BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819094.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 907,095 number of mapped reads = 797,210 (87.89%) number of supplementary alignments = 3,656 (0.4%) number of secondary alignments = 0 number of mapped bases = 44,939,312 bp number of sequenced bases = 44,923,220 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,559 duplication rate = 6.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2118 >>>>>>> ACTG content number of A's = 10,803,329 bp (24.05%) number of C's = 8,642,280 bp (19.24%) number of T's = 14,219,883 bp (31.65%) number of G's = 11,257,171 bp (25.06%) number of N's = 557 bp (0%) GC percentage = 44.3% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 251,496 number of insertions = 2,675 mapped reads with insertion percentage = 0.33% number of deletions = 9,460 mapped reads with deletion percentage = 1.18% homopolymer indels = 42.37% >>>>>>> Coverage mean coverageData = 0.0145X std coverageData = 0.1802X There is a 1.17% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 4502013 0.018062193714654777 0.26727049985242335 chr2 243199373 3561031 0.014642434953974983 0.21828620496612758 chr3 198022430 2482058 0.012534226552012315 0.13492359617871105 chr4 191154276 2437844 0.012753279973710868 0.16607527906722655 chr5 180915260 2504279 0.013842276212631262 0.1408463688170246 chr6 171115067 1765305 0.010316479027530637 0.13158607018471888 chr7 159138663 2307966 0.01450286157047832 0.19725269594393927 chr8 146364022 4218475 0.028821802942802434 0.23094041555327482 chr9 141213431 2075427 0.01469709350805307 0.15890011254481815 chr10 135534747 2354702 0.017373419378574558 0.22668712755880366 chr11 135006516 1467384 0.010868986501362645 0.15138129451265112 chr12 133851895 2179575 0.016283482576021805 0.15415620752717013 chr13 115169878 936928 0.00813518270810359 0.10791273820727422 chr14 107349540 1055646 0.009833726348524642 0.12050834677450452 chr15 102531392 1170781 0.011418756511176596 0.13008388010055977 chr16 90354753 1393508 0.015422630838247103 0.15546900659268306 chr17 81195210 1572437 0.019366130095605394 0.17508165601817713 chr18 78077248 1047331 0.013414035802081548 0.22857079345930542 chr19 59128983 920124 0.015561302652541817 0.2011697108786135 chr20 63025520 1168634 0.018542234954983316 0.1666140116383825 chr21 48129895 603827 0.0125457784605597 0.15770666153830973 chr22 51304566 348153 0.006786004193077084 0.09906684028389652 chrMT 16571 38813 2.342224367871583 2.172979637848081 chrX 155270560 2628364 0.01692763908367433 0.16330448303382475 chrY 59373566 198707 0.003346725039220316 0.14683561933875408