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Table 2 Attributes used to train prediction model: total 15-features are calculated with samtools-bcftools(v1.2) pipeline [23]

From: RDDpred: a condition-specific RNA-editing prediction model from RNA-seq data

Categories

Attributes

Description

Read depth

Read depth

Read depth

Allele segregation

VAF

Variant read ratio

Allele segregation

SGB

Segregation based metric

Allele segregation

FQ

Phred probability of all samples

  

being the same

Allele segregation

CallQual

Variant/reference QUALity

Mapping quality

PV3

Mapping quality bias

Mapping quality

MQB

Mann-Whitney U test of Mapping

  

Quality Bias

Mapping quality

MQ0F

Fraction of MQ0 reads

Mapping quality

MQ

Root-mean-square mapping quality

  

of covering reads

Read position

VDB

Variant Distance Bias for filtering

  

splice-site artefacts in

  

RNA-seq data

Read position

RPB

Mann-Whitney U test of Read

  

Position Bias

Read position

PV4

Tail distance bias

Base quality

PV2

Base quality bias

Base quality

BQB

Mann-Whitney U test of Base

  

Quality Bias

Read strand

PV1

Read strand bias