msec_summarized: 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_homology function.

Usage

msec_summarized

Format

A list with 52 factors, each contains 29 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_farthest

5'-farthest supported base from the mutated base

post_farthest

3'-farthest supported base from the mutated base

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_rep_status

5'-repeat sequence length

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

distant_homology_rate

rate of reads derived from homologous regions

pre_minimum_length_adj

adjusted pre_minimum_length

post_minimum_length_adj

adjusted pre_minimum_length

pre_support_length_adj

adjusted pre_minimum_length

post_support_length_adj

adjusted pre_minimum_length

shortest_support_length_adj

the shortest short_support_length

minimum_length_1

theoretically minimum 5'-supporting length

minimum_length_2

theoretically minimum 3'-supporting length

minimum_length

theoretically minimum supporting length

short_support_length_adj

adjusted short_support_length

altered_length

substituted/inserted length

half_length

half of the read length

short_support_length_total

range of short_support_length

pre_support_length_total

range of pre_support_length

post_support_length_total

range of post_support_length

half_length_total

range of possible short_support_length

total_length_total

range of possible supporting length

soft_clipped_rate

rate of soft clipped reads

...

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