Brachypodium distachyon vs Triticum urartu LastZ results

Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) and Triticum urartu (Triticum urartu, ASM34745v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. Brachypodium distachyon 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

ParameterValue
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

ParameterBrachypodium distachyonTriticum urartu
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 664,428 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Brachypodium distachyon

Uncovered: 152,594,016 out of 271,163,419
Covered: 118,569,403 out of 271,163,419

Uncovered: 4,267,091 out of 39,007,317
Matches: 25,027,959 out of 39,007,317
Mismatches: 8,888,781 out of 39,007,317
Insertions: 823,486 out of 39,007,317
Identity over aligned base-pairs: 72.0%

Triticum urartu

Uncovered: 3,506,636,321 out of 3,747,163,292
Covered: 240,526,971 out of 3,747,163,292

Uncovered: 4,457,588 out of 36,194,921
Matches: 25,681,771 out of 36,194,921
Mismatches: 5,428,881 out of 36,194,921
Insertions: 626,681 out of 36,194,921
Identity over aligned base-pairs: 80.9%

Block size distribution

Size range All 664,428 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4,374
24.4 kb
10 bp - 100 bp
120,028
7.9 Mb
75,475
5.2 Mb
100 bp - 1 kb
470,386
159.2 Mb
297,335
98.4 Mb
1 kb - 10 kb
69,441
125.4 Mb
63,558
162.5 Mb
10 kb - 100 kb
199
3.1 Mb
2,051
29.5 Mb