Skip to content

Latest commit

 

History

History
105 lines (62 loc) · 7.34 KB

ega-4-defs-ega-file-object-properties-sequence-quality-details.md

File metadata and controls

105 lines (62 loc) · 7.34 KB

Sequence quality details Schema

https://raw.githubusercontent.com/EbiEga/ega-metadata-schema/main/schemas/EGA.common-definitions.json#/$defs/fileObject/properties/sequenceQualityDetails

Sequencing quality scores measure the probability that a base is called (i.e. sequenced) incorrectly. New sequencing technologies assign a quality score to each of the bases in the sequence.

Abstract Extensible Status Identifiable Custom Properties Additional Properties Access Restrictions Defined In
Can be instantiated No Unknown status No Forbidden Forbidden none EGA.common-definitions.json*

sequenceQualityDetails Type

object (Sequence quality details)

sequenceQualityDetails Properties

Property Type Required Nullable Defined by
qualityScoringSystem string Required cannot be null EGA common metadata definitions
qualityEncoding string Optional cannot be null EGA common metadata definitions
asciiOffset string Optional cannot be null EGA common metadata definitions

qualityScoringSystem

How the quality score was computed for the data.

qualityScoringSystem

qualityScoringSystem Type

string (Quality scoring system)

qualityScoringSystem Constraints

enum: the value of this property must be equal to one of the following values:

Value Explanation
"phred" The quality score is expressed as a probability of error in log form: -10 log(1/p) where p is the probability of error, with value range 0..63 (0 meaning no base call).
"logOdds" The quality score is expressed as the ratio of error to non-error in log form: -10 log(p/(1-p)) where p is the of error, with value range -40..40. The SRA will convert these into phred scale during loadtime.

qualityEncoding

Encoding system used to represent the quality score.

qualityEncoding

qualityEncoding Type

string (Quality encoding format)

qualityEncoding Constraints

enum: the value of this property must be equal to one of the following values:

Value Explanation
"ascii" ASCII character based encoding.
"decimal" Single decimal value per quality score.
"hexadecimal" Single hexadecimal value per quality score.

asciiOffset

Character used in representing the minimum quality value. Helps specify how to decode text rendering of quality data.

asciiOffset

asciiOffset Type

string (ASCII offset)

asciiOffset Constraints

enum: the value of this property must be equal to one of the following values:

Value Explanation
"!" ASCII value 33. Typically used for range 0..63.
"@" ASCII value 64. Typically used for range 0..60.