BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365338.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 122,090,618 number of mapped reads = 119,096,413 (97.55%) number of supplementary alignments = 903,554 (0.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 59,833,932 number of mapped paired reads (second in pair) = 59,262,481 number of mapped paired reads (both in pair) = 118,345,500 number of mapped paired reads (singletons) = 750,913 number of mapped bases = 15,619,489,179 bp number of sequenced bases = 15,613,808,843 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,621,804 duplication rate = 34.37% >>>>>>> Insert size mean insert size = 73,078.4604 std insert size = 2,672,574.8081 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 54.2304 >>>>>>> ACTG content number of A's = 4,616,944,590 bp (29.57%) number of C's = 3,144,763,779 bp (20.14%) number of T's = 4,548,053,178 bp (29.13%) number of G's = 3,303,139,308 bp (21.16%) number of N's = 907,988 bp (0.01%) GC percentage = 41.3% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 113,540,133 number of insertions = 4,529,215 mapped reads with insertion percentage = 3.69% number of deletions = 2,363,573 mapped reads with deletion percentage = 1.92% homopolymer indels = 50.24% >>>>>>> Coverage mean coverageData = 5.0456X std coverageData = 46.8898X There is a 67.73% of reference with a coverageData >= 1X There is a 61.18% of reference with a coverageData >= 2X There is a 52.91% of reference with a coverageData >= 3X There is a 46.69% of reference with a coverageData >= 4X There is a 39.91% of reference with a coverageData >= 5X There is a 34.59% of reference with a coverageData >= 6X There is a 29.26% of reference with a coverageData >= 7X There is a 25.06% of reference with a coverageData >= 8X There is a 21.04% of reference with a coverageData >= 9X There is a 17.87% of reference with a coverageData >= 10X There is a 14.92% of reference with a coverageData >= 11X There is a 12.6% of reference with a coverageData >= 12X There is a 10.48% of reference with a coverageData >= 13X There is a 8.8% of reference with a coverageData >= 14X There is a 7.3% of reference with a coverageData >= 15X There is a 6.12% of reference with a coverageData >= 16X There is a 5.07% of reference with a coverageData >= 17X There is a 4.24% of reference with a coverageData >= 18X There is a 3.51% of reference with a coverageData >= 19X There is a 2.93% of reference with a coverageData >= 20X There is a 2.43% of reference with a coverageData >= 21X There is a 2.04% of reference with a coverageData >= 22X There is a 1.69% of reference with a coverageData >= 23X There is a 1.42% of reference with a coverageData >= 24X There is a 1.19% of reference with a coverageData >= 25X There is a 1% of reference with a coverageData >= 26X There is a 0.84% of reference with a coverageData >= 27X There is a 0.71% of reference with a coverageData >= 28X There is a 0.6% of reference with a coverageData >= 29X There is a 0.52% of reference with a coverageData >= 30X There is a 0.44% of reference with a coverageData >= 31X There is a 0.38% of reference with a coverageData >= 32X There is a 0.33% of reference with a coverageData >= 33X There is a 0.28% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.12% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1353428020 5.429988557581167 128.5564661326776 chr2 243199373 1353612234 5.5658541274281985 28.038887934251964 chr3 198022430 1093024366 5.51969979360419 7.194677550773611 chr4 191154276 1028553334 5.380749808599625 23.66021984012777 chr5 180915260 974766999 5.387975558280711 7.2673714917433285 chr6 171115067 904342352 5.284995458640705 23.158866262982695 chr7 159138663 842885075 5.2965449068778465 31.002690382081312 chr8 146364022 789141147 5.391633382416889 16.747982338809877 chr9 141213431 669215234 4.739033881274367 39.60624889081411 chr10 135534747 795806445 5.8716046077837145 80.08501869332305 chr11 135006516 748918521 5.547276851437304 35.21633052715582 chr12 133851895 742856488 5.549839156180792 26.765737532528064 chr13 115169878 487130740 4.229671407657478 5.632374785665531 chr14 107349540 480917637 4.479922661988119 6.16903898005243 chr15 102531392 459649265 4.483010091192364 13.709230641377975 chr16 90354753 435545144 4.820389957792259 14.64220039789301 chr17 81195210 463352388 5.70664683298436 27.06837952788006 chr18 78077248 429242528 5.4976646717876125 47.7550494248386 chr19 59128983 302333862 5.113124675254435 67.52950060420895 chr20 63025520 329915134 5.234627719057296 10.308271726038795 chr21 48129895 202121662 4.199503489463254 18.27638139722935 chr22 51304566 199725429 3.892936722240278 16.449482059398342 chrMT 16571 14026153 846.42767485366 212.56490328284016 chrX 155270560 394562316 2.541127667730444 11.673253417454967 chrY 59373566 124416706 2.0954898683363568 41.66715829869157