BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013269.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 = 2,002,099 number of mapped reads = 1,767,215 (88.27%) number of supplementary alignments = 13,716 (0.69%) number of secondary alignments = 0 number of mapped bases = 118,642,545 bp number of sequenced bases = 118,591,895 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,744 duplication rate = 3.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9084 >>>>>>> ACTG content number of A's = 33,411,978 bp (28.17%) number of C's = 21,810,470 bp (18.39%) number of T's = 37,822,516 bp (31.89%) number of G's = 25,521,567 bp (21.52%) number of N's = 25,364 bp (0.02%) GC percentage = 39.91% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 982,853 number of insertions = 8,403 mapped reads with insertion percentage = 0.47% number of deletions = 29,942 mapped reads with deletion percentage = 1.68% homopolymer indels = 47.31% >>>>>>> Coverage mean coverageData = 0.0383X std coverageData = 0.3849X There is a 3.16% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 10769507 0.04320754330236955 0.6621042976197912 chr2 243199373 12175044 0.05006198761869341 0.5577665503169099 chr3 198022430 7594416 0.0383512918208306 0.23040534804955326 chr4 191154276 5487501 0.028707184138533213 0.20471860867115205 chr5 180915260 5385316 0.02976706332014226 0.20124907264923483 chr6 171115067 8067801 0.047148396347821316 0.37682583273247533 chr7 159138663 2329524 0.014638328336338982 0.430049264960621 chr8 146364022 7923070 0.054132633769793506 0.4830170578967991 chr9 141213431 2111389 0.014951757669566147 0.3286471659246902 chr10 135534747 3325228 0.024534136622544476 0.4271576686404029 chr11 135006516 5870134 0.043480375421287076 0.3087741687892137 chr12 133851895 9850711 0.07359410936991218 0.32250574273840343 chr13 115169878 2537731 0.02203467646288555 0.1714268059995678 chr14 107349540 6651973 0.06196554731394285 0.29904451895632217 chr15 102531392 1836851 0.017915010848579917 0.1554819874631331 chr16 90354753 3425166 0.037907978122634016 0.2498376951493119 chr17 81195210 3197691 0.03938275422897484 0.24084077295815123 chr18 78077248 4838262 0.06196762980170613 0.6397609280038465 chr19 59128983 1100183 0.01860649285985521 0.4619860709957467 chr20 63025520 4410684 0.06998250867267736 0.31662396870689963 chr21 48129895 1597225 0.033185715447748225 0.21594748595008673 chr22 51304566 1252637 0.02441570210339563 0.17851385613530582 chrMT 16571 34454 2.079174461408485 2.233382864297193 chrX 155270560 6668210 0.042945745800105316 0.26964447802259517 chrY 59373566 201837 0.003399442101894301 0.07450437643225352