BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231865.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 = 1,261,358 number of mapped reads = 944,359 (74.87%) number of supplementary alignments = 5,245 (0.42%) number of secondary alignments = 0 number of mapped bases = 60,948,525 bp number of sequenced bases = 60,908,607 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,136 duplication rate = 4.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6975 >>>>>>> ACTG content number of A's = 16,719,333 bp (27.45%) number of C's = 10,457,281 bp (17.17%) number of T's = 20,163,463 bp (33.1%) number of G's = 13,565,840 bp (22.27%) number of N's = 2,690 bp (0%) GC percentage = 39.44% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 486,585 number of insertions = 4,956 mapped reads with insertion percentage = 0.52% number of deletions = 22,888 mapped reads with deletion percentage = 2.39% homopolymer indels = 45.91% >>>>>>> Coverage mean coverageData = 0.0197X std coverageData = 0.2118X There is a 1.69% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 6122796 0.024564817433293376 0.3870210140098529 chr2 243199373 5047680 0.02075531666769552 0.22385322131855107 chr3 198022430 4418489 0.022313073322047405 0.17033053859692185 chr4 191154276 1492237 0.007806453673053069 0.10809464390356806 chr5 180915260 3590954 0.019848817617706765 0.16043522233493027 chr6 171115067 5092444 0.029760348339167585 0.22043102344186496 chr7 159138663 3430450 0.02155635805486188 0.23078663574478483 chr8 146364022 4243339 0.02899168075608089 0.34435783059848885 chr9 141213431 2413806 0.017093317419644028 0.16559839694173403 chr10 135534747 2528692 0.01865714922535695 0.17751154803983324 chr11 135006516 2311294 0.017119869977238727 0.16955693633661423 chr12 133851895 1625970 0.012147530671866842 0.126645800196783 chr13 115169878 2646190 0.022976407077551997 0.17396800291854198 chr14 107349540 3835954 0.03573330635604028 0.2172850795888644 chr15 102531392 1081141 0.010544487682367562 0.11889437178146632 chr16 90354753 649769 0.007191309570621039 0.10481561417235877 chr17 81195210 1281432 0.01578211325520311 0.1463523056060876 chr18 78077248 1805395 0.023123189485367106 0.23148207446093247 chr19 59128983 2023699 0.03422516162674403 0.26219531882292235 chr20 63025520 1352674 0.02146232192927563 0.16822657227343096 chr21 48129895 974789 0.020253295794640733 0.16410439217904885 chr22 51304566 280607 0.005469435215571261 0.08360716207082199 chrMT 16571 8544 0.5155995413674491 0.772810977028641 chrX 155270560 2486791 0.016015856450830087 0.14842076675565935 chrY 59373566 203389 0.00342558168057482 0.07209009356495115