BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013272.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 = 1,797,533 number of mapped reads = 1,282,639 (71.36%) number of supplementary alignments = 16,719 (0.93%) number of secondary alignments = 0 number of mapped bases = 79,193,358 bp number of sequenced bases = 79,127,232 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 205,933 duplication rate = 12.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2672 >>>>>>> ACTG content number of A's = 21,910,300 bp (27.69%) number of C's = 14,394,526 bp (18.19%) number of T's = 25,297,777 bp (31.97%) number of G's = 17,509,330 bp (22.13%) number of N's = 15,299 bp (0.02%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 816,127 number of insertions = 5,228 mapped reads with insertion percentage = 0.4% number of deletions = 38,316 mapped reads with deletion percentage = 2.93% homopolymer indels = 42.14% >>>>>>> Coverage mean coverageData = 0.0256X std coverageData = 0.3048X There is a 1.37% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 3205001 0.012858547702474932 0.360921366526494 chr2 243199373 12101359 0.049759005752041965 0.4629529406710685 chr3 198022430 2402185 0.012130873255115594 0.17938674532854984 chr4 191154276 5749814 0.030079442219749244 0.29621057836577613 chr5 180915260 2331725 0.012888492656727797 0.1864830415205245 chr6 171115067 6912328 0.04039578817451534 0.390703621931086 chr7 159138663 3750722 0.02356889224336389 0.2805420505498699 chr8 146364022 4289411 0.029306457566463977 0.3205153770193515 chr9 141213431 3017807 0.0213705380474751 0.2599133053478767 chr10 135534747 3574691 0.026374719982323058 0.2997176274330803 chr11 135006516 1918587 0.014211069634594526 0.19911526075927405 chr12 133851895 6047591 0.04518121316100904 0.36785077904271596 chr13 115169878 1979329 0.017186169112725812 0.2238556522940646 chr14 107349540 1278166 0.011906581062201105 0.177682241935504 chr15 102531392 3566776 0.034787160599555694 0.3166166616774318 chr16 90354753 2052291 0.022713702731277458 0.2513092677792157 chr17 81195210 1699087 0.020925951173720717 0.24471195964699277 chr18 78077248 1128265 0.014450624591686428 0.28021859455273773 chr19 59128983 1133492 0.019169820661383605 0.2873874214000372 chr20 63025520 1266228 0.020090718807238717 0.2411840504038824 chr21 48129895 2161746 0.04491482892285553 0.37009677413223674 chr22 51304566 332525 0.00648139192913161 0.12960300149187354 chrMT 16571 24390 1.4718484098726692 1.8478880007414338 chrX 155270560 7015120 0.0451799748774011 0.3693866580732148 chrY 59373566 254722 0.004290158350940215 0.1176458172850492