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Table 4 SV features and their contributions in the random forest classifier for CHM13

From: Evaluating nanopore sequencing data processing pipelines for structural variation identification

Feature

Description

SV caller

Contribution

Sniffles

NanoSV

Picky

Deletion (%)

Insertion (%)

SVLEN

Length of the SV

Yes

Yes

Yes

52

55

DEPTHPVAL

P value of the significance test of the depth of coverage at possible breakpoint junctions

No

Yes

No

20

15

RE

Read support

Yes

No

Yes

7

14

MAPQ

Median mapping quality of read pairs

Yes

Yes

No

10

8

CIEND

Confidence interval around the END position

No

Yes

Yes

3

3

CIPOS

Confidence interval around the POS position

No

Yes

Yes

2

2

PRECISE

Precise structural variant

Yes

Yes

Yes

5

1

  1. “Yes/No” under SV callers indicates whether a feature is provided by an SV caller