BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080712.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,070,923 number of mapped reads = 1,868,254 (90.21%) number of supplementary alignments = 12,419 (0.6%) number of secondary alignments = 0 number of mapped bases = 126,419,616 bp number of sequenced bases = 126,372,810 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,861 duplication rate = 4.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.203 >>>>>>> ACTG content number of A's = 35,310,101 bp (27.94%) number of C's = 23,322,414 bp (18.46%) number of T's = 40,281,909 bp (31.88%) number of G's = 27,456,508 bp (21.73%) number of N's = 1,878 bp (0%) GC percentage = 40.18% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,010,678 number of insertions = 8,912 mapped reads with insertion percentage = 0.47% number of deletions = 26,637 mapped reads with deletion percentage = 1.41% homopolymer indels = 48.38% >>>>>>> Coverage mean coverageData = 0.0408X std coverageData = 0.3477X There is a 3.39% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 15200019 0.06098287313795699 0.4939479046824453 chr2 243199373 8410902 0.03458439014972296 0.34904566225814887 chr3 198022430 7783298 0.03930513326192391 0.22952316542234877 chr4 191154276 5464653 0.028587657646748116 0.20077050859437368 chr5 180915260 5982532 0.03306814472145689 0.20959311336276193 chr6 171115067 7614334 0.04449832579617317 0.334289326003773 chr7 159138663 8016380 0.050373553785606456 0.8398391925548597 chr8 146364022 14952154 0.10215730475075357 0.47117987221881963 chr9 141213431 3856554 0.027310107634166896 0.24361770871594973 chr10 135534747 5888373 0.04344548634454602 0.3142271310759273 chr11 135006516 5382888 0.03987131998873299 0.2506244193612541 chr12 133851895 4113880 0.030734566738857154 0.20424337111208496 chr13 115169878 2709882 0.02352943362499698 0.17757952942179403 chr14 107349540 2545514 0.023712388520714667 0.18841995487653923 chr15 102531392 2206990 0.021525017430759158 0.16935839166072425 chr16 90354753 3046881 0.03372131402982199 0.22729970173916733 chr17 81195210 1974755 0.024321077561102435 0.18508473357695793 chr18 78077248 4182654 0.053570714992413664 0.37448095943091103 chr19 59128983 2067662 0.03496867179332342 0.3281965365950695 chr20 63025520 3118625 0.0494819400141403 0.2610640665727519 chr21 48129895 1926152 0.040019867070144245 0.23711512504770502 chr22 51304566 1161747 0.02264412489134008 0.1725305619465517 chrMT 16571 14760 0.8907126908454529 1.1961206576435068 chrX 155270560 8528998 0.054929910731306694 0.28679056788096274 chrY 59373566 269029 0.004531124170645233 0.0947946065724616