 0.89% of reference with a coverageData >= 47X There is a 0.88% of reference with a coverageData >= 48X There is a 0.87% of reference with a coverageData >= 49X There is a 0.86% of reference with a coverageData >= 50X There is a 0.85% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 870272535 3.491556135380702 42.047933447603405 chr2 243199373 527417636 2.168663633849089 28.081815448533863 chr3 198022430 441041976 2.227232420084937 30.894955974520784 chr4 191154276 319124220 1.6694589662226547 26.552187617214777 chr5 180915260 368675455 2.0378350339269335 30.39787776850357 chr6 171115067 592529555 3.4627550068399295 48.23949352073373 chr7 159138663 403423656 2.535044899805398 36.214306282227426 chr8 146364022 250258705 1.7098375788006153 25.029274211324342 chr9 141213431 294008504 2.0820151590254894 29.620710703542958 chr10 135534747 302130211 2.2291716160432276 30.778483443879463 chr11 135006516 357061281 2.6447707235108564 33.043249514113015 chr12 133851895 402486761 3.0069560165733926 34.760642080971586 chr13 115169878 142494686 1.2372565507102473 23.209352626379072 chr14 107349540 244247993 2.275258869297437 31.97756541477651 chr15 102531392 280076769 2.731619687753776 33.81349280342734 chr16 90354753 241110651 2.6684888508300166 33.400483326053234 chr17 81195210 299231100 3.685329467095411 38.255190519390695 chr18 78077248 114789232 1.4702007939624102 23.172255185977356 chr19 59128983 300895822 5.088804284017535 46.801185663471756 chr20 63025520 189339077 3.004165249251414 39.20824584463002 chr21 48129895 70121506 1.4569220647582963 22.38687336481164 chr22 51304566 130401398 2.54171135567154 31.506709497881904 chrMT 16571 145656 8.78981352966025 24.754104830027117 chrX 155270560 172171686 1.1088495204757425 18.407692550917165 chrY 59373566 2136503 0.03598407749334106 2.329504903601889