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Mouse Whole Exome Sequencing

Overview

Whole Exome Sequencing (WES) enables researchers to focus on the genes most likely to affect disorder or phenotype by selectively sequencing the coding regions of a genome. Mice, Mus musculus, are important model organisms for human disease research and drug development. Novogene’s mouse whole exome sequencing (mWES) empowers you to identify causative mutations in mice with phenotypes, which may directly lead to the discovery of human disease genes.

Service Specifications

Applications

  • Drug development
  • Model research on human health and disease

Advantages

  • State-of-the-art NGS technologies: Novogene is a world leader in sequencing capacity using state-of-the-art technology, including Illumina HiSeq and NovaSeq 6000 Systems.
  • Highest data quality: We guarantee a Q30 score ≥ 80%, exceeding Illumina’s official guarantee of ≥ 75%. See our data example.
  • Extraordinary informatics expertise: Novogene uses its cutting-edge bioinformatics pipeline and internationally recognized, best-in-class software to provide customers with highly reliable, publication-ready data.

 

Sample Requirements

Sample Type Amount (Qubit?) Purity
Genomic DNA ≥ 400 ng OD260/280=1.8-2.0
Genomic DNA from FFPE ≥ 0.8 μg

Sequencing Parameters and Analysis Contents

Platform Illumina Novaseq 6000
Read length Paired-end 150 bp
Recommended sequencing depth Effective sequencing depth above 50× (6G)
Standard analysis
  • Data Quality Control
  • Alignment with reference genome, statistics of sequencing depth and coverage
  • SNP and InDel calling, annotation and statistics
  • Somatic SNP/InDel/CNV calling, annotation and statistics (tumor-normal paired samples)

Note: For detailed information, please refer to the Service Specifications and contact us for customized requests.

Project Workflow


Sequencing error rate distribution


Note: The x-axis represents position in reads, and the y-axis represents the average error rate of bases of all reads at a position.


GC content distribution


Note: The x-axis is position in reads, and the y-axis is percentage of each type of bases (A, T, G, C); different bases are distinguishable by different colors.


Sequencing depth & coverage distribution


Note: Average sequencing depth (bar plot) and coverage (dot-line plot) in each chromosome. The x-axis represents chromosome; the left y-axis is the average depth; the right y-axis is the coverage (proportion of covered bases).


SNP detection

Sample Sample_1 Sample_2 Sample_3 Sample_4 Sample_5
CDS 22849 22726 22681 22679 22496
Synonymous SNP 11491 11441 11416 11,408.00 11532
missense SNP 10697 10657 10,628.00 10639 10359
stopgain 91 87 87 87 79
stoploss 12 12 12 13 15
unknown 564 535 544 536 520
intronic 130230 128685 129046 132820 182248
UTR3 6431 6217 6301 6413 7612
UTR5 3177 3150 3163 3234 3730
splicing 81 81 81 81 76
ncRNA exonic 3328 3289 3312 3343 4037
ncRNA intronic 11066 10967 10946 11426 17658
ncRNA splicing 8 10 13 13 13
upstream 4488 4204 4270 4458 6344
downstream 2392 2352 2436 2406 3501
intergenic 66631 64399 64589 68470 137307
Total 250922 246335 247081 255588 385335

Heatmap of significantly mutated genes

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