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Brachypodium distachyon vs Triticum turgidum LastZ results

Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) and Triticum turgidum (Triticum turgidum subsp. durum, Svevo.v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 98. 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 turgidum
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 1,747,583 alignment blocks

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

Uncovered: 148,077,163 out of 271,163,419
Covered: 123,086,256 out of 271,163,419

Uncovered: 2,695,527 out of 39,007,317
Matches: 29,374,172 out of 39,007,317
Mismatches: 6,029,515 out of 39,007,317
Insertions: 908,103 out of 39,007,317
Identity over aligned base-pairs: 80.9%

Triticum turgidum

Uncovered: 9,789,027,155 out of 10,463,058,104
Covered: 674,030,949 out of 10,463,058,104

Uncovered: 5,622,236 out of 88,577,667
Matches: 67,097,581 out of 88,577,667
Mismatches: 14,097,550 out of 88,577,667
Insertions: 1,760,300 out of 88,577,667
Identity over aligned base-pairs: 80.9%

Block size distribution

Size range All 1,747,583 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
10,993
60.5 kb
10 bp - 100 bp
330,722
21.5 Mb
219,087
14.8 Mb
100 bp - 1 kb
1,229,298
416.3 Mb
805,146
269.0 Mb
1 kb - 10 kb
176,558
311.0 Mb
162,391
385.4 Mb
10 kb - 100 kb
12
130.3 kb
4,002
73.8 Mb
100 kb - 1 Mb
32
6.0 Mb