BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618594.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 50,908,148 number of mapped reads = 49,232,334 (96.71%) number of supplementary alignments = 179,310 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 24,838,215 number of mapped paired reads (second in pair) = 24,394,119 number of mapped paired reads (both in pair) = 48,344,634 number of mapped paired reads (singletons) = 887,700 number of mapped bases = 4,639,053,197 bp number of sequenced bases = 4,635,903,981 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,668,942 duplication rate = 20.48% >>>>>>> Insert size mean insert size = 65,152.9724 std insert size = 2,529,469.9958 median insert size = 188 >>>>>>> Mapping quality mean mapping quality = 53.3152 >>>>>>> ACTG content number of A's = 1,267,528,056 bp (27.34%) number of C's = 1,010,200,387 bp (21.79%) number of T's = 1,282,011,860 bp (27.65%) number of G's = 1,075,940,522 bp (23.21%) number of N's = 223,156 bp (0%) GC percentage = 45% >>>>>>> Mismatches and indels general error rate = 0.013 number of mismatches = 59,078,052 number of insertions = 828,299 mapped reads with insertion percentage = 1.66% number of deletions = 2,310,675 mapped reads with deletion percentage = 4.58% homopolymer indels = 52.64% >>>>>>> Coverage mean coverageData = 1.4986X std coverageData = 5.8493X There is a 26.06% of reference with a coverageData >= 1X There is a 18.38% of reference with a coverageData >= 2X There is a 13.84% of reference with a coverageData >= 3X There is a 11.04% of reference with a coverageData >= 4X There is a 9.01% of reference with a coverageData >= 5X There is a 7.53% of reference with a coverageData >= 6X There is a 6.37% of reference with a coverageData >= 7X There is a 5.47% of reference with a coverageData >= 8X There is a 4.74% of reference with a coverageData >= 9X There is a 4.14% of reference with a coverageData >= 10X There is a 3.64% of reference with a coverageData >= 11X There is a 3.23% of reference with a coverageData >= 12X There is a 2.87% of reference with a coverageData >= 13X There is a 2.57% of reference with a coverageData >= 14X There is a 2.3% of reference with a coverageData >= 15X There is a 2.08% of reference with a coverageData >= 16X There is a 1.88% of reference with a coverageData >= 17X There is a 1.7% of reference with a coverageData >= 18X There is a 1.55% of reference with a coverageData >= 19X There is a 1.41% of reference with a coverageData >= 20X There is a 1.29% of reference with a coverageData >= 21X There is a 1.18% of reference with a coverageData >= 22X There is a 1.08% of reference with a coverageData >= 23X There is a 1% of reference with a coverageData >= 24X There is a 0.92% of reference with a coverageData >= 25X There is a 0.85% of reference with a coverageData >= 26X There is a 0.78% of reference with a coverageData >= 27X There is a 0.72% of reference with a coverageData >= 28X There is a 0.67% of reference with a coverageData >= 29X There is a 0.62% of reference with a coverageData >= 30X There is a 0.58% of reference with a coverageData >= 31X There is a 0.54% of reference with a coverageData >= 32X There is a 0.5% of reference with a coverageData >= 33X There is a 0.47% of reference with a coverageData >= 34X There is a 0.44% of reference with a coverageData >= 35X There is a 0.41% of reference with a coverageData >= 36X There is a 0.38% of reference with a coverageData >= 37X There is a 0.36% of reference with a coverageData >= 38X There is a 0.34% of reference with a coverageData >= 39X There is a 0.31% of reference with a coverageData >= 40X There is a 0.3% of reference with a coverageData >= 41X There is a 0.28% of reference with a coverageData >= 42X There is a 0.26% of reference with a coverageData >= 43X There is a 0.25% of reference with a coverageData >= 44X There is a 0.23% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 413424162 1.6586685334677662 7.337785397377588 chr2 243199373 398685485 1.6393359903933633 6.5020036652962405 chr3 198022430 311265914 1.5718720046006909 5.026947634109466 chr4 191154276 239128904 1.250973344692535 4.974343944898002 chr5 180915260 260706082 1.4410397552975907 4.797745861806219 chr6 171115067 252030146 1.4728693996303668 4.8923643186106505 chr7 159138663 235262735 1.4783505815931104 4.9736608232880455 chr8 146364022 163861564 1.119548108619207 4.267131489165247 chr9 141213431 204294074 1.4467042727685018 6.608508015070087 chr10 135534747 239199267 1.7648556720292545 5.7222373480158515 chr11 135006516 236183284 1.7494213686693463 6.524130181065969 chr12 133851895 208347979 1.5565560651942956 5.204563471426148 chr13 115169878 127570823 1.1076752464737352 4.038574458131305 chr14 107349540 146934804 1.368751128323419 4.997053254366482 chr15 102531392 150073874 1.4636870822937817 5.239123840263751 chr16 90354753 166094777 1.838251685553277 9.287417851833187 chr17 81195210 145134308 1.7874737684649131 6.13066982015743 chr18 78077248 120744035 1.5464688893747895 6.802912656974178 chr19 59128983 93687081 1.5844527716636019 6.508738163875773 chr20 63025520 130009333 2.0628046067688137 6.412755499828174 chr21 48129895 60417391 1.255298624690538 8.885319712634105 chr22 51304566 82811238 1.6141104867742182 6.492453869480267 chrMT 16571 528 0.0318628930058536 0.22206675542584428 chrX 155270560 247117126 1.5915259531491353 5.061483468701043 chrY 59373566 6068283 0.10220512946788475 2.9899746459629903