BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068070.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,569,825 number of mapped reads = 4,310,390 (94.32%) number of supplementary alignments = 33,584 (0.73%) number of secondary alignments = 0 number of mapped bases = 276,822,023 bp number of sequenced bases = 276,717,746 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 821,182 duplication rate = 14.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3954 >>>>>>> ACTG content number of A's = 70,944,504 bp (25.64%) number of C's = 50,123,050 bp (18.11%) number of T's = 89,896,296 bp (32.49%) number of G's = 65,722,093 bp (23.75%) number of N's = 31,803 bp (0.01%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,477,382 number of insertions = 16,827 mapped reads with insertion percentage = 0.39% number of deletions = 60,020 mapped reads with deletion percentage = 1.38% homopolymer indels = 43.82% >>>>>>> Coverage mean coverageData = 0.0894X std coverageData = 1.0493X There is a 5.49% of reference with a coverageData >= 1X There is a 1.96% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% 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 31813084 0.12763492372602755 2.1210017649980597 chr2 243199373 25460917 0.1046915404670883 1.9286572117191663 chr3 198022430 21356847 0.10785064601015147 0.49714041287023814 chr4 191154276 15378938 0.08045301586661864 0.453246386077261 chr5 180915260 13229968 0.0731279826809524 0.4099257341173287 chr6 171115067 17883151 0.10450950529096308 0.6837160273009464 chr7 159138663 22266076 0.1399161937159168 1.611309269150175 chr8 146364022 12562196 0.08582844218369456 1.2386286322097038 chr9 141213431 7491598 0.05305159677056497 0.6036248957615864 chr10 135534747 11887467 0.08770789235324282 0.5576548279287482 chr11 135006516 9991889 0.0740104203563034 0.49223639645133377 chr12 133851895 11869862 0.0886790732398671 0.4766517970821619 chr13 115169878 6252367 0.05428821414571612 0.41629436995861685 chr14 107349540 3646572 0.033969144162145457 0.33553791054568954 chr15 102531392 5102111 0.04976145257054542 0.3862286668950608 chr16 90354753 7092041 0.07849106731551798 0.4448603676001752 chr17 81195210 9439557 0.11625756002108992 0.5305303953828013 chr18 78077248 7154633 0.09163531224871041 1.1700016750304527 chr19 59128983 7601431 0.12855676885225642 1.2658332065955402 chr20 63025520 3962769 0.06287562561959029 0.4070010093105808 chr21 48129895 4501828 0.09353496408001721 0.46999766592896636 chr22 51304566 2867993 0.05590132075184107 0.3460355076330943 chrMT 16571 350737 21.165711182185746 13.32901778899868 chrX 155270560 16846841 0.10849990494012517 0.5834341483920119 chrY 59373566 811150 0.01366180363833966 0.3381477144483453