Base quality scores represent the sequencer's confidence that a nucleotide was accurately called (sometimes called Phred quality score). Inside
FASTQ files, these numerical scores are stored as characters. Here is an example FASTQ record, with the base quality highlighted:
@read1
ACGTACGTACGT
+
!!IIIIII87II
Read name
DNA sequence
Ignored line
Base quality
Calculator
Quality
ASCII
Prob.
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
!
"
#
$
%
&
'
(
)
*
+
,
-
.
/
0
1
2
3
4
5
6
7
8
9
:
;
<
=
>
?
@
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
[
\
]
^
_
`
a
b
c
d
e
f
g
h
i
j
k
l
m
n
o
p
q
r
s
t
u
v
w
x
y
z
{
|
}
~
1
10-1
10-2
10-3
10-4
10-5
10-6
10-7
10-8
10-9
A quality score of 20 is represented as the character
5 in FASTQ files, and
corresponds to a base calling error probability of
1.0e-2, or
1 in 100.