BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080617.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,567,638 number of mapped reads = 1,790,107 (69.72%) number of supplementary alignments = 15,095 (0.59%) number of secondary alignments = 0 number of mapped bases = 118,264,327 bp number of sequenced bases = 118,218,835 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 118,821 duplication rate = 5.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3214 >>>>>>> ACTG content number of A's = 32,514,699 bp (27.5%) number of C's = 20,718,282 bp (17.53%) number of T's = 39,080,858 bp (33.06%) number of G's = 25,812,933 bp (21.83%) number of N's = 92,063 bp (0.08%) GC percentage = 39.36% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,084,553 number of insertions = 9,825 mapped reads with insertion percentage = 0.54% number of deletions = 28,031 mapped reads with deletion percentage = 1.55% homopolymer indels = 49.24% >>>>>>> Coverage mean coverageData = 0.0382X std coverageData = 0.278X There is a 2.97% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.15% 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 8464446 0.03395957837954594 0.2972597818116049 chr2 243199373 10165021 0.041797069106753 0.3061300723774768 chr3 198022430 6988816 0.03529305240825496 0.23504944863295912 chr4 191154276 7443812 0.03894138366018032 0.247560633211761 chr5 180915260 7653821 0.042306110606700614 0.25684197853767626 chr6 171115067 6735832 0.03936434189047771 0.28102701165585897 chr7 159138663 6766306 0.04251830367583269 0.3747060277168731 chr8 146364022 6013867 0.04108842403907157 0.385956318778607 chr9 141213431 4662179 0.03301512446078872 0.2546274858551971 chr10 135534747 7041575 0.051954020322183506 0.3003764027729724 chr11 135006516 5835068 0.04322063980971111 0.2715228414149027 chr12 133851895 4612092 0.034456680646919494 0.23302169249849103 chr13 115169878 4581283 0.0397784827036111 0.2519083457323346 chr14 107349540 3079448 0.02868617788208501 0.21359791483906732 chr15 102531392 3542018 0.034545693088805424 0.23097545359729926 chr16 90354753 3114070 0.034464927373549455 0.23809516634008365 chr17 81195210 2838952 0.03496452561672049 0.23857621735402007 chr18 78077248 3053676 0.039110958419026245 0.3336470221729577 chr19 59128983 2007059 0.033943742952588916 0.2810831477921182 chr20 63025520 2532121 0.040176122307281244 0.2530341272689217 chr21 48129895 1651856 0.034320789604880705 0.233905042033233 chr22 51304566 1351649 0.026345588811724868 0.1994717295263219 chrMT 16571 48756 2.9422485064268904 4.208519555220534 chrX 155270560 7823218 0.05038442574046233 0.2890213963093162 chrY 59373566 257386 0.00433502680300523 0.09112033501912958