BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695980.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 15,349,065 number of mapped reads = 14,008,186 (91.26%) number of supplementary alignments = 217,713 (1.42%) number of secondary alignments = 0 number of mapped bases = 1,880,087,105 bp number of sequenced bases = 1,865,876,513 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,130,253 duplication rate = 18.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.4507 >>>>>>> ACTG content number of A's = 520,484,820 bp (27.89%) number of C's = 409,613,077 bp (21.95%) number of T's = 515,449,302 bp (27.63%) number of G's = 420,329,314 bp (22.53%) number of N's = 0 bp (0%) GC percentage = 44.48% >>>>>>> Mismatches and indels general error rate = 0.0172 number of mismatches = 21,315,240 number of insertions = 9,994,912 mapped reads with insertion percentage = 44.14% number of deletions = 12,809,340 mapped reads with deletion percentage = 53.22% homopolymer indels = 37.3% >>>>>>> Coverage mean coverageData = 0.6073X std coverageData = 1.5157X There is a 26.51% of reference with a coverageData >= 1X There is a 13.92% of reference with a coverageData >= 2X There is a 7.72% of reference with a coverageData >= 3X There is a 4.47% of reference with a coverageData >= 4X There is a 2.69% of reference with a coverageData >= 5X There is a 1.66% of reference with a coverageData >= 6X There is a 1.05% of reference with a coverageData >= 7X There is a 0.68% of reference with a coverageData >= 8X There is a 0.45% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 214448232 0.8603719065558517 2.2345403027711033 chr2 243199373 140671029 0.5784185512682223 1.3899555578322453 chr3 198022430 119983725 0.6059097699184885 1.3661735036353921 chr4 191154276 64394254 0.3368705913751048 0.9894655099167383 chr5 180915260 143401479 0.7926444623853178 1.645140300871873 chr6 171115067 91280549 0.533445421261472 1.3799899104138014 chr7 159138663 112847173 0.7091122350324132 1.5179627742583348 chr8 146364022 75338625 0.5147345909912205 1.2670555096795837 chr9 141213431 74771981 0.5294962417562109 1.329469215570071 chr10 135534747 80563184 0.5944098158090781 1.6105379750155382 chr11 135006516 102344221 0.7580687512890119 1.591386328858821 chr12 133851895 98908586 0.7389404983769561 1.58136402994178 chr13 115169878 48462610 0.4207924054586565 1.1303927411791652 chr14 107349540 40660600 0.37876827418170583 1.0800044352625404 chr15 102531392 71061409 0.6930697771078734 1.5021439131949677 chr16 90354753 78304993 0.8666394450771173 1.7527096854854398 chr17 81195210 69356411 0.8541933816046537 1.7921382791295042 chr18 78077248 35128921 0.4499251945970227 1.4205132116893469 chr19 59128983 44752531 0.7568628569173936 1.9539888193017778 chr20 63025520 63696148 1.0106405786100614 1.9665613392174564 chr21 48129895 15549876 0.32308144449515214 1.0873328225006147 chr22 51304566 23416821 0.4564276208866088 1.219326859533198 chrMT 16571 267927 16.168426769657835 10.134056312071715 chrX 155270560 68757266 0.44282229677023127 1.1536912755748696 chrY 59373566 1718554 0.028944766430232607 0.6085682877220322