BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365347.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 = 296,349,006 number of mapped reads = 291,182,840 (98.26%) number of supplementary alignments = 1,226,730 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 145,617,959 number of mapped paired reads (second in pair) = 145,564,881 number of mapped paired reads (both in pair) = 290,249,974 number of mapped paired reads (singletons) = 932,866 number of mapped bases = 30,712,934,481 bp number of sequenced bases = 30,702,713,782 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 178,272,272 duplication rate = 39.79% >>>>>>> Insert size mean insert size = 83,246.5297 std insert size = 2,800,632.6926 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 54.0091 >>>>>>> ACTG content number of A's = 9,291,988,268 bp (30.26%) number of C's = 5,887,414,146 bp (19.18%) number of T's = 9,019,451,670 bp (29.38%) number of G's = 6,503,787,071 bp (21.18%) number of N's = 72,627 bp (0%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 142,640,734 number of insertions = 9,535,699 mapped reads with insertion percentage = 3.2% number of deletions = 4,801,842 mapped reads with deletion percentage = 1.61% homopolymer indels = 50.57% >>>>>>> Coverage mean coverageData = 9.9212X std coverageData = 63.036X There is a 84.85% of reference with a coverageData >= 1X There is a 79.2% of reference with a coverageData >= 2X There is a 73.15% of reference with a coverageData >= 3X There is a 67.72% of reference with a coverageData >= 4X There is a 62.13% of reference with a coverageData >= 5X There is a 57.04% of reference with a coverageData >= 6X There is a 51.96% of reference with a coverageData >= 7X There is a 47.36% of reference with a coverageData >= 8X There is a 42.9% of reference with a coverageData >= 9X There is a 38.88% of reference with a coverageData >= 10X There is a 35.05% of reference with a coverageData >= 11X There is a 31.63% of reference with a coverageData >= 12X There is a 28.43% of reference with a coverageData >= 13X There is a 25.58% of reference with a coverageData >= 14X There is a 22.94% of reference with a coverageData >= 15X There is a 20.61% of reference with a coverageData >= 16X There is a 18.46% of reference with a coverageData >= 17X There is a 16.57% of reference with a coverageData >= 18X There is a 14.84% of reference with a coverageData >= 19X There is a 13.33% of reference with a coverageData >= 20X There is a 11.94% of reference with a coverageData >= 21X There is a 10.73% of reference with a coverageData >= 22X There is a 9.63% of reference with a coverageData >= 23X There is a 8.66% of reference with a coverageData >= 24X There is a 7.78% of reference with a coverageData >= 25X There is a 7.01% of reference with a coverageData >= 26X There is a 6.32% of reference with a coverageData >= 27X There is a 5.7% of reference with a coverageData >= 28X There is a 5.15% of reference with a coverageData >= 29X There is a 4.66% of reference with a coverageData >= 30X There is a 4.22% of reference with a coverageData >= 31X There is a 3.83% of reference with a coverageData >= 32X There is a 3.47% of reference with a coverageData >= 33X There is a 3.16% of reference with a coverageData >= 34X There is a 2.87% of reference with a coverageData >= 35X There is a 2.62% of reference with a coverageData >= 36X There is a 2.39% of reference with a coverageData >= 37X There is a 2.19% of reference with a coverageData >= 38X There is a 2% of reference with a coverageData >= 39X There is a 1.84% of reference with a coverageData >= 40X There is a 1.68% of reference with a coverageData >= 41X There is a 1.55% of reference with a coverageData >= 42X There is a 1.43% of reference with a coverageData >= 43X There is a 1.32% of reference with a coverageData >= 44X There is a 1.22% of reference with a coverageData >= 45X There is a 1.13% of reference with a coverageData >= 46X There is a 1.04% of reference with a coverageData >= 47X There is a 0.97% of reference with a coverageData >= 48X There is a 0.9% of reference with a coverageData >= 49X There is a 0.84% of reference with a coverageData >= 50X There is a 0.78% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2494246169 10.006980760942618 161.97122604567468 chr2 243199373 2712345381 11.152764694833321 43.1804492613685 chr3 198022430 2147609649 10.845284794252853 11.781831510178987 chr4 191154276 2179001678 11.399178316052947 56.18963093862436 chr5 180915260 1906505322 10.538112274221644 11.477091340313104 chr6 171115067 1839691213 10.75119359886643 34.26509195912256 chr7 159138663 1733244382 10.891409726120422 57.80659813867034 chr8 146364022 1584078418 10.8228675076994 21.0699715331442 chr9 141213431 1316610337 9.323548954773289 45.881345104950256 chr10 135534747 1450440721 10.701615291317141 95.96672062437085 chr11 135006516 1424173993 10.548927823602233 38.06867789499094 chr12 133851895 1397240783 10.438707520726547 18.60865347499481 chr13 115169878 1050398891 9.1204306997703 10.434245470324637 chr14 107349540 956494333 8.91009251646537 11.000703232020108 chr15 102531392 875103569 8.534981842439045 12.520875011603666 chr16 90354753 820704500 9.08313589214283 24.108867069768237 chr17 81195210 827711367 10.194091092319363 50.888511428763465 chr18 78077248 792637092 10.15195991539046 80.88034199605978 chr19 59128983 555643845 9.397148687641051 77.82689026752963 chr20 63025520 640107390 10.156320645985943 17.751864894477563 chr21 48129895 443414733 9.212875552710015 33.25314143714523 chr22 51304566 356511024 6.9489141375837775 26.537030226777198 chrMT 16571 32055838 1934.4540462253335 366.396133636258 chrX 155270560 863123282 5.558834089347008 17.364205837432852 chrY 59373566 313840571 5.285863594583488 106.1236110631831