BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819106.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,139,065 number of mapped reads = 1,802,537 (84.27%) number of supplementary alignments = 9,282 (0.43%) number of secondary alignments = 0 number of mapped bases = 99,798,698 bp number of sequenced bases = 99,752,109 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 307,823 duplication rate = 11.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5115 >>>>>>> ACTG content number of A's = 23,463,860 bp (23.52%) number of C's = 19,833,629 bp (19.88%) number of T's = 32,805,931 bp (32.89%) number of G's = 23,647,350 bp (23.71%) number of N's = 1,339 bp (0%) GC percentage = 43.59% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 630,424 number of insertions = 6,741 mapped reads with insertion percentage = 0.37% number of deletions = 27,912 mapped reads with deletion percentage = 1.53% homopolymer indels = 41.76% >>>>>>> Coverage mean coverageData = 0.0322X std coverageData = 0.3738X There is a 1.96% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9941640 0.039886119280721874 0.52917005387993 chr2 243199373 8119271 0.03338524643318057 0.5289546156226662 chr3 198022430 5548173 0.028017901810416124 0.26326075284749106 chr4 191154276 5934074 0.03104337566584176 0.3732964231688995 chr5 180915260 5482639 0.030305011307503855 0.2691067944612545 chr6 171115067 4198843 0.024538125564360736 0.28043627527853154 chr7 159138663 5234191 0.03289075640908206 0.39904403654052273 chr8 146364022 9118521 0.062300289889546764 0.4576549199559995 chr9 141213431 4218462 0.029872951674122274 0.3068213727334271 chr10 135534747 5373896 0.03964958152022817 0.5051192972505819 chr11 135006516 3476407 0.025749920100152795 0.3041330798594258 chr12 133851895 4618605 0.034505338904615435 0.293720591755333 chr13 115169878 2321895 0.020160610051180222 0.2214179571650561 chr14 107349540 2418881 0.022532756078880264 0.23587034292725415 chr15 102531392 2695443 0.026288953533372492 0.2533039827599739 chr16 90354753 3177567 0.03516767955748825 0.3141861768445702 chr17 81195210 3513924 0.043277479053259425 0.3498223069926996 chr18 78077248 2399842 0.030736764697444255 0.4667351919572929 chr19 59128983 2213804 0.03744025159370659 0.4075272690368122 chr20 63025520 2964857 0.04704216641132037 0.35666394661610706 chr21 48129895 1434342 0.02980147785487585 0.32364066631625776 chr22 51304566 844503 0.016460581695594112 0.20737163180830262 chrMT 16571 157709 9.517168547462434 7.42271693094118 chrX 155270560 3927256 0.02529298535408129 0.2626071781234977 chrY 59373566 463953 0.007814133986831784 0.3520382630682064