Edith,
We have noticed a skewing of quality values in the 60-70 range with the latest version of Phred (0.02.0425.C) versus the old version in our 3700 data. See the distributions below. We asked the author but have not recieved a response yet.
Mark
- - - - - - - - -
Mark Jung
DuPont Crop Genetics
Trait & Technology Development
Analytical Biochemistry Department
Structural Genomics Group
1 Innovation Way, Suite 100 Rm 104
Newark, DE 19714-6104
Mark.T.Jung at usa.dupont.com
OLD version:
Quality Value Distribution
==========================
quality val. num base (%) rcum base (%)
------------ ------------- -------------
0-4 14096 (1.2) 1199547 (100.0) |X
5-9 60548 (5.0) 1185451 (98.8) |XXX
10-14 57548 (4.8) 1124903 (93.8) |XX
15-19 58161 (4.8) 1067355 (89.0) |XX
20-24 58093 (4.8) 1009194 (84.1) |XX
25-29 99040 (8.3) 951101 (79.3) |XXXX
30-34 66216 (5.5) 852061 (71.0) |XXX
35-39 75014 (6.3) 785845 (65.5) |XXX
40-44 188692 (15.7) 710831 (59.3) |XXXXXXXX
45-49 121623 (10.1) 522139 (43.5) |XXXXX
50-54 191927 (16.0) 400516 (33.4) |XXXXXXXX
55-59 208589 (17.4) 208589 (17.4) |XXXXXXXXX
NEW Version:
Quality Value Distribution
==========================
quality val. num base (%) rcum base (%)
------------ ------------- -------------
0-4 12009 (1.0) 1199011 (100.0) |X
5-9 38315 (3.2) 1187002 (99.0) |XX
10-14 60391 (5.0) 1148687 (95.8) |XXX
15-19 41122 (3.4) 1088296 (90.8) |XX
20-24 42174 (3.5) 1047174 (87.3) |XX
25-29 44772 (3.7) 1005000 (83.8) |XX
30-34 66895 (5.6) 960228 (80.1) |XXX
35-39 96554 (8.1) 893333 (74.5) |XXXX
40-44 73692 (6.1) 796779 (66.5) |XXX
45-49 58815 (4.9) 723087 (60.3) |XX
50-54 70355 (5.9) 664272 (55.4) |XXX
55-59 172017 (14.3) 593917 (49.5) |XXXXXXX
60-64 27153 (2.3) 421900 (35.2) |X
65-69 394747 (32.9) 394747 (32.9) |XXXXXXXXXXXXXXXX
> -----Original Message-----
> From: owner-autoseq at hgmp.mrc.ac.uk@DUPONT_MHUB at DUPONT On Behalf Of Edith Schlagenhauf <ediths at botinst.unizh.ch>
> Sent: Wednesday, May 28, 2003 9:09 AM
> To: autoseq at net.bio.net> Subject: Data from ABI 3100, Phred quality values
>> Hi all,
>> I have PHRED processed for the first time a batch of traces coming
> from an ABI 3100. I was surprised to see that the average
> quality for good quality traces is in the range of 60-70.
> For traces from an ABI377 these values are usually around 40-50.
> Is this real or some sort of artefact?
>> Any comments on that?
>> Edith Schlagenhauf
> ---
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