Table 1.
Numbers and types of sequence variants observed in TAR-cloned rDNA loci
| A. Variants in rDNA | |||||
|---|---|---|---|---|---|
| Validated by deep sequencing | |||||
| Features | Total variants (variants/kb) | All | Any | Any RNA-seq | |
| 5′ ETS | 19 (5.2) | 9 | 12 | 7 | |
| 18S | 4 (2.1) | 0 | 0 | 0 | |
| ITS-1 | 14 (13.1) | 5 | 11 | 3 | |
| 5.8S | 0 (0) | 0 | 0 | 0 | |
| ITS-2 | 13 (11.1) | 5 | 5 | 4 | |
| 28S | 43 (8.5) | 18 | 27 | 7 | |
| 3′ ETS | 8 (22.2) | 1 | 5 | 1 | |
| 45S (total) | 101 (7.6) | 38 | 60 | 22 | |
| IGS (total) | 235 (7.5) | 108 | 148 | 3 | |
| B. Variant breakdown into types | |||||
| Deletions | Insertions | ||||
| Features | SNPs | Single nucleotide | Multiple nucleotide | Single nucleotide | Multiple nucleotide |
| 5′ ETS | 8 | 5 | 2 | 3 | 1 |
| 18S | 0 | 4 | 0 | 0 | 0 |
| ITS-1 | 3 | 6 | 0 | 3 | 2 |
| 5.8S | 0 | 0 | 0 | 0 | 0 |
| ITS-2 | 2 | 9 | 0 | 2 | 0 |
| 28S | 9 | 16 | 2 | 6 | 10 |
| 3′ ETS | 3 | 0 | 2 | 2 | 1 |
| 45S (total) | 25 | 40 | 6 | 16 | 14 |
| IGS (total) | 88 | 14 | 59 | 8 | 66 |
(A) A summary of distribution of variants in the 45S pre-rDNA and IGS regions and their frequencies per kilobases are shown. The number of variants validated in all deep sequenced individuals versus any deep-sequenced individuals are also listed. The last column lists variants validated in deep-sequenced RNA samples. (B) Variants categorized as SNPs, insertions and deletions are listed for transcribed rDNA and IGS regions.