Table 1

Frequencies of putative MSG alleles in five populations of P. carinii

Groupa (no. reads)

Nucleotide position of polymorphismb

Haplotypesc

Frequency of haplotypes in 5 P. carinii populationsd


A

B

C

D

E


1(49)

HV1, 81

1-C

15

3

1

1

5


1-T

0

2

0

0

0


2-C

4

15

0

0

1


2-T

0

1

0

0

0


3-C

1

0

0

0

0


4-C

1

0

0

0

0



2 (40)

57,83,173,204

5-GTAA

6

24

0

0

0


5-TTAA

0

2

0

0

0


5-GCAA

0

2

0

0

0

5-GTGA

4

0

0

0

0


5-GTAT

2

0

0

0

0



3 (34)

HV1, 85, 203

4-CT

9

16

1

0

1


4-CG

1

0

1

0

0


6-CT

0

0

0

0

1


6-CG

2

0

0

0

0


5-GG

1

0

1

0

0



4 (32)

HV1

7

10

16

1

0

0


8

2

0

0

0

0


9

0

0

1

1

0


10

1

0

0

0

0



5 (29)

153

11-T

5

22

0

0

0


11-C

0

2

0

0

0



6 (28)

HV1, 300

12-T

4

20

1

0

0


12-C

0

2

0

0

0


13-T

1

0

0

0

0



7 (26)

193

14-A

2

22

0

0

0


14-G

0

2

0

0

0



8 (24)

HV1

9

13

7

0

0

1


7

2

0

0

1

1


9 (25)

HV1,302,313

4-AA

3

14

0

0

0


4-GA

0

4

0

0

0


4-AG

0

2

0

0

0


1-AA

1

0

0

0

0


15-AA

1

0

0

0

0



10 (19)

97 to 107

16

8

10

0

0

0


16-indel

1

0

0

0

0



12 (18)

65,216,228,282

18-T-TA

2

11

0

0

0


18-A-TA

0

1

0

0

0


18-AATG

0

1

0

0

0


18-TATA

0

1

0

0

0


18-T-AA

0

2

0

0

0



13 (16)

HV1

9

1

0

0

0

0


16

15

0

0

0

0


a 581 reads were assembled (maximum mismatch of 5%) into groups. Groups containing less than 16 reads are not listed.

b "HV1" means that a polymorphism was seen in hypervariable region 1 (see Table 2 for sequences). Numbers in this column refer to the location of the polymorphisms that were not in HV1. Each number refers to a nucleotide site where position 1 is the A in the ATG at the beginning of the CRJE. Because the HV1 sequences varied in length, the position-numbers of polymorphisms downstream of HV1 cannot be compared between groups.

c An haplotype designated as 1-C had a type 1 hypervariable region and a C at a polymorphic site located outside of HV1.

d Populations A and B were the source of ADAM plasmids and Lucigen genome project reads, respectively. Populations C, D and E were smaller populations that had been analyzed in the past using the same methods as those used to produce the ADAM plasmid library.

Keely and Stringer BMC Genomics 2009 10:367   doi:10.1186/1471-2164-10-367

Open Data