BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236078.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 = 3,904,933 number of mapped reads = 3,421,683 (87.62%) number of supplementary alignments = 39,057 (1%) number of secondary alignments = 0 number of mapped bases = 217,547,266 bp number of sequenced bases = 217,437,431 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 341,800 duplication rate = 8.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8244 >>>>>>> ACTG content number of A's = 61,217,650 bp (28.15%) number of C's = 40,292,028 bp (18.53%) number of T's = 68,288,275 bp (31.41%) number of G's = 47,637,481 bp (21.91%) number of N's = 1,997 bp (0%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,642,474 number of insertions = 15,790 mapped reads with insertion percentage = 0.46% number of deletions = 64,158 mapped reads with deletion percentage = 1.85% homopolymer indels = 45.46% >>>>>>> Coverage mean coverageData = 0.0703X std coverageData = 0.603X There is a 4.66% of reference with a coverageData >= 1X There is a 1.47% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% 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% 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 24526868 0.09840243487297069 0.9221573561191426 chr2 243199373 16800185 0.06907988615579203 0.6614331295278754 chr3 198022430 20329142 0.10266080463713126 0.45135099123322475 chr4 191154276 15481176 0.0809878613439963 0.45035039976380725 chr5 180915260 13527850 0.07477451045312596 0.38326106147542516 chr6 171115067 22174189 0.12958642034719245 0.8851234862722198 chr7 159138663 12470907 0.07836503565447198 0.6619064818179478 chr8 146364022 12848987 0.08778787863591231 1.3170817514081379 chr9 141213431 8507052 0.06024251333430175 0.4150555781627384 chr10 135534747 9531349 0.0703240254692769 0.5340557206927716 chr11 135006516 3666188 0.027155637436047902 0.2669263026693608 chr12 133851895 4277239 0.03195501266530444 0.2634216770035258 chr13 115169878 5156996 0.04477729845298612 0.30020199618338306 chr14 107349540 4549577 0.04238096409169522 0.3178375451181522 chr15 102531392 6093309 0.059428716231610314 0.35876404606022566 chr16 90354753 4742871 0.05249166028930432 0.3333234295860777 chr17 81195210 6595639 0.08123187316099066 0.46325995612729237 chr18 78077248 4636308 0.059381037610342004 0.6361244228550549 chr19 59128983 4044100 0.06839454688405515 0.6440988422764649 chr20 63025520 3614019 0.05734215282952049 0.34587422153085307 chr21 48129895 1880437 0.0390700416030411 0.3094893756428838 chr22 51304566 1433284 0.027936772723113963 0.22283801073622972 chrMT 16571 140642 8.487236738881178 6.038842458725966 chrX 155270560 10022066 0.0645458224662808 0.3769774627868388 chrY 59373566 496886 0.008368808435727104 0.24048163245885912