HWI-K00288_BSF_0436
Instrument name/ID
4
Flowcell lane
1101
Tile number within the flowcell lane
10003
“x”-coordinate of the cluster within the tile
10669
“y”-coordinate of the cluster within the tile
The Phred Score represents the probability that the corresponding base call is incorrect
[2].
The ASCII table and an example for Phred Score calculation are depicted in Fig. 7.2.
Qualities are based on the Phred scale and are encoded: Q ¼ À10*log 10 (P err ).
The formula for getting Phred quality from encoded quality is: Q ¼ ascii(char) À33.
Review Question 2
Determine the Phred-Scores for the following quality values in a FASTQ file format:
#4¼DBDDDHFHFFHIGHIII.
7.2.4 SAM
SAM stands for Sequence Alignment/Map format. As the name suggests, you get this file
format after mapping the fastq files to a reference genome. It is a TAB-delimited text format
Fig. 7.2 ASCII table and Phred Score calculation
7 NGS Data
83
Instrument name/ID
4
Flowcell lane
1101
Tile number within the flowcell lane
10003
“x”-coordinate of the cluster within the tile
10669
“y”-coordinate of the cluster within the tile
The Phred Score represents the probability that the corresponding base call is incorrect
[2].
The ASCII table and an example for Phred Score calculation are depicted in Fig. 7.2.
Qualities are based on the Phred scale and are encoded: Q ¼ À10*log 10 (P err ).
The formula for getting Phred quality from encoded quality is: Q ¼ ascii(char) À33.
Review Question 2
Determine the Phred-Scores for the following quality values in a FASTQ file format:
#4¼DBDDDHFHFFHIGHIII.
7.2.4 SAM
SAM stands for Sequence Alignment/Map format. As the name suggests, you get this file
format after mapping the fastq files to a reference genome. It is a TAB-delimited text format
Fig. 7.2 ASCII table and Phred Score calculation
7 NGS Data
83