msec_analyzed {MicroSEC}R Documentation

An example mutation file.

Description

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

Usage

msec_analyzed

Format

A list with 37 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

total_read

number of mutation supporting reads

soft_clipped_read

number of soft-clipped reads

flag_hairpin

number of reads produced by hairpin structure

pre_support_length

maximum 5'-supporting length

post_support_length

maximum 3'-supporting length

short_support_length

minimum 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

distant_homology_rate

rate of reads derived from homologous regions

soft_clipped_rate

rate of soft clipped reads

prob_filter_1

possibility of short-supporting length

prob_filter_3_pre

possibility of 5'-supporting length

prob_filter_3_post

possibility of 3'-supporting length

filter_1_mutation_intra_hairpin_loop

filter 1

filter_2_hairpin_structure

filter 2

filter_3_microhomology_induced_mutation

filter 3

filter_4_highly_homologous_region

filter 4

filter_5_soft_clipping

filter 5

filter_6_simple_repeat

filter 6

filter_7_mutation_at_homopolymer

filter 7

filter_8_low_quality

filter 8

msec_filter_123

any of filter 1-3

msec_filter_1234

any of filter 1-4

msec_filter_all

any of filter 1-8

comment

comment

...


[Package MicroSEC version 2.1.3 Index]