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Brachypodium distachyon vs Triticum dicoccoides LastZ results

Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) and Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) 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 dicoccoides
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 932,208 alignment blocks

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

Uncovered: 154,569,800 out of 271,163,419
Covered: 116,593,619 out of 271,163,419

Uncovered: 2,928,706 out of 39,007,317
Matches: 29,336,751 out of 39,007,317
Mismatches: 5,847,443 out of 39,007,317
Insertions: 894,417 out of 39,007,317
Identity over aligned base-pairs: 81.3%

Triticum dicoccoides

Uncovered: 9,657,511,005 out of 10,079,039,394
Covered: 421,528,389 out of 10,079,039,394

Uncovered: 5,052,599 out of 81,268,905
Matches: 62,507,456 out of 81,268,905
Mismatches: 12,130,613 out of 81,268,905
Insertions: 1,578,237 out of 81,268,905
Identity over aligned base-pairs: 82.0%

Block size distribution

Size range All 932,208 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7,582
44.2 kb
2
9.0 bp
10 bp - 100 bp
139,967
9.1 Mb
69,993
5.0 Mb
100 bp - 1 kb
655,700
238.3 Mb
361,749
126.7 Mb
1 kb - 10 kb
128,950
231.4 Mb
104,796
268.2 Mb
10 kb - 100 kb
9
96.8 kb
3,937
71.9 Mb
100 kb - 1 Mb
35
7.2 Mb