BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525153.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 852,154 number of mapped reads = 762,458 (89.47%) number of supplementary alignments = 2,588 (0.3%) number of secondary alignments = 0 number of mapped bases = 46,558,906 bp number of sequenced bases = 46,543,678 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,791 duplication rate = 1.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5487 >>>>>>> ACTG content number of A's = 12,136,351 bp (26.08%) number of C's = 9,183,361 bp (19.73%) number of T's = 14,155,091 bp (30.41%) number of G's = 11,067,711 bp (23.78%) number of N's = 1,164 bp (0%) GC percentage = 43.51% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 224,983 number of insertions = 4,044 mapped reads with insertion percentage = 0.53% number of deletions = 9,419 mapped reads with deletion percentage = 1.23% homopolymer indels = 40.25% >>>>>>> Coverage mean coverageData = 0.015X std coverageData = 0.1701X There is a 1.41% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5215066 0.02092298097022595 0.29579540555192874 chr2 243199373 3999831 0.016446715921426328 0.18441895832948965 chr3 198022430 3522661 0.01778920196060618 0.1396180958611819 chr4 191154276 1950757 0.0102051444561983 0.10861504239115347 chr5 180915260 2130336 0.011775325088663057 0.11325217633053376 chr6 171115067 2944021 0.017204919774831986 0.14344589759647203 chr7 159138663 3605571 0.02265678831296955 0.2898550450320588 chr8 146364022 2295418 0.01568293880308919 0.14357109240989183 chr9 141213431 1618755 0.011463180156000884 0.1284024559093309 chr10 135534747 2560969 0.018895294798462272 0.18371969203982882 chr11 135006516 2210357 0.016372224582108318 0.1491885480345463 chr12 133851895 2195251 0.016400597092779298 0.13433919445306602 chr13 115169878 1074989 0.009333942335165104 0.10066487175196877 chr14 107349540 1802716 0.016792955051321133 0.13809972533365103 chr15 102531392 915652 0.008930455172207162 0.09908942626891029 chr16 90354753 1344910 0.01488477313418144 0.13480476183921772 chr17 81195210 896014 0.011035306146754223 0.11181900787293927 chr18 78077248 1020407 0.01306919782828411 0.22636164875162543 chr19 59128983 805981 0.013630895697969303 0.20570814188664832 chr20 63025520 865696 0.013735642323934812 0.12317218148707058 chr21 48129895 612668 0.012729468867530253 0.11975253000791444 chr22 51304566 570169 0.011113416299048315 0.10950960711032044 chrMT 16571 52312 3.156840263110253 2.3371843714695424 chrX 155270560 2230045 0.014362316977539077 0.12952392705153493 chrY 59373566 118354 0.001993378669558099 0.06213153885307324