BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238612.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 = 3,500,548 number of mapped reads = 2,562,470 (73.2%) number of supplementary alignments = 21,401 (0.61%) number of secondary alignments = 0 number of mapped bases = 154,520,628 bp number of sequenced bases = 154,454,238 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,257,725 duplication rate = 21.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0824 >>>>>>> ACTG content number of A's = 37,833,344 bp (24.49%) number of C's = 26,482,643 bp (17.15%) number of T's = 53,171,800 bp (34.43%) number of G's = 36,963,060 bp (23.93%) number of N's = 3,391 bp (0%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 902,826 number of insertions = 10,708 mapped reads with insertion percentage = 0.42% number of deletions = 39,171 mapped reads with deletion percentage = 1.51% homopolymer indels = 41.75% >>>>>>> Coverage mean coverageData = 0.0499X std coverageData = 1.6013X There is a 1% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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% 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 8205360 0.032920118582171955 0.9068049457943413 chr2 243199373 12480049 0.05131612325332763 2.4260995111049035 chr3 198022430 17806407 0.08992116196129903 1.2458214486251669 chr4 191154276 7284498 0.03810795213390884 0.7457187066301837 chr5 180915260 8946535 0.04945152222095582 0.8879662303601056 chr6 171115067 10902330 0.06371344260409284 1.498134248427373 chr7 159138663 7057916 0.04435073078375681 1.0665838106776506 chr8 146364022 3588951 0.024520718623050684 0.8889295589183173 chr9 141213431 5871252 0.04157714998086832 0.8516515649233026 chr10 135534747 13693048 0.10102979717813618 1.3866353849587356 chr11 135006516 5569876 0.04125634943427471 0.7824431962187892 chr12 133851895 4098845 0.030622241097146962 0.6567761970708109 chr13 115169878 4206610 0.036525262273873385 1.2968453436696248 chr14 107349540 4745182 0.044203095793423984 0.9460054516419023 chr15 102531392 3034105 0.029591961455082947 0.877849189532428 chr16 90354753 2187392 0.02420893121139958 0.6577859470094937 chr17 81195210 6144342 0.07567370045597517 1.1019091677646549 chr18 78077248 3751593 0.04804975964316775 6.82595559729627 chr19 59128983 1608369 0.027201025933424224 0.7391262712415718 chr20 63025520 1445971 0.022942627050121917 0.520270134241834 chr21 48129895 2691909 0.05593008254017592 0.9745354855855315 chr22 51304566 1564983 0.030503776213602507 0.7345358155572073 chrMT 16571 66875 4.03566471546678 8.42205476016713 chrX 155270560 17023869 0.10964003092408503 1.3187969812221678 chrY 59373566 544361 0.009168406694656002 0.5828444822233797