Exercise 10

We have several candidate profiles of mutations to explore:

1. Description of variants. How many SNVs, INDELs, MNVs, SVs, CNVs?
2. Recessive heritage
3. Dominant heritage (father is affected).
4. For this chromosome: 5
5. Evaluate these regions at the same time: 5,6:10000-500000
6. For theses genes: SDHA,AHRR
7. Are there variants for these SNPs: rs6682385,rs75478250,rs147502335?
8. Variants with MAF (Minimum Allelic Frequency) < 0.001 for African population in 1000 Genomes phase 1
9. Variants with MAF (Minimum Allelic Frequency) < 0.001 for African population in 1000 Genomes phase 3
10. Variants with MAF (Minimum Allelic Frequency) < 0.001 for African American population in ESP 6500

1. There are clear information about our candidate variants:
   • Recessive heritage
   • Chromosome 1
   • SNV
   • Variants with MAF (Minimum Allelic Frequency) < 0.001 for all populations in 1000 Genomes phase 1
     • How many variants do you have including both characteristics?
     • Download these final results in a csv file

1. 36424 SNVs, 3552 INDELs, 19 MNVs, 3 SVs, 0 CNVs
2. Candidate variants: 980
3. Candidate variants: 1107
4. Candidate variants: 1826
5. Candidate variants: 1832
6. Candidate variants: 16
7. Candidate variants: 2
8. Candidate variants in 1000 Genomes, phase 1: 11925
9. Candidate variants in 1000 Genomes, phase 3: 12894
10. Candidate variants in African American MAF population: 21319

1. 980 → 106 → 94 → 14