Data from ABI 3100, Phred quality values

Jung, Mark T. MARK.T.JUNG at USA.dupont.com
Wed May 28 12:28:25 EST 2003


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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