msec_read_checked: An example mutation file.

In MicroSEC: Sequence Error Filter for Formalin-Fixed and Paraffin-Embedded Samples

An example mutation file.

Description

A dataset containing the information of eight mutations processed by the fun_read_check function.

Usage

msec_read_checked

Format

A list with 34 factors, each contains 46527 variables

Sample

sample name

Mut_type

mutation type

Chr

altered chromosome

Pos

altered position

Ref

reference base

Alt

altered base

SimpleRepeat_TRF

mutation locating repeat sequence

Neighborhood_sequence

neighborhood sequence

read_length

read length

mut_type

mutation type

alt_length

length of the mutated bases

total_read

number of mutation supporting reads

soft_clipped_read

number of soft-clipped reads

flag_hairpin

number of reads produced by hairpin structure

hairpin_length

maximum length of palindromic sequences

pre_support_length

maximum 5'-supporting length

post_support_length

maximum 3'-supporting length

short_support_length

minimum supporting length

pre_minimum_length

minimum 5'-supporting length

post_minimum_length

minimum 3'-supporting length

pre_minimum_length

minimum 5'-supporting length

low_quality_base_rate_under_q18

low quality base rate

low_quality_pre

low quality base rate of 5'- side

low_quality_post

low quality base rate of 3'- side

pre_farthest

5'-farthest supported base from the mutated base

post_farthest

3'-farthest supported base from the mutated base

post_rep_status

3'-repeat sequence length

homopolymer_status

homopolymer sequence length

indel_status

whether the mutation is indel or not

indel_length

length of indel mutation

distant_homology

number of reads derived from homologous regions

penalty_pre

5'-penalty score by the mapper

penalty_post

3'-penalty score by the mapper

caution

comment

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MicroSEC documentation built on Sept. 11, 2024, 6:06 p.m.