Vitis vinifera vs Nicotiana attenuata LastZ results
Vitis vinifera (Vitis vinifera, 12X) and Nicotiana attenuata (Nicotiana attenuata, NIATTr2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. Vitis vinifera was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.
Configuration parameters
Parameter | Value |
---|---|
Gap open penalty (O) | 400 |
Gap extend penalty (E) | 30 |
HSP threshold (K) | |
Threshold for gapped extension (L) | 3000 |
Threshold for alignments between gapped alignment blocks (H) | 2200 |
Masking count (M) | |
Seed and Transition value (T) | 1 |
Scoring matrix (Q) | Default: A C G T 91 -114 -31 -123 -114 100 -125 -31 -31 -125 100 -114 -123 -31 -114 91 |
Chunking parameters
Parameter | Vitis vinifera | Nicotiana attenuata |
---|---|---|
Chunk size | 10,000,000 | 10,100,000 |
Overlap | 0 | 100,000 |
Group set size | 0 | 10,100,000 |
Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 218,979 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Vitis vinifera |
Uncovered: 438,569,948 out of 486,265,422 |
Uncovered: 9,277,381 out of 32,794,161 |
Nicotiana attenuata |
Uncovered: 1,435,622,376 out of 1,492,146,380 |
Uncovered: 4,791,913 out of 23,314,391 |
Block size distribution
Size range | All 218,979 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 1,305 |
7.0 kb |
1 |
5.0 bp |
|
10 bp - 100 bp | 37,440 |
2.6 Mb |
17,231 |
1.2 Mb |
|
100 bp - 1 kb | 164,603 |
54.6 Mb |
75,221 |
25.6 Mb |
|
1 kb - 10 kb | 15,566 |
25.5 Mb |
24,252 |
54.0 Mb |
|
10 kb - 100 kb | 64 |
1.3 Mb |
191 |
2.8 Mb |
|
100 kb - 1 Mb | 1 |
139.4 kb |
3 |
469.3 kb |