BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068163.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 = 1,235,025 number of mapped reads = 1,027,164 (83.17%) number of supplementary alignments = 9,495 (0.77%) number of secondary alignments = 0 number of mapped bases = 68,126,573 bp number of sequenced bases = 68,094,435 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,332 duplication rate = 6.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3731 >>>>>>> ACTG content number of A's = 20,351,913 bp (29.89%) number of C's = 13,037,868 bp (19.15%) number of T's = 20,777,129 bp (30.51%) number of G's = 13,857,132 bp (20.35%) number of N's = 70,393 bp (0.1%) GC percentage = 39.5% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 612,156 number of insertions = 4,925 mapped reads with insertion percentage = 0.48% number of deletions = 18,525 mapped reads with deletion percentage = 1.78% homopolymer indels = 47.97% >>>>>>> Coverage mean coverageData = 0.022X std coverageData = 0.2902X There is a 1.19% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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% 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 5251543 0.021069327646730317 0.42789561925660063 chr2 243199373 8420797 0.03462507693225015 0.34275259796488383 chr3 198022430 4299587 0.021712626190881507 0.24530860886090625 chr4 191154276 4672757 0.024444951469461244 0.26443275135078315 chr5 180915260 3915342 0.021641855971685307 0.24493451929340612 chr6 171115067 4163376 0.024330855680873502 0.2687185898448411 chr7 159138663 3915874 0.02460667901929024 0.35228867966954347 chr8 146364022 3396844 0.023208189783142198 0.35810269602070055 chr9 141213431 2659263 0.018831516104158674 0.25257487955591607 chr10 135534747 3046364 0.02247662734044134 0.2789598595255867 chr11 135006516 2968614 0.02198867201343082 0.27417794473951373 chr12 133851895 3201863 0.023920938885474877 0.2593948224265747 chr13 115169878 1925120 0.01671548180332361 0.21678260347533712 chr14 107349540 2178173 0.02029047353160526 0.24414095823889226 chr15 102531392 1909158 0.018620229012398466 0.22943341842615178 chr16 90354753 1674137 0.018528488479183824 0.22729594272159082 chr17 81195210 1264910 0.015578628345194254 0.208083961319799 chr18 78077248 1764983 0.022605599521130663 0.406503416957702 chr19 59128983 1030076 0.0174208306609975 0.2704867001023013 chr20 63025520 1328540 0.02107939767890848 0.24372640292707154 chr21 48129895 1188624 0.024696168566334914 0.26422776743706433 chr22 51304566 570026 0.011110629022765732 0.16871900815782767 chrMT 16571 16259 0.9811719268601774 1.544420992014273 chrX 155270560 3112779 0.020047451364894928 0.23857281321533066 chrY 59373566 251564 0.004236969697929209 0.10250609011057692