Table 1. Distribution of SNPs relative to R1, in seven B. microti isolates and in the re-sequenced R1 isolate.
Isolate | Total counta | Non coding region | Coding region | Unique SNPs | Ambiguous | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Inter-genic | Intronic | 5′ UTR 3′ UTR | Syn. | Non-syn. | RTH NON | Unique ALT | Unique REF | QUAL | UNC | ||
R1b | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 515 | 0 | 0 |
ATCC_30222 | 523 | 106 | 49 | 33 | 163 | 170 | 2 | 25 | 0 | 22 | 0 |
ATCC_PRA-99 | 507 | 102 | 53 | 32 | 154 | 164 | 2 | 6 | 0 | 31 | 0 |
GI | 528 | 106 | 53 | 33 | 163 | 171 | 2 | 6 | 0 | 7 | 0 |
Greenwich_Lab_Strain_1 | 456 | 85 | 44 | 30 | 146 | 149 | 2 | 3 | 0 | 79 | 1 |
Nan_Hs_2011_N11–50 | 524 | 104 | 54 | 33 | 164 | 167 | 2 | 5 | 0 | 12 | 0 |
Naushon | 523 | 107 | 53 | 33 | 162 | 166 | 2 | 3 | 0 | 11 | 0 |
Bm1438 | 508 | 106 | 48 | 34 | 160 | 158 | 2 | 6 | 0 | 26 | 2 |
Total number of variable genomic positions | 588 | 121 | 63 | 38 | 171 | 193 | 2 | 54 | 515 | 98 | 2 |
aDifferences were identified against the R1 reference genome25.
bR1 reference isolate was re-sequenced, using Illumina HiSeq technology, to identify potential errors in the original assembly. The sequence variants identified are based on these Illumina data mapped against the reference genome assembly.