BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013194.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 = 1,903,569 number of mapped reads = 1,599,696 (84.04%) number of supplementary alignments = 14,158 (0.74%) number of secondary alignments = 0 number of mapped bases = 103,783,240 bp number of sequenced bases = 103,735,979 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,896 duplication rate = 5.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5974 >>>>>>> ACTG content number of A's = 28,097,627 bp (27.09%) number of C's = 18,738,945 bp (18.06%) number of T's = 33,397,823 bp (32.2%) number of G's = 23,500,202 bp (22.65%) number of N's = 1,382 bp (0%) GC percentage = 40.72% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 758,871 number of insertions = 6,709 mapped reads with insertion percentage = 0.42% number of deletions = 27,360 mapped reads with deletion percentage = 1.69% homopolymer indels = 46.62% >>>>>>> Coverage mean coverageData = 0.0335X std coverageData = 0.345X There is a 2.57% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 6703794 0.026895796580583043 0.5907564239964166 chr2 243199373 12300431 0.05057756049395736 0.4204932086815101 chr3 198022430 5217338 0.026347207233039207 0.202371926329135 chr4 191154276 6150705 0.03217665400275953 0.2266747371896624 chr5 180915260 6734605 0.03722519040129617 0.24553949077313558 chr6 171115067 4143343 0.024213782413444632 0.22091281863781262 chr7 159138663 8478012 0.05327436991223183 0.6596815721547155 chr8 146364022 6037622 0.04125072485368023 0.3614335267972019 chr9 141213431 2494524 0.017664920272350015 0.2450080959109791 chr10 135534747 3737808 0.027578226858681488 0.30736667856661487 chr11 135006516 3257925 0.02413161302525576 0.2440694217513029 chr12 133851895 6081446 0.04543414196713465 0.26892712373884986 chr13 115169878 2759785 0.023962732686058762 0.19175965066489678 chr14 107349540 3068975 0.028588618078847845 0.21714088309125293 chr15 102531392 3633696 0.03543983875689506 0.23680987119262437 chr16 90354753 3868338 0.04281277820548079 0.26570584970759326 chr17 81195210 2118581 0.02609243821156445 0.21443471865367644 chr18 78077248 3229289 0.04136017960059248 0.47011894760430023 chr19 59128983 2576683 0.04357732653714 0.43219947779602963 chr20 63025520 1498353 0.023773750696543243 0.19876159104528165 chr21 48129895 1711250 0.03555482512480029 0.2398552826239936 chr22 51304566 822031 0.016022569998935376 0.15404694110078762 chrMT 16571 14483 0.8739967412950335 1.3208018784067688 chrX 155270560 6916161 0.04454264221111845 0.29068876625314777 chrY 59373566 228062 0.003841136980049337 0.08994274714400174