BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975212.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 92,240,876 number of mapped reads = 92,123,141 (99.87%) number of supplementary alignments = 838,345 (0.91%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 46,063,051 number of mapped paired reads (second in pair) = 46,060,090 number of mapped paired reads (both in pair) = 92,059,848 number of mapped paired reads (singletons) = 63,293 number of mapped bases = 9,012,234,841 bp number of sequenced bases = 9,011,055,740 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,158,246 duplication rate = 60.85% >>>>>>> Insert size mean insert size = 136,265.0695 std insert size = 3,660,814.0593 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 55.8604 >>>>>>> ACTG content number of A's = 2,193,272,597 bp (24.34%) number of C's = 2,317,690,764 bp (25.72%) number of T's = 2,177,702,653 bp (24.17%) number of G's = 2,322,051,921 bp (25.77%) number of N's = 337,805 bp (0%) GC percentage = 51.49% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 37,980,384 number of insertions = 820,568 mapped reads with insertion percentage = 0.88% number of deletions = 522,007 mapped reads with deletion percentage = 0.56% homopolymer indels = 32.01% >>>>>>> Coverage mean coverageData = 2.9112X std coverageData = 25.8343X There is a 11.91% of reference with a coverageData >= 1X There is a 7.9% of reference with a coverageData >= 2X There is a 5.58% of reference with a coverageData >= 3X There is a 4.5% of reference with a coverageData >= 4X There is a 3.86% of reference with a coverageData >= 5X There is a 3.54% of reference with a coverageData >= 6X There is a 3.3% of reference with a coverageData >= 7X There is a 3.15% of reference with a coverageData >= 8X There is a 3.03% of reference with a coverageData >= 9X There is a 2.93% of reference with a coverageData >= 10X There is a 2.85% of reference with a coverageData >= 11X There is a 2.78% of reference with a coverageData >= 12X There is a 2.71% of reference with a coverageData >= 13X There is a 2.65% of reference with a coverageData >= 14X There is a 2.6% of reference with a coverageData >= 15X There is a 2.55% of reference with a coverageData >= 16X There is a 2.5% of reference with a coverageData >= 17X There is a 2.45% of reference with a coverageData >= 18X There is a 2.41% of reference with a coverageData >= 19X There is a 2.37% of reference with a coverageData >= 20X There is a 2.33% of reference with a coverageData >= 21X There is a 2.29% of reference with a coverageData >= 22X There is a 2.25% of reference with a coverageData >= 23X There is a 2.22% of reference with a coverageData >= 24X There is a 2.18% of reference with a coverageData >= 25X There is a 2.15% of reference with a coverageData >= 26X There is a 2.12% of reference with a coverageData >= 27X There is a 2.09% of reference with a coverageData >= 28X There is a 2.06% of reference with a coverageData >= 29X There is a 2.03% of reference with a coverageData >= 30X There is a 2% of reference with a coverageData >= 31X There is a 1.97% of reference with a coverageData >= 32X There is a 1.94% of reference with a coverageData >= 33X There is a 1.92% of reference with a coverageData >= 34X There is a 1.89% of reference with a coverageData >= 35X There is a 1.86% of reference with a coverageData >= 36X There is a 1.84% of reference with a coverageData >= 37X There is a 1.81% of reference with a coverageData >= 38X There is a 1.79% of reference with a coverageData >= 39X There is a 1.77% of reference with a coverageData >= 40X There is a 1.74% of reference with a coverageData >= 41X There is a 1.72% of reference with a coverageData >= 42X There is a 1.7% of reference with a coverageData >= 43X There is a 1.67% of reference with a coverageData >= 44X There is a 1.65% of reference with a coverageData >= 45X There is a 1.63% of reference with a coverageData >= 46X There is a 1.61% of reference with a coverageData >= 47X There is a 1.59% of reference with a coverageData >= 48X There is a 1.57% of reference with a coverageData >= 49X There is a 1.55% of reference with a coverageData >= 50X There is a 1.53% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 952306407 3.8206781719512746 31.447978778049478 chr2 243199373 611129423 2.512874171760303 22.07660819065378 chr3 198022430 467771281 2.3622136189319565 20.515651934797624 chr4 191154276 306861779 1.6053095197305447 16.712485654020494 chr5 180915260 436743861 2.414079724396936 22.810850457978173 chr6 171115067 450722046 2.6340289835494146 24.879420651433584 chr7 159138663 471889256 2.9652709599552183 26.87804180499665 chr8 146364022 296395912 2.0250599016744704 19.609093272675953 chr9 141213431 336615612 2.3837365158275916 21.832472838047398 chr10 135534747 336450147 2.4823903423083085 22.834762429841977 chr11 135006516 558327505 4.135559686615422 31.788553119478497 chr12 133851895 469870232 3.5103741489801097 28.055738888479276 chr13 115169878 145209752 1.260830996104728 14.462992670227502 chr14 107349540 290086269 2.7022590781478897 24.76988512517447 chr15 102531392 272975442 2.662359660541817 22.496885627612798 chr16 90354753 396045820 4.383231726614316 33.26868544934702 chr17 81195210 583931704 7.191701382384503 44.06890059751869 chr18 78077248 110485612 1.4150807671909749 15.012094878484865 chr19 59128983 578606997 9.785505646190465 50.95490047479614 chr20 63025520 237663071 3.7709021837503283 28.91838089616247 chr21 48129895 95319568 1.9804649064786033 22.21608093419907 chr22 51304566 209726632 4.087874595801083 30.07771888750246 chrMT 16571 5264788 317.7109408001931 443.8387430112948 chrX 155270560 389190445 2.5065308259337766 26.3563027595964 chrY 59373566 2645280 0.0445531602396932 1.802833802019974