SnpEff html result

Question

[Sudhir Jadhao]

Hello everyone,

I have snpeff output (.vcf and html). from that I want to extract below information with their co-ordinate (detail information)

Nonsynonymous (missense, nonsene)

I know their numeric values (missense and nonsense mutation) from html file but I want detaile information

Note: I have below information

synonymous_variant  130673

splice_region_variant&intron_variant    9440

upstream_gene_variant   1248890

intron_variant  343467

downstream_gene_variant 1198401

3_prime_UTR_variant 41314

missense_variant    189835

5_prime_UTR_premature_start_codon_gain_variant  3257

splice_region_variant&synonymous_variant    1321

start_lost  619

5_prime_UTR_variant 22475

missense_variant&splice_region_variant  2083

intergenic_region   1351028

splice_acceptor_variant&intron_variant  1164

stop_gained 7423

stop_lost&splice_region_variant 929

splice_donor_variant&intron_variant 1066

splice_region_variant&stop_retained_variant 136

stop_lost   1094

stop_gained&splice_region_variant   134

splice_region_variant   14560

stop_retained_variant   197

initiator_codon_variant 29

start_lost&splice_region_variant    1

But I dont know which category falls under Nonsynonymous (missense, nonsense).

Can anyone please tell me how to get detailed information of Nonsynonymous from snpeff output.

Thank you Inadvance

Answer 1

[Noushin N]

The SnpEff manual page might have the information you are looking for.

Take a look at http://snpeff.sourceforge.net/SnpEff_manual.html and look under 'Effect prediction details'.

My guess is that you are referring to sequence ontologies which Nonsynonymous as part of their 'Effect Classic'.

However more generally, nonsynonymous mutations are those that alter the protein sequence of proteins. Following this definition, many ontologies other than the three with 'NON_SYNONYMOUS_CODING' in their 'Effect Classic' attribute would be considered nonsynonymous; e.g. indels of all kinds, stop_lost, start_lost, etc.

[Sudhir Jadhao]

Thank you for reply,

As you want to say that missense_variant are the non_synonymous snp. But snpeff out showing below result

snpeff html output: 205,104 (Non_synonomous snp count ) snpeff .vcf output: 189835 (missense_variant)

Numbers are not matching

I think with missense_Variant , there are other ontologies come under non_synonymous snp category.

I want to know which ontologies are come under non_synonymous snp