Triticum aestivum vs Brachypodium distachyon LastZ results
Triticum aestivum (Triticum aestivum, IWGSC) and Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. Triticum aestivum 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 | Triticum aestivum | Brachypodium distachyon |
---|---|---|
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 2,227,317 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Triticum aestivum |
Uncovered: 13,651,982,362 out of 14,547,261,565 |
Uncovered: 8,433,093 out of 136,655,258 |
Brachypodium distachyon |
Uncovered: 145,247,128 out of 271,163,419 |
Uncovered: 2,592,219 out of 39,007,317 |
Block size distribution
Size range | All 2,227,317 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 15,172 |
84.8 kb |
|||
10 bp - 100 bp | 408,693 |
26.5 Mb |
261,669 |
17.8 Mb |
|
100 bp - 1 kb | 1,564,420 |
536.1 Mb |
986,043 |
330.8 Mb |
|
1 kb - 10 kb | 239,011 |
422.6 Mb |
211,414 |
511.9 Mb |
|
10 kb - 100 kb | 21 |
231.9 kb |
5,950 |
113.9 Mb |
|
100 kb - 1 Mb | 59 |
11.2 Mb |