BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504421.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 133,556,838 number of mapped reads = 132,207,827 (98.99%) number of supplementary alignments = 2,189,502 (1.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 66,129,993 number of mapped paired reads (second in pair) = 66,077,834 number of mapped paired reads (both in pair) = 131,784,254 number of mapped paired reads (singletons) = 423,573 number of mapped bases = 12,619,227,541 bp number of sequenced bases = 12,615,401,353 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,047,946 duplication rate = 33.51% >>>>>>> Insert size mean insert size = 80,894.055 std insert size = 2,643,918.9445 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 52.7308 >>>>>>> ACTG content number of A's = 3,749,185,425 bp (29.72%) number of C's = 2,544,239,397 bp (20.17%) number of T's = 3,769,726,975 bp (29.88%) number of G's = 2,550,353,084 bp (20.22%) number of N's = 1,896,472 bp (0.02%) GC percentage = 40.38% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 73,315,677 number of insertions = 1,252,783 mapped reads with insertion percentage = 0.94% number of deletions = 2,421,492 mapped reads with deletion percentage = 1.81% homopolymer indels = 48.08% >>>>>>> Coverage mean coverageData = 4.0764X std coverageData = 153.8157X There is a 27.25% of reference with a coverageData >= 1X There is a 21.15% of reference with a coverageData >= 2X There is a 16.47% of reference with a coverageData >= 3X There is a 13.96% of reference with a coverageData >= 4X There is a 11.94% of reference with a coverageData >= 5X There is a 10.51% of reference with a coverageData >= 6X There is a 9.36% of reference with a coverageData >= 7X There is a 8.44% of reference with a coverageData >= 8X There is a 7.68% of reference with a coverageData >= 9X There is a 7.04% of reference with a coverageData >= 10X There is a 6.49% of reference with a coverageData >= 11X There is a 6.02% of reference with a coverageData >= 12X There is a 5.61% of reference with a coverageData >= 13X There is a 5.24% of reference with a coverageData >= 14X There is a 4.92% of reference with a coverageData >= 15X There is a 4.63% of reference with a coverageData >= 16X There is a 4.38% of reference with a coverageData >= 17X There is a 4.14% of reference with a coverageData >= 18X There is a 3.93% of reference with a coverageData >= 19X There is a 3.74% of reference with a coverageData >= 20X There is a 3.56% of reference with a coverageData >= 21X There is a 3.4% of reference with a coverageData >= 22X There is a 3.25% of reference with a coverageData >= 23X There is a 3.11% of reference with a coverageData >= 24X There is a 2.98% of reference with a coverageData >= 25X There is a 2.86% of reference with a coverageData >= 26X There is a 2.75% of reference with a coverageData >= 27X There is a 2.65% of reference with a coverageData >= 28X There is a 2.55% of reference with a coverageData >= 29X There is a 2.46% of reference with a coverageData >= 30X There is a 2.38% of reference with a coverageData >= 31X There is a 2.29% of reference with a coverageData >= 32X There is a 2.22% of reference with a coverageData >= 33X There is a 2.15% of reference with a coverageData >= 34X There is a 2.08% of reference with a coverageData >= 35X There is a 2.01% of reference with a coverageData >= 36X There is a 1.95% of reference with a coverageData >= 37X There is a 1.9% of reference with a coverageData >= 38X There is a 1.84% of reference with a coverageData >= 39X There is a 1.79% of reference with a coverageData >= 40X There is a 1.74% of reference with a coverageData >= 41X There is a 1.69% of reference with a coverageData >= 42X There is a 1.65% of reference with a coverageData >= 43X There is a 1.6% of reference with a coverageData >= 44X There is a 1.56% of reference with a coverageData >= 45X There is a 1.52% of reference with a coverageData >= 46X There is a 1.48% of reference with a coverageData >= 47X There is a 1.45% of reference with a coverageData >= 48X There is a 1.41% of reference with a coverageData >= 49X There is a 1.38% of reference with a coverageData >= 50X There is a 1.34% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 896293874 3.5959544269299935 33.52707778685438 chr2 243199373 944739820 3.884630985458996 22.082495597857893 chr3 198022430 914730524 4.619327840790561 34.6176429692446 chr4 191154276 749905022 3.9230355589848274 34.16332608302693 chr5 180915260 834850534 4.614594335491655 30.874521764492936 chr6 171115067 750858440 4.38803229408197 38.81983847717607 chr7 159138663 648320794 4.073936413554009 152.74585138129552 chr8 146364022 655310295 4.477263510837383 36.455199782440765 chr9 141213431 1197628401 8.480980828232974 636.2239343024168 chr10 135534747 859149870 6.338963911593829 269.5027020265328 chr11 135006516 563117345 4.171038270478737 26.36588231567301 chr12 133851895 504507184 3.769144874639242 19.98402347415409 chr13 115169878 310543192 2.696392471649575 17.32111880334751 chr14 107349540 331359738 3.086736449918649 20.50843961440031 chr15 102531392 278829803 2.7194578905161064 18.866399400343035 chr16 90354753 228010391 2.523501901443967 14.745603504996067 chr17 81195210 202964282 2.4997075812723435 16.160640886204607 chr18 78077248 305917337 3.9181367791036896 31.342008490972145 chr19 59128983 144320167 2.4407686328716327 24.229941720569084 chr20 63025520 175557602 2.7855002545000818 17.32141029939804 chr21 48129895 137384974 2.8544623668927596 21.090671656810578 chr22 51304566 59976005 1.169018854968971 8.330436741328159 chrMT 16571 5077 0.3063786132399976 1.3555509219087518 chrX 155270560 916113092 5.900108120947075 60.78279224432371 chrY 59373566 8833778 0.14878301229203583 1.8168278519534962