BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013301.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 = 2,591,566 number of mapped reads = 2,247,317 (86.72%) number of supplementary alignments = 19,719 (0.76%) number of secondary alignments = 0 number of mapped bases = 147,203,007 bp number of sequenced bases = 147,143,855 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,302 duplication rate = 4.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1341 >>>>>>> ACTG content number of A's = 41,272,782 bp (28.05%) number of C's = 27,099,381 bp (18.42%) number of T's = 46,652,501 bp (31.71%) number of G's = 32,089,247 bp (21.81%) number of N's = 29,944 bp (0.02%) GC percentage = 40.23% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,251,972 number of insertions = 11,038 mapped reads with insertion percentage = 0.49% number of deletions = 35,460 mapped reads with deletion percentage = 1.56% homopolymer indels = 46.33% >>>>>>> Coverage mean coverageData = 0.0476X std coverageData = 0.4064X There is a 3.84% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12655655 0.050774818330342295 0.4600885029142119 chr2 243199373 16822918 0.06917336090336056 0.6307317724714422 chr3 198022430 6424986 0.032445748696246175 0.21321693971066408 chr4 191154276 10843301 0.0567253907519181 0.2876716994656841 chr5 180915260 7370391 0.04073946553762242 0.24203804662493653 chr6 171115067 10373462 0.06062272704483703 0.4252993359084071 chr7 159138663 8845684 0.05558475755197215 0.6622597917997338 chr8 146364022 6549902 0.04475076532127547 0.48109371813037427 chr9 141213431 5225002 0.03700074393065345 0.3971697925630879 chr10 135534747 8267587 0.06099975971475418 0.44253759217448224 chr11 135006516 5859002 0.0433979201418693 0.37772527867022615 chr12 133851895 5866574 0.04382884530697156 0.2548265070515182 chr13 115169878 1878145 0.016307606056507242 0.15300060234172072 chr14 107349540 4806752 0.04477664273177137 0.27652598538665907 chr15 102531392 3020154 0.029455895809938872 0.20696771638959002 chr16 90354753 4006445 0.04434127554972122 0.270897894700129 chr17 81195210 4427605 0.05453037192711245 0.3372551047828221 chr18 78077248 4413378 0.056525788408935726 0.71369207389515 chr19 59128983 1661821 0.028105015775427764 0.40395386167481145 chr20 63025520 3997917 0.06343330447729745 0.30698489868007944 chr21 48129895 2152453 0.04472174726331732 0.2650885355298872 chr22 51304566 1334233 0.02600612584852584 0.18901242763072093 chrMT 16571 30811 1.8593325689457485 1.8874332763635824 chrX 155270560 10024420 0.06456098309943624 0.3739896907155514 chrY 59373566 344409 0.005800712727950347 0.10500353016307928