BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365364.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 638,624,950 number of mapped reads = 582,686,126 (91.24%) number of supplementary alignments = 46,405,961 (7.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 290,927,682 number of mapped paired reads (second in pair) = 291,758,444 number of mapped paired reads (both in pair) = 577,414,572 number of mapped paired reads (singletons) = 5,271,554 number of mapped bases = 78,914,820,277 bp number of sequenced bases = 78,848,205,255 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 314,454,052 duplication rate = 37.75% >>>>>>> Insert size mean insert size = 113,696.1153 std insert size = 2,909,996.2319 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 53.3638 >>>>>>> ACTG content number of A's = 21,797,627,212 bp (27.65%) number of C's = 17,699,868,171 bp (22.45%) number of T's = 21,239,925,858 bp (26.94%) number of G's = 18,106,195,903 bp (22.96%) number of N's = 4,588,111 bp (0.01%) GC percentage = 45.41% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 796,994,435 number of insertions = 18,397,128 mapped reads with insertion percentage = 2.87% number of deletions = 16,811,961 mapped reads with deletion percentage = 2.64% homopolymer indels = 36.6% >>>>>>> Coverage mean coverageData = 25.4918X std coverageData = 455.0059X There is a 82.56% of reference with a coverageData >= 1X There is a 79.56% of reference with a coverageData >= 2X There is a 73.77% of reference with a coverageData >= 3X There is a 70.64% of reference with a coverageData >= 4X There is a 66.12% of reference with a coverageData >= 5X There is a 63.08% of reference with a coverageData >= 6X There is a 59.42% of reference with a coverageData >= 7X There is a 56.62% of reference with a coverageData >= 8X There is a 53.58% of reference with a coverageData >= 9X There is a 51.05% of reference with a coverageData >= 10X There is a 48.47% of reference with a coverageData >= 11X There is a 46.22% of reference with a coverageData >= 12X There is a 43.99% of reference with a coverageData >= 13X There is a 41.99% of reference with a coverageData >= 14X There is a 40.05% of reference with a coverageData >= 15X There is a 38.28% of reference with a coverageData >= 16X There is a 36.59% of reference with a coverageData >= 17X There is a 35.02% of reference with a coverageData >= 18X There is a 33.52% of reference with a coverageData >= 19X There is a 32.12% of reference with a coverageData >= 20X There is a 30.79% of reference with a coverageData >= 21X There is a 29.55% of reference with a coverageData >= 22X There is a 28.37% of reference with a coverageData >= 23X There is a 27.25% of reference with a coverageData >= 24X There is a 26.19% of reference with a coverageData >= 25X There is a 25.19% of reference with a coverageData >= 26X There is a 24.24% of reference with a coverageData >= 27X There is a 23.34% of reference with a coverageData >= 28X There is a 22.48% of reference with a coverageData >= 29X There is a 21.67% of reference with a coverageData >= 30X There is a 20.9% of reference with a coverageData >= 31X There is a 20.16% of reference with a coverageData >= 32X There is a 19.46% of reference with a coverageData >= 33X There is a 18.79% of reference with a coverageData >= 34X There is a 18.15% of reference with a coverageData >= 35X There is a 17.54% of reference with a coverageData >= 36X There is a 16.96% of reference with a coverageData >= 37X There is a 16.41% of reference with a coverageData >= 38X There is a 15.87% of reference with a coverageData >= 39X There is a 15.37% of reference with a coverageData >= 40X There is a 14.88% of reference with a coverageData >= 41X There is a 14.42% of reference with a coverageData >= 42X There is a 13.97% of reference with a coverageData >= 43X There is a 13.54% of reference with a coverageData >= 44X There is a 13.13% of reference with a coverageData >= 45X There is a 12.74% of reference with a coverageData >= 46X There is a 12.36% of reference with a coverageData >= 47X There is a 12% of reference with a coverageData >= 48X There is a 11.65% of reference with a coverageData >= 49X There is a 11.31% of reference with a coverageData >= 50X There is a 10.99% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6239232791 25.031964879236952 221.17640957916228 chr2 243199373 5935987930 24.407908033545795 281.41769369035467 chr3 198022430 4569046165 23.073376914928275 106.53300615990253 chr4 191154276 4537971495 23.739837737137513 753.9184795875275 chr5 180915260 3825518268 21.145359810996595 63.30254812958739 chr6 171115067 3613271446 21.11603325965445 126.39139835586003 chr7 159138663 4094305296 25.727910608373026 107.75333172082725 chr8 146364022 3171074139 21.665666846733686 74.31154459917117 chr9 141213431 3148396867 22.295307498052363 197.2149866395248 chr10 135534747 4865856831 35.9011761832558 1190.0505254310717 chr11 135006516 3793943469 28.101928569136618 108.76197326196976 chr12 133851895 3327866356 24.862302890818242 58.906743764439 chr13 115169878 1764972458 15.32494857726601 29.402841006098956 chr14 107349540 2113655611 19.68947059298065 48.47801354338658 chr15 102531392 2151325510 20.9821155066343 41.045618659892 chr16 90354753 4153722123 45.971263105550186 882.4719525298165 chr17 81195210 2749961402 33.8685176379247 377.39267333512316 chr18 78077248 1990963658 25.499921026929638 787.8494611991308 chr19 59128983 2389187153 40.40636303519714 161.59960530415626 chr20 63025520 2086377523 33.10369391636912 297.7227667186381 chr21 48129895 1273365843 26.45685894390586 465.20964642063933 chr22 51304566 1332728193 25.976794989358257 71.7350464753114 chrMT 16571 32974872 1989.914428821435 1040.2288578300697 chrX 155270560 1782363609 11.479082763661058 82.48364644074229 chrY 59373566 3970751269 66.87742604175064 1551.0225569806128