Which quality score?

[baohua100]

@5_5cChx69L221/1
AAAACTTTTACATATATGTTTTNAACGATTTAAAAGATAATTAA
+
WRUTWWWWWNWWWNWWWWWWWWEWPWWWWWSPQQPQQQQQQQQL
@5_WaChx69L221/1
TCATACATTTTCTCTTTTAAAANAGTTAGATTAGATTAGAGATA
+
WWSWPWTWWWWWWWWWWWWSWQEQWWWQWNSTNTQQQQQLQQQL
@3_9aChx69L221/1
TTTCATTGGGAAACATTACGCTNGCTACAAACCGTCTTTCAGCC
+
WWWWWWWWWWWSWTSWWWWWWPEWWWQTWKMQQSQQQQQNKQQN

Is the quality score as Phred's sanger score or Solexa' score ?


If solexa: ASCII-64

! -31 0.10%
+ -21 0.10%
C 3 0.06%
D 4 0.06%
E 5 0.16%
F 6 0.16%
G 7 0.17%
H 8 0.13%
I 9 0.20%
J 10 0.25%
K 11 0.25%
L 12 0.31%
M 13 0.48%
N 14 0.60%
O 15 0.66%
P 16 1.04%
Q 17 3.98%
R 18 14.83%
S 19 0.77%
T 20 11.11%
U 21 0.50%
V 22 0.93%
W 23 63.17%

If Phred' sanger score ASCII-33

! 0 0.10%
+ 10 0.10%
C 34 0.06%
D 35 0.06%
E 36 0.16%
F 37 0.16%
G 38 0.17%
H 39 0.13%
I 40 0.20%
J 41 0.25%
K 42 0.25%
L 43 0.31%
M 44 0.48%
N 45 0.60%
O 46 0.66%
P 47 1.04%
Q 48 3.98%
R 49 14.83%
S 50 0.77%
T 51 11.11%
U 52 0.50%
V 53 0.93%
W 54 63.17%

[dvh]

Which version of solexa/illumina Pipeline?

Base call quality score output in GERALD folder 'fastq' files seems to have changed from Pipeline 1.0 to 1.3.2.

See http://seqanswers.com/forums/showthread.php?t=1110

[Torst]

Base call quality score output in GERALD folder 'fastq' files seems to have changed from Pipeline 1.0 to 1.3.2.
See http://seqanswers.com/forums/showthread.php?t=1110

*sigh*

--Torst