BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514708.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 = 78,349,227 number of mapped reads = 77,501,993 (98.92%) number of supplementary alignments = 4,261,553 (5.44%) number of secondary alignments = 0 number of mapped bases = 7,332,016,134 bp number of sequenced bases = 7,323,005,476 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,447,624 duplication rate = 32.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.5435 >>>>>>> ACTG content number of A's = 2,145,581,650 bp (29.3%) number of C's = 1,508,110,034 bp (20.59%) number of T's = 2,123,335,508 bp (29%) number of G's = 1,531,534,653 bp (20.91%) number of N's = 14,443,631 bp (0.2%) GC percentage = 41.51% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 51,485,818 number of insertions = 3,199,151 mapped reads with insertion percentage = 3.93% number of deletions = 3,606,086 mapped reads with deletion percentage = 4.36% homopolymer indels = 35.62% >>>>>>> Coverage mean coverageData = 2.3685X std coverageData = 164.8076X There is a 13.6% of reference with a coverageData >= 1X There is a 9.95% of reference with a coverageData >= 2X There is a 8.23% of reference with a coverageData >= 3X There is a 7.24% of reference with a coverageData >= 4X There is a 6.52% of reference with a coverageData >= 5X There is a 5.97% of reference with a coverageData >= 6X There is a 5.52% of reference with a coverageData >= 7X There is a 5.14% of reference with a coverageData >= 8X There is a 4.81% of reference with a coverageData >= 9X There is a 4.52% of reference with a coverageData >= 10X There is a 4.26% of reference with a coverageData >= 11X There is a 4.03% of reference with a coverageData >= 12X There is a 3.82% of reference with a coverageData >= 13X There is a 3.62% of reference with a coverageData >= 14X There is a 3.45% of reference with a coverageData >= 15X There is a 3.28% of reference with a coverageData >= 16X There is a 3.13% of reference with a coverageData >= 17X There is a 2.99% of reference with a coverageData >= 18X There is a 2.86% of reference with a coverageData >= 19X There is a 2.74% of reference with a coverageData >= 20X There is a 2.62% of reference with a coverageData >= 21X There is a 2.52% of reference with a coverageData >= 22X There is a 2.42% of reference with a coverageData >= 23X There is a 2.32% of reference with a coverageData >= 24X There is a 2.23% of reference with a coverageData >= 25X There is a 2.15% of reference with a coverageData >= 26X There is a 2.07% of reference with a coverageData >= 27X There is a 1.99% of reference with a coverageData >= 28X There is a 1.92% of reference with a coverageData >= 29X There is a 1.85% of reference with a coverageData >= 30X There is a 1.78% of reference with a coverageData >= 31X There is a 1.72% of reference with a coverageData >= 32X There is a 1.66% of reference with a coverageData >= 33X There is a 1.61% of reference with a coverageData >= 34X There is a 1.56% of reference with a coverageData >= 35X There is a 1.51% of reference with a coverageData >= 36X There is a 1.46% of reference with a coverageData >= 37X There is a 1.41% of reference with a coverageData >= 38X There is a 1.37% of reference with a coverageData >= 39X There is a 1.32% of reference with a coverageData >= 40X There is a 1.28% of reference with a coverageData >= 41X There is a 1.24% of reference with a coverageData >= 42X There is a 1.21% of reference with a coverageData >= 43X There is a 1.17% of reference with a coverageData >= 44X There is a 1.14% of reference with a coverageData >= 45X There is a 1.1% of reference with a coverageData >= 46X There is a 1.07% of reference with a coverageData >= 47X There is a 1.04% of reference with a coverageData >= 48X There is a 1.01% of reference with a coverageData >= 49X There is a 0.99% of reference with a coverageData >= 50X There is a 0.96% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 705418821 2.8301587300759423 93.5072048205537 chr2 243199373 666821844 2.7418732037602744 22.12650935033723 chr3 198022430 502998472 2.5401085725490793 16.1936679878018 chr4 191154276 738778620 3.864829160295635 407.1838324123294 chr5 180915260 584090330 3.2285299205827083 19.070035930297408 chr6 171115067 417176312 2.4379870184079113 35.12280954464251 chr7 159138663 337578619 2.121286007034004 34.8241139170007 chr8 146364022 461972468 3.1563253160670866 402.5197831754054 chr9 141213431 578636894 4.097605234165013 377.26490454205555 chr10 135534747 247173760 1.8236929309352679 15.073795226375209 chr11 135006516 279186904 2.0679513276233275 13.230132528250335 chr12 133851895 258180572 1.9288525724645138 48.38270863712063 chr13 115169878 220647229 1.915841475494139 24.40550773383185 chr14 107349540 131399425 1.2240334238972985 10.153158515729748 chr15 102531392 107830274 1.0516805818846193 8.43679021118933 chr16 90354753 151613899 1.677984765228676 12.000819288001445 chr17 81195210 168001234 2.0691027709639522 16.28032883724908 chr18 78077248 104940451 1.344059296249786 54.0121597057212 chr19 59128983 135797685 2.2966348837760324 63.33365573606915 chr20 63025520 86178673 1.367361554494116 15.996894970508782 chr21 48129895 52336998 1.0874114310866458 8.84374388863409 chr22 51304566 39136379 0.7628244823277522 22.462526373474997 chrMT 16571 2792494 168.51692716190936 82.66820868408907 chrX 155270560 307299115 1.9791202852620613 174.94108651487696 chrY 59373566 46028662 0.7752382937551704 6.990960403635973