BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038489.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 13,913,612 number of mapped reads = 13,560,845 (97.46%) number of supplementary alignments = 133,679 (0.96%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,838,597 number of mapped paired reads (second in pair) = 6,722,248 number of mapped paired reads (both in pair) = 13,428,080 number of mapped paired reads (singletons) = 132,765 number of mapped bases = 1,994,586,447 bp number of sequenced bases = 1,993,860,117 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,327,584 duplication rate = 7.12% >>>>>>> Insert size mean insert size = 89,865.6014 std insert size = 3,001,664.0991 median insert size = 268 >>>>>>> Mapping quality mean mapping quality = 54.4383 >>>>>>> ACTG content number of A's = 576,503,032 bp (28.91%) number of C's = 423,721,004 bp (21.25%) number of T's = 571,270,794 bp (28.65%) number of G's = 422,319,920 bp (21.18%) number of N's = 45,367 bp (0%) GC percentage = 42.43% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 20,471,304 number of insertions = 249,812 mapped reads with insertion percentage = 1.73% number of deletions = 263,251 mapped reads with deletion percentage = 1.86% homopolymer indels = 44.32% >>>>>>> Coverage mean coverageData = 0.6443X std coverageData = 6.7255X There is a 37.67% of reference with a coverageData >= 1X There is a 15.49% of reference with a coverageData >= 2X There is a 5.33% of reference with a coverageData >= 3X There is a 2.09% of reference with a coverageData >= 4X There is a 0.74% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 149141435 0.5983593316704314 17.5796125905063 chr2 243199373 194755280 0.8008050251017711 5.298522178177208 chr3 198022430 119115098 0.6015232617840313 0.9942758700284922 chr4 191154276 111184666 0.5816488562358919 4.52023454344771 chr5 180915260 113468467 0.6271912441216955 1.0835204952359587 chr6 171115067 138325972 0.8083798488650915 5.591311819207427 chr7 159138663 111352397 0.6997193196225358 4.216964655109557 chr8 146364022 93674470 0.6400102205444996 4.738152820586655 chr9 141213431 79096071 0.5601171959344292 7.586946842403427 chr10 135534747 88568132 0.6534717772410052 10.367585995061678 chr11 135006516 96996973 0.7184614185584939 3.5716038421036957 chr12 133851895 76885029 0.5744037392970791 1.006482303677911 chr13 115169878 108275524 0.9401375245009811 1.2948162737118558 chr14 107349540 45290743 0.4218997398591554 0.9304262478621859 chr15 102531392 44617874 0.4351630571835014 0.8484068874987611 chr16 90354753 73093775 0.808964360734847 4.303270221805923 chr17 81195210 66514399 0.8191911690357103 3.679253015743398 chr18 78077248 36126759 0.46270533254450774 7.738014241615178 chr19 59128983 45671038 0.7723968125749769 7.978023522979232 chr20 63025520 61071826 0.9690015409630892 1.950997630811325 chr21 48129895 21887353 0.454755885089714 2.8015205339541867 chr22 51304566 20386713 0.39736644492811807 2.1847311849290785 chrMT 16571 4392576 265.07609679560676 32.436689204975934 chrX 155270560 76538844 0.4929385454654121 1.267809227638772 chrY 59373566 18155033 0.3057763618240481 5.676272058009691