BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234104.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 = 5,233,950 number of mapped reads = 4,942,295 (94.43%) number of supplementary alignments = 35,953 (0.69%) number of secondary alignments = 0 number of mapped bases = 317,910,498 bp number of sequenced bases = 317,790,148 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 631,158 duplication rate = 10.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8284 >>>>>>> ACTG content number of A's = 82,215,189 bp (25.87%) number of C's = 57,463,043 bp (18.08%) number of T's = 103,019,237 bp (32.42%) number of G's = 75,061,914 bp (23.62%) number of N's = 30,765 bp (0.01%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,682,851 number of insertions = 19,932 mapped reads with insertion percentage = 0.4% number of deletions = 68,540 mapped reads with deletion percentage = 1.37% homopolymer indels = 44.06% >>>>>>> Coverage mean coverageData = 0.1027X std coverageData = 1.0207X There is a 7.56% of reference with a coverageData >= 1X There is a 1.8% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% 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 25340556 0.10166697237636972 2.1082073064154088 chr2 243199373 21357691 0.0878196795351113 1.6829762485779838 chr3 198022430 29705437 0.15001046598610066 0.4990087926323424 chr4 191154276 9101611 0.04761395450029064 0.340908419938455 chr5 180915260 24297203 0.13430156748524144 0.47790155621812547 chr6 171115067 26062657 0.15231070797523633 0.8709554153883483 chr7 159138663 24650578 0.1548999943527237 1.464715896361292 chr8 146364022 18315081 0.1251337640885545 0.9787382546461803 chr9 141213431 11647194 0.0824793641618976 0.6021332827839343 chr10 135534747 15092438 0.11135475097024382 0.7673882764207899 chr11 135006516 18275143 0.1353648960173152 0.8662620831161565 chr12 133851895 9733271 0.07271672171693946 0.3689423161027634 chr13 115169878 12098798 0.10505175667547377 0.4601874732378727 chr14 107349540 12060528 0.11234820382090133 0.474637148574188 chr15 102531392 4500637 0.043895210161586415 0.32092667308371436 chr16 90354753 10778228 0.11928789180575813 0.5463307225375801 chr17 81195210 6276729 0.07730417841150974 0.46185049951087975 chr18 78077248 4733986 0.060632080679892814 1.4780029668308543 chr19 59128983 7335817 0.12406465709041538 1.2292113737322943 chr20 63025520 7824637 0.12415029657827496 0.5109766439640826 chr21 48129895 4872931 0.10124541098624877 0.4331375841530141 chr22 51304566 2455605 0.04786328374749335 0.271814981946014 chrMT 16571 549840 33.18085812564118 18.152418361159697 chrX 155270560 10189181 0.0656221050532696 0.44239258934924025 chrY 59373566 654721 0.011027146322994985 0.24110319764929067