BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038397.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 = 17,527,258 number of mapped reads = 16,248,191 (92.7%) number of supplementary alignments = 288,182 (1.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,235,721 number of mapped paired reads (second in pair) = 8,012,470 number of mapped paired reads (both in pair) = 15,963,576 number of mapped paired reads (singletons) = 284,615 number of mapped bases = 2,182,104,017 bp number of sequenced bases = 2,180,438,513 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,324,820 duplication rate = 13.76% >>>>>>> Insert size mean insert size = 86,931.8174 std insert size = 2,825,482.2288 median insert size = 252 >>>>>>> Mapping quality mean mapping quality = 53.5057 >>>>>>> ACTG content number of A's = 626,425,951 bp (28.73%) number of C's = 430,769,705 bp (19.76%) number of T's = 635,746,722 bp (29.16%) number of G's = 487,320,841 bp (22.35%) number of N's = 175,294 bp (0.01%) GC percentage = 42.11% >>>>>>> Mismatches and indels general error rate = 0.0138 number of mismatches = 28,842,328 number of insertions = 430,128 mapped reads with insertion percentage = 2.49% number of deletions = 809,377 mapped reads with deletion percentage = 4.79% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 0.7049X std coverageData = 10.5247X There is a 27.71% of reference with a coverageData >= 1X There is a 15.65% of reference with a coverageData >= 2X There is a 8.67% of reference with a coverageData >= 3X There is a 5.21% of reference with a coverageData >= 4X There is a 3.1% of reference with a coverageData >= 5X There is a 1.91% of reference with a coverageData >= 6X There is a 1.19% of reference with a coverageData >= 7X There is a 0.76% of reference with a coverageData >= 8X There is a 0.49% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% 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 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% 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 171007293 0.6860857249378729 15.163186349422952 chr2 243199373 196485324 0.807918711204901 10.332112209725684 chr3 198022430 145980567 0.7371920797053142 1.6910124221243303 chr4 191154276 148454325 0.776620476959668 13.893265129400865 chr5 180915260 130346056 0.7204812684126259 1.5685409050935886 chr6 171115067 123688953 0.7228408062979048 6.285938628855085 chr7 159138663 112697097 0.7081691832486993 8.264987679380411 chr8 146364022 111003598 0.7584076775370384 3.1826783282328783 chr9 141213431 90249412 0.6390993502593957 15.212612657166574 chr10 135534747 125377597 0.9250587009986451 28.056816016447964 chr11 135006516 99800976 0.7392308086818565 6.731386690857794 chr12 133851895 91876216 0.6864020565416724 1.647460033616817 chr13 115169878 65560092 0.5692468650526833 1.3641704139760236 chr14 107349540 62127297 0.5787383625491083 1.5278951042345064 chr15 102531392 58961364 0.5750567006834356 1.3889044501492018 chr16 90354753 74208133 0.8212975027445429 13.414684656816505 chr17 81195210 53722746 0.6616492031980704 9.887481909251362 chr18 78077248 60985700 0.7810943848840574 11.775390279141988 chr19 59128983 29306972 0.4956447838786607 7.30816082274143 chr20 63025520 44638426 0.7082595431184067 4.362052524399894 chr21 48129895 27625148 0.5739706683340988 6.152273977975437 chr22 51304566 20339353 0.39644333020963474 1.2263900840146509 chrMT 16571 4478079 270.2358940317422 151.61229233448617 chrX 155270560 124341844 0.8008075967524043 3.176469457425996 chrY 59373566 8841449 0.14891221120186718 13.99234845123514