Mappability and Read Length

Frontiers in Genetics

卷:5

Jan eFreudenberg¹  Wentian eLi¹ 

[1] Feinstein Institute for Medical Research, North Shore LIJ Health System;

关键词: Next-generation sequencing;    Repeats;    Copy Number Variations;    power-law distribution;    mappability;   

DOI  :  10.3389/fgene.2014.00381

来源: DOAJ

【 摘 要 】

Power-law distributions are the main functional formforthe distribution of repeat size and repeat copy number in the human genome. When the genome is broken into fragments for sequencing, the limited size offragments and reads may prevent an unique alignment of repeatsequences to the reference sequence. Repeats in the human genome canbe as long as $10^4$ bases, or $10^5-10^6$ bases when allowing for mismatches between repeat units.Sequence reads from these regions are therefore unmappable when the read length is in the range of $10^3$ bases.With the read length of exactly 1000 bases, slightly more than 1% of theassembled genome, and slightly less than 1% of the 1kbreads, are unmappable, excluding the unassembled portion of the humangenome (8% in GRCh37). The slow decay (long tail) ofthe power-law function implies a diminishing return in convertingunmappable regions/reads to become mappable with the increase of theread length, with the understanding that increasing read length willalways move towards the direction of 100% mappability.

【 授权许可】

Unknown