Anyone knows sequence quality score 0-99?

[holywoool]

hi,everyone!
I've just get the quality score file(panTro2.quals.fa.gz) in chimpanee database from UCSC ftp.
I find that the qualities in the file are from 0 to 99,and most of them are 97 and 99.
I wondered whether the quality score is the same as Phred which has the following formular:
Phred= -10logPe
Can anyone tell me?
Thanks,

[simonandrews]

Difficult to say from the information you provided. I'm not aware of any sequencers which will generate qualities as high as 99, so this is only going to be possible if this is the consensus from an assembly where the depth of coverage was used to add confidence to the calls.

If you provide more information about where you got the file and its format we might be able to provide more information.

[holywoool]

Difficult to say from the information you provided. I'm not aware of any sequencers which will generate qualities as high as 99, so this is only going to be possible if this is the consensus from an assembly where the depth of coverage was used to add confidence to the calls.

If you provide more information about where you got the file and its format we might be able to provide more information.

hi,
The quality score file is from UCSC ftp chimpazee page,and data in this file is of FASTA format.Here is part of it:

99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99
99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 99 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 22
24 20 19 16 12 12 23 25 13 10 10 19 27 39 50 47 48 43 44 40
28 40 41 45 56 53 51 55 63 60 80 82 80 80 79 79 74 76 74 68
76 76 80 81 78 74 71 52 72 70 58 58 57 79 60 61 73 84 62 80
65 65 66 81 84 88 84 72 59 58 70 70 68 91 78 91 86 79 85 84
83 97 97 97 97 90 79 78 81 76 77 59 58 54 76 61 75 78 97 97
86 70 77 77 78 90 97 97 97 97 97 80 80 59 87 97 97 97 97 97
97 97 97 97 97 97 97 97 97 97 97 97 97 97 97 97 97 97 97 97
97 97 97 97 97 97 97 97 97 97 97 97 97 97 97 97 97 97 97 97
I've checked that the number of the scores in each chromosome are equal with correspanding chromosome lengh in panTro2 genome.
I wondered can quality scores reach 99?Or they are not in Phred's methord. Then,how do they work out?

[kmcarr]

I wondered can quality scores reach 99?Or they are not in Phred's methord. Then,how do they work out?

These represent the consensus quality scores of the assembly, assigned by the assembly program. Yes, they are "Phred" like scores. Can quality scores reach 99... in theory I suppose they could. All assemblers will have some cap, or maximum Q score they will assign to a consensus base call. I believe Phrap uses 64 as its maximum. Apparently PCAP (the assembler used for P. troglodytes) uses 99.

[holywoool]

These represent the consensus quality scores of the assembly, assigned by the assembly program. Yes, they are "Phred" like scores. Can quality scores reach 99... in theory I suppose they could. All assemblers will have some cap, or maximum Q score they will assign to a consensus base call. I believe Phrap uses 64 as its maximum. Apparently PCAP (the assembler used for P. troglodytes) uses 99.

Yes,these quality scores are used by the Phrap assembly program, which gives quality scores for the bases on the assembly.The program takes PHRED score as input and outputs 0~97,with two additional score 99 and 98 which represents "FINISHED" and "Manually assigned" respectively.
Still I'm not quite sure the exact meaning of these score.For example score 50 and 70,how to precisely describe their difference in accuricy?