BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472393.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 20,700,192 number of mapped reads = 20,506,361 (99.06%) number of supplementary alignments = 74,936 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,291,359 number of mapped paired reads (second in pair) = 10,215,002 number of mapped paired reads (both in pair) = 20,384,800 number of mapped paired reads (singletons) = 121,561 number of mapped bases = 2,016,181,382 bp number of sequenced bases = 2,015,915,884 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,155,514 duplication rate = 49.45% >>>>>>> Insert size mean insert size = 17,243.0416 std insert size = 1,311,418.3679 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 54.9657 >>>>>>> ACTG content number of A's = 540,745,454 bp (26.82%) number of C's = 468,664,684 bp (23.25%) number of T's = 542,378,950 bp (26.9%) number of G's = 463,874,432 bp (23.01%) number of N's = 252,364 bp (0.01%) GC percentage = 46.26% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 11,464,343 number of insertions = 117,673 mapped reads with insertion percentage = 0.57% number of deletions = 98,158 mapped reads with deletion percentage = 0.47% homopolymer indels = 45.56% >>>>>>> Coverage mean coverageData = 0.6513X std coverageData = 18.6303X There is a 5.05% of reference with a coverageData >= 1X There is a 2.15% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.46% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.42% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.38% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.37% of reference with a coverageData >= 14X There is a 0.36% of reference with a coverageData >= 15X There is a 0.35% of reference with a coverageData >= 16X There is a 0.34% of reference with a coverageData >= 17X There is a 0.33% of reference with a coverageData >= 18X There is a 0.33% of reference with a coverageData >= 19X There is a 0.32% of reference with a coverageData >= 20X There is a 0.32% of reference with a coverageData >= 21X There is a 0.31% of reference with a coverageData >= 22X There is a 0.3% of reference with a coverageData >= 23X There is a 0.3% of reference with a coverageData >= 24X There is a 0.29% of reference with a coverageData >= 25X There is a 0.29% of reference with a coverageData >= 26X There is a 0.29% of reference with a coverageData >= 27X There is a 0.28% of reference with a coverageData >= 28X There is a 0.28% of reference with a coverageData >= 29X There is a 0.27% of reference with a coverageData >= 30X There is a 0.27% of reference with a coverageData >= 31X There is a 0.27% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.26% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.25% of reference with a coverageData >= 36X There is a 0.25% of reference with a coverageData >= 37X There is a 0.25% of reference with a coverageData >= 38X There is a 0.24% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.24% of reference with a coverageData >= 41X There is a 0.23% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.23% of reference with a coverageData >= 44X There is a 0.23% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.22% of reference with a coverageData >= 47X There is a 0.22% of reference with a coverageData >= 48X There is a 0.22% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 188507192 0.7562957766913648 20.49189546830448 chr2 243199373 170773846 0.7021969008119112 19.35181226166007 chr3 198022430 100537432 0.5077072935626534 11.220033500189189 chr4 191154276 65606526 0.34321244270779483 14.368905402479522 chr5 180915260 60767957 0.3358918258194472 11.623863988249623 chr6 171115067 180920788 1.057304836867463 23.434026184451366 chr7 159138663 152275489 0.9568729944652105 22.821232541452847 chr8 146364022 107326720 0.7332862170185512 20.593558378563255 chr9 141213431 82959632 0.5874769234946214 14.447018055002475 chr10 135534747 53396474 0.39396889123938084 13.491281884254901 chr11 135006516 64910329 0.48079404552592114 13.439124321871597 chr12 133851895 104617938 0.7815947469402655 17.126639721827768 chr13 115169878 44617274 0.38740402243023997 11.622920205956492 chr14 107349540 45411601 0.42302557607605956 13.961513262279125 chr15 102531392 32444525 0.31643503874403656 14.07415169685075 chr16 90354753 129699403 1.435446378786515 39.394512804196054 chr17 81195210 106357558 1.309899414017157 27.127711124021406 chr18 78077248 23738281 0.3040358312833977 11.850274843803911 chr19 59128983 63296157 1.070475996517647 20.794542934693965 chr20 63025520 74398339 1.1804478408111507 29.818021613568266 chr21 48129895 13827092 0.28728697621301685 11.901834190670291 chr22 51304566 19980360 0.38944603877947237 11.137335771448264 chrMT 16571 15850 0.9564902540582946 1.3245423482256422 chrX 155270560 129484748 0.8339298061396829 21.28867096871959 chrY 59373566 309871 0.005219006047236577 0.28708652330491613