Statistic of Variants Quality


DNArails Genomics Analysis Platform provides a summary of results to evaluate the quality of total variants in each sample. This summary page provides an overview of variant quality and types, including Ti/Tv ratio, mutation types, distribution of InDel length, quality score, genotype quality, and variants coverage. Each graph is dynamic and can be shown the real-time status of your setting.

 

Ratio of Transitions to Transversions

The ratio of transition to transversion (Ti/Tv, also called Ts/Tv) could be an evaluation criteria of sequencing results. Transitions are mutations with the same type of nucleotide (T↔C, A↔G) and occur at higher frequencies than transversions (T↔A, T↔G, C↔A, C↔G). The general Ti/Tv ratio should be around 2.0~2.1 for human whole genome and 2.8~3.0 or higher for human exomes. There might be some bias of sample in sequencing or variants calling procedure if ratio is out of the range.


 

Variants Types

The variant type is based on the result of each allele with alignment to reference sequence. There are five variant types including SNP, INS, DEL, INDEL, and MNP. SNP: Single Nucleotide Polymorphism. INS: Insertion of one or several nucleotides. DEL: Deletion of one or several nucleotides. INDEL: An insertion and a deletion, affecting 2 or more nucleotides. MNP: Multiple Nucleotide Polymorphism, a sequence alteration where the length of the change in the variant is the same as that of the reference.


 

InDel Length (Insertion and Deletion Length)

InDel is a term for the insertion or deletion of bases in DNA sequence. It defined as a mutation which has a net change in total number of nucleotides. Deletions occurred much more frequently than insertions.


 

Variants Quality Score

This is a Phred-scaled base quality score and scores range from 0 to infinity. The Phred quality score (Q) is logarithmically related to the error probability (e), is defined by the following equation: Q= -10 * log(e). Higher Q score indicate a smaller probability that variant is incorrect. Q30 represents an error rate of 1 in 1,000 , with a corresponding call accuracy of 99.9%. A vast majority quality score of variants above Q30 is ideal for clinical research and analysis. The quality score of variants under Q19 are shown in red bars.


 

Genotype Quality

The Genotype Quality represents the Phred-scaled confidence that the called genotype is the true genotype. Higher values reflect more accurate genotype calls. The genotype quality of variants under Q19 are shown in red bars.


 

Read Depth of Variants

The number of aligned reads after filtering on a given position of the target region. For detecting human genome SNVs or structure variation, publication often recommend over 10X to 30X depth of coverage depending on your applications.