BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238603.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 = 3,312,239 number of mapped reads = 3,035,736 (91.65%) number of supplementary alignments = 22,475 (0.68%) number of secondary alignments = 0 number of mapped bases = 189,184,017 bp number of sequenced bases = 189,086,271 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 409,750 duplication rate = 11.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5723 >>>>>>> ACTG content number of A's = 47,776,437 bp (25.27%) number of C's = 33,631,389 bp (17.79%) number of T's = 62,431,284 bp (33.02%) number of G's = 45,237,442 bp (23.92%) number of N's = 9,719 bp (0.01%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,060,562 number of insertions = 11,962 mapped reads with insertion percentage = 0.39% number of deletions = 56,030 mapped reads with deletion percentage = 1.82% homopolymer indels = 42.13% >>>>>>> Coverage mean coverageData = 0.0611X std coverageData = 0.6406X There is a 4.41% of reference with a coverageData >= 1X There is a 1.11% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 19120878 0.07671346182924856 1.0548759396770728 chr2 243199373 18811495 0.07735009662216523 1.2765895409995236 chr3 198022430 12454120 0.06289247132256684 0.3358155521757263 chr4 191154276 6945052 0.03633218228401022 0.2770566003347617 chr5 180915260 11401571 0.06302161022790449 0.33853855593242727 chr6 171115067 22139990 0.12938656068200002 0.857118941647884 chr7 159138663 6440355 0.04047008362763485 0.39425844951581684 chr8 146364022 10930038 0.07467708150299396 0.49401294515563454 chr9 141213431 10749266 0.07612070554393655 0.6173219301614994 chr10 135534747 6085785 0.044902027964828825 0.3965201499785509 chr11 135006516 8351619 0.06186085862700138 0.37898479643724853 chr12 133851895 6708995 0.05012252534788544 0.3437695360666062 chr13 115169878 4052062 0.03518334889614105 0.3387081233065874 chr14 107349540 4331878 0.04035301874605145 0.3651615163942364 chr15 102531392 3826263 0.037317965994258614 0.35780984105517816 chr16 90354753 5276776 0.05840064661567942 0.40420884581444705 chr17 81195210 3215064 0.03959672005282085 0.28726910657449867 chr18 78077248 6225528 0.07973549477563553 1.1858868864091092 chr19 59128983 1847733 0.03124919297191362 0.6173414458855302 chr20 63025520 2675061 0.04244409248824921 0.3036139611089188 chr21 48129895 2981333 0.061943476086951776 0.3837473523679665 chr22 51304566 295007 0.005750111988083088 0.09234221990233873 chrMT 16571 21809 1.3160943817512523 1.5881982012104952 chrX 155270560 13824403 0.08903428312488858 0.4336516799223846 chrY 59373566 471936 0.0079485877604185 0.24125545632054227