BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617407.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 22,751,592 number of mapped reads = 17,556,503 (77.17%) number of supplementary alignments = 241,739 (1.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,682,134 number of mapped paired reads (second in pair) = 7,874,369 number of mapped paired reads (both in pair) = 15,540,502 number of mapped paired reads (singletons) = 2,016,001 number of mapped bases = 1,699,247,776 bp number of sequenced bases = 1,698,870,971 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 505,292 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 58,838.7155 std insert size = 2,319,329.5603 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 53.1074 >>>>>>> ACTG content number of A's = 508,011,106 bp (29.9%) number of C's = 340,345,077 bp (20.03%) number of T's = 502,621,923 bp (29.59%) number of G's = 347,452,710 bp (20.45%) number of N's = 440,155 bp (0.03%) GC percentage = 40.49% >>>>>>> Mismatches and indels general error rate = 0.0199 number of mismatches = 33,506,025 number of insertions = 149,370 mapped reads with insertion percentage = 0.84% number of deletions = 169,873 mapped reads with deletion percentage = 0.95% homopolymer indels = 42.8% >>>>>>> Coverage mean coverageData = 0.5489X std coverageData = 1.7429X There is a 22.56% of reference with a coverageData >= 1X There is a 11.07% of reference with a coverageData >= 2X There is a 6.24% of reference with a coverageData >= 3X There is a 3.89% of reference with a coverageData >= 4X There is a 2.59% of reference with a coverageData >= 5X There is a 1.81% of reference with a coverageData >= 6X There is a 1.32% of reference with a coverageData >= 7X There is a 0.98% of reference with a coverageData >= 8X There is a 0.75% of reference with a coverageData >= 9X There is a 0.59% of reference with a coverageData >= 10X There is a 0.47% of reference with a coverageData >= 11X There is a 0.38% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% 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 109055487 0.4375334615515361 1.6179844032549087 chr2 243199373 169902577 0.698614371016491 1.8858100122111154 chr3 198022430 143592531 0.7251326579519299 2.0253763322336424 chr4 191154276 82892390 0.4336413065643376 1.398167955652632 chr5 180915260 109636767 0.6060117150979967 1.7375092258027776 chr6 171115067 78353339 0.45789853794698276 1.5658320140268878 chr7 159138663 127219287 0.7994241286292572 1.9605325115099628 chr8 146364022 75278417 0.514323233068848 1.8869784384092296 chr9 141213431 67986430 0.48144450225842894 1.5506356113368291 chr10 135534747 54549461 0.40247583890793703 1.4398846932823033 chr11 135006516 125755519 0.9314774036536133 2.2825111324546583 chr12 133851895 80867970 0.6041600681111015 1.684355357951713 chr13 115169878 74407208 0.64606483302865 1.6876647994963478 chr14 107349540 49173305 0.4580672166829965 1.7044235331626194 chr15 102531392 38713473 0.3775767815577887 1.4302219205035387 chr16 90354753 42188575 0.466921480046545 1.9296079528096868 chr17 81195210 51406103 0.6331174338978863 2.1178988304008026 chr18 78077248 24536194 0.3142553641234896 1.2018608816190444 chr19 59128983 23664265 0.4002143077617283 1.3614813633092442 chr20 63025520 56639979 0.8986832476749101 2.705308481917123 chr21 48129895 23301166 0.48413082970573695 1.5208741655149283 chr22 51304566 13404762 0.26127814822563744 1.216146179747683 chrMT 16571 100658 6.074346750346992 3.3899057450861645 chrX 155270560 75190412 0.4842541432194229 1.5514602289576287 chrY 59373566 1431501 0.02411007282264299 0.3705265289359274