BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514762.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 20,479,126 number of mapped reads = 18,200,717 (88.87%) number of supplementary alignments = 2,744,801 (13.4%) number of secondary alignments = 0 number of mapped bases = 1,724,895,248 bp number of sequenced bases = 1,723,851,634 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,205,905 duplication rate = 37.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1152 >>>>>>> ACTG content number of A's = 536,217,305 bp (31.11%) number of C's = 325,283,867 bp (18.87%) number of T's = 526,702,437 bp (30.55%) number of G's = 335,532,481 bp (19.46%) number of N's = 115,544 bp (0.01%) GC percentage = 38.33% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 8,887,138 number of insertions = 982,431 mapped reads with insertion percentage = 5.18% number of deletions = 371,494 mapped reads with deletion percentage = 1.94% homopolymer indels = 53.2% >>>>>>> Coverage mean coverageData = 0.5572X std coverageData = 22.0235X There is a 2.85% of reference with a coverageData >= 1X There is a 1.8% of reference with a coverageData >= 2X There is a 1.45% of reference with a coverageData >= 3X There is a 1.25% of reference with a coverageData >= 4X There is a 1.12% of reference with a coverageData >= 5X There is a 1.01% of reference with a coverageData >= 6X There is a 0.93% of reference with a coverageData >= 7X There is a 0.87% of reference with a coverageData >= 8X There is a 0.81% of reference with a coverageData >= 9X There is a 0.76% of reference with a coverageData >= 10X There is a 0.72% of reference with a coverageData >= 11X There is a 0.68% of reference with a coverageData >= 12X There is a 0.65% of reference with a coverageData >= 13X There is a 0.62% of reference with a coverageData >= 14X There is a 0.59% of reference with a coverageData >= 15X There is a 0.57% of reference with a coverageData >= 16X There is a 0.54% of reference with a coverageData >= 17X There is a 0.52% of reference with a coverageData >= 18X There is a 0.5% of reference with a coverageData >= 19X There is a 0.49% of reference with a coverageData >= 20X There is a 0.47% of reference with a coverageData >= 21X There is a 0.45% of reference with a coverageData >= 22X There is a 0.44% of reference with a coverageData >= 23X There is a 0.42% of reference with a coverageData >= 24X There is a 0.41% of reference with a coverageData >= 25X There is a 0.4% of reference with a coverageData >= 26X There is a 0.39% of reference with a coverageData >= 27X There is a 0.38% of reference with a coverageData >= 28X There is a 0.37% of reference with a coverageData >= 29X There is a 0.36% of reference with a coverageData >= 30X There is a 0.35% of reference with a coverageData >= 31X There is a 0.34% of reference with a coverageData >= 32X There is a 0.33% of reference with a coverageData >= 33X There is a 0.32% of reference with a coverageData >= 34X There is a 0.32% of reference with a coverageData >= 35X There is a 0.31% of reference with a coverageData >= 36X There is a 0.3% of reference with a coverageData >= 37X There is a 0.29% of reference with a coverageData >= 38X There is a 0.29% of reference with a coverageData >= 39X There is a 0.28% of reference with a coverageData >= 40X There is a 0.28% of reference with a coverageData >= 41X There is a 0.27% of reference with a coverageData >= 42X There is a 0.26% of reference with a coverageData >= 43X There is a 0.26% of reference with a coverageData >= 44X There is a 0.25% of reference with a coverageData >= 45X There is a 0.25% of reference with a coverageData >= 46X There is a 0.24% of reference with a coverageData >= 47X There is a 0.24% of reference with a coverageData >= 48X There is a 0.23% of reference with a coverageData >= 49X There is a 0.23% of reference with a coverageData >= 50X There is a 0.23% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 137001480 0.5496535152062871 13.60604311670983 chr2 243199373 170116145 0.6994925311752346 33.004496536152935 chr3 198022430 142032379 0.7172539949136065 13.658265131478851 chr4 191154276 168279678 0.8803343640609954 15.946999543306347 chr5 180915260 66501419 0.3675832486435915 13.254877626402907 chr6 171115067 111148172 0.6495522220728815 11.504698271560745 chr7 159138663 119377301 0.7501464367587404 14.956768917454365 chr8 146364022 91762581 0.6269476593093349 38.20213157916879 chr9 141213431 60367084 0.42748826065985185 13.904164019055832 chr10 135534747 52588149 0.38800492245726476 12.63723671719611 chr11 135006516 66097374 0.489586547067106 10.697445935380715 chr12 133851895 69816143 0.5215924884739211 12.774325338655853 chr13 115169878 136145653 1.1821290025157447 25.384808311977764 chr14 107349540 33259345 0.3098228925806296 7.372812620931163 chr15 102531392 41177479 0.40160850444710633 7.445024806321077 chr16 90354753 33623073 0.37212290315264324 8.199305304621783 chr17 81195210 20640861 0.25421279161664834 9.495607053676526 chr18 78077248 51450155 0.6589647601308899 13.724279518792235 chr19 59128983 6862867 0.11606604158911375 8.184368222479051 chr20 63025520 22424040 0.3557930184471306 18.09446828116206 chr21 48129895 6122232 0.12720227210136237 6.033757471978616 chr22 51304566 7735379 0.15077369526915013 4.093589876456576 chrMT 16571 66298488 4000.874298473236 4233.430439787942 chrX 155270560 38032584 0.24494394816377296 8.444366376988699 chrY 59373566 6035187 0.1016477096895275 3.4493931116415406