BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068132.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 = 1,429,046 number of mapped reads = 1,222,167 (85.52%) number of supplementary alignments = 10,758 (0.75%) number of secondary alignments = 0 number of mapped bases = 87,426,121 bp number of sequenced bases = 87,390,150 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 140,959 duplication rate = 9.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9437 >>>>>>> ACTG content number of A's = 25,674,497 bp (29.38%) number of C's = 16,923,967 bp (19.37%) number of T's = 26,912,725 bp (30.8%) number of G's = 17,826,432 bp (20.4%) number of N's = 52,529 bp (0.06%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 782,075 number of insertions = 7,328 mapped reads with insertion percentage = 0.6% number of deletions = 21,169 mapped reads with deletion percentage = 1.72% homopolymer indels = 48.04% >>>>>>> Coverage mean coverageData = 0.0282X std coverageData = 0.5001X There is a 0.78% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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% 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 8356907 0.03352812910343762 0.6294740032022915 chr2 243199373 7372285 0.03031375002763679 0.5187986592985537 chr3 198022430 5352617 0.027030357116615528 0.4600824467205305 chr4 191154276 4781486 0.025013753812130262 0.46896217360765347 chr5 180915260 8246615 0.04558274962543237 0.5959135948178126 chr6 171115067 4377053 0.02557958849994197 0.46264027713082256 chr7 159138663 3537211 0.02222722582506553 0.4860409803655865 chr8 146364022 3200217 0.021864779037023184 0.4565144491427587 chr9 141213431 3701604 0.026212832404022533 0.45669362945255365 chr10 135534747 3693381 0.02725043637702736 0.576162316276495 chr11 135006516 4096491 0.030342913226499377 0.47403866308753145 chr12 133851895 2794155 0.020874975285183672 0.3995550867662741 chr13 115169878 4707218 0.04087195438376691 0.5708149298799303 chr14 107349540 1762600 0.016419259924169215 0.34781719018590945 chr15 102531392 4125517 0.04023662333580724 0.5858316123833153 chr16 90354753 2720646 0.030110712604128308 0.48331868854702137 chr17 81195210 2323519 0.028616454098708534 0.47785714132946183 chr18 78077248 2401195 0.03075409368936774 0.5613181383944622 chr19 59128983 1147631 0.019408941973515764 0.46812310355537484 chr20 63025520 1448302 0.022979612068254256 0.4145115247499409 chr21 48129895 1522929 0.03164205947260014 0.5079737043120023 chr22 51304566 799120 0.01557600155900354 0.335921014171848 chrMT 16571 19046 1.1493573109649386 2.492527429856179 chrX 155270560 4633988 0.029844601578045447 0.47863595442747947 chrY 59373566 304388 0.005126658553740902 0.22430849125957122