Triticum dicoccoides vs Hordeum vulgare LastZ results
Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) and Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. Triticum dicoccoides 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) | |
Gap extend penalty (E) | |
HSP threshold (K) | |
Threshold for gapped extension (L) | |
Threshold for alignments between gapped alignment blocks (H) | |
Masking count (M) | |
Seed and Transition value (T) | |
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 | Triticum dicoccoides | Hordeum vulgare |
---|---|---|
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 3,357,299 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Triticum dicoccoides |
Uncovered: 8,832,852,184 out of 10,079,039,394 |
Uncovered: 2,715,730 out of 81,268,905 |
Hordeum vulgare |
Uncovered: 3,995,118,014 out of 4,834,432,680 |
Uncovered: 2,032,746 out of 44,420,163 |
Block size distribution
Size range | All 3,357,299 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 45,877 |
248.2 kb |
|||
10 bp - 100 bp | 608,517 |
37.4 Mb |
246,340 |
16.5 Mb |
|
100 bp - 1 kb | 2,182,930 |
823.2 Mb |
1,055,311 |
415.5 Mb |
|
1 kb - 10 kb | 519,801 |
1.0 Gb |
475,605 |
1.2 Gb |
|
10 kb - 100 kb | 174 |
2.0 Mb |
12,360 |
193.0 Mb |
|
100 kb - 1 Mb | 66 |
11.3 Mb |