BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231829.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 = 5,675,645 number of mapped reads = 5,013,826 (88.34%) number of supplementary alignments = 26,087 (0.46%) number of secondary alignments = 0 number of mapped bases = 319,148,206 bp number of sequenced bases = 319,019,082 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 491,465 duplication rate = 7.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0236 >>>>>>> ACTG content number of A's = 80,754,564 bp (25.31%) number of C's = 57,754,324 bp (18.1%) number of T's = 103,787,520 bp (32.53%) number of G's = 76,602,065 bp (24.01%) number of N's = 120,609 bp (0.04%) GC percentage = 42.12% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,983,262 number of insertions = 20,612 mapped reads with insertion percentage = 0.41% number of deletions = 72,039 mapped reads with deletion percentage = 1.42% homopolymer indels = 44.23% >>>>>>> Coverage mean coverageData = 0.1031X std coverageData = 1.0418X There is a 7.97% of reference with a coverageData >= 1X There is a 1.57% of reference with a coverageData >= 2X There is a 0.36% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 29389147 0.1179100251870586 2.342458018330172 chr2 243199373 22119117 0.09095055109373164 1.4825504377905205 chr3 198022430 30801362 0.15554481378700383 0.49217436886144683 chr4 191154276 11803227 0.061747125133627664 0.3774075979548336 chr5 180915260 15225403 0.08415764927734676 0.372964601645936 chr6 171115067 25533718 0.14921957749050818 0.8739694944173807 chr7 159138663 18988822 0.11932249298839466 1.3925703726161882 chr8 146364022 19610521 0.13398457306673356 0.900674333588446 chr9 141213431 15733696 0.11141784381685337 0.7327975481800783 chr10 135534747 14909285 0.11000341484387026 0.9703735474492126 chr11 135006516 11123759 0.08239423791959789 0.6325377799567224 chr12 133851895 11013245 0.08227933567918481 0.3904600152731748 chr13 115169878 10120267 0.08787251645781895 0.39957546150477413 chr14 107349540 13781312 0.12837793249975735 0.4992374826724907 chr15 102531392 6029144 0.05880290789380876 0.36130130203001803 chr16 90354753 8676483 0.09602685760205663 0.5171529105406835 chr17 81195210 8084286 0.09956604582955078 0.45648635950251415 chr18 78077248 6048367 0.07746644707559365 1.7127434544427063 chr19 59128983 8820987 0.14918211936775574 1.3874661417740828 chr20 63025520 7865273 0.12479505127446787 0.4873604077002293 chr21 48129895 6468946 0.1344059861339818 0.49956398185010903 chr22 51304566 3492553 0.06807489610184014 0.3173691394780163 chrMT 16571 261232 15.764407700199143 8.924984429352461 chrX 155270560 12449044 0.08017646101102488 0.46655316422918075 chrY 59373566 799010 0.013457335542217558 0.286463849264011