Understanding the textual output file of FastQC - Per Base N Content
Hi,
I know that the fastqc_report.html generated by FastQC shows the Module of Per Base N Content with percents, but the textual output file generated as fastqc_data.txt shows the data of the same module as follows:
Per base N content pass
#Base N-Count
1 0.005880142888664921
2 7.156360513588139E-5
3 1.19272675226469E-5
4 0.0039121437474281835
5 0.009816141171138397
6 0.011378613216605141
7 0.02527387988048878
8 0.025476643428373778
9 0.024379334816290264
10 0.03693874751763745
Does the N-Count column in the textual data file represent percents or does it represent counts of N in that base's reads?
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antonioggsousa
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amitfinkelstein •
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amitfinkelstein •
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Hi,
It is the percentage of N ambiguous bases found a each bp position.
You can test it by creating some fake fastq data:
@fake_1
ATGCAGTCGATGTGCTANNN
+
ATGCAGTCGATGTGCTA!!!
@fake_2
ATGCAGTCGATGTGCTNNNN
+
ATGCAGTCGATGTGCT!!!!
@fake_3
ATGCAGTCGATGTGCTATGT
+
ATGCAGTCGATGTGCTATGC
@fake_4
NNGCAGTCGATGTGCTATGC
+
!!GCAGTCGATGTGCTATGT
The result is this:
>>Per base N content fail
#Base N-Count
1 25.0
2 25.0
3 0.0
4 0.0
5 0.0
6 0.0
7 0.0
8 0.0
9 0.0
10 0.0
11 0.0
12 0.0
13 0.0
14 0.0
15 0.0
16 0.0
17 25.0
18 50.0
19 50.0
20 50.0
António
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Well, as counts should be integer and that fastqc outputed float numbers I would say it's a percentage
It does not make sense to have 0.1 N counts on a given base.