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Table 1 Frequencies of putative MSG alleles in five populations of P. carinii

From: Complexity of the MSG gene family of Pneumocystis 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
  1. a 581 reads were assembled (maximum mismatch of 5%) into groups. Groups containing less than 16 reads are not listed.
  2. 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.
  3. c An haplotype designated as 1-C had a type 1 hypervariable region and a C at a polymorphic site located outside of HV1.
  4. 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.