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Arabidopsis thaliana vs Brachypodium distachyon LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. Arabidopsis thaliana 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)3000
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

ParameterArabidopsis thalianaBrachypodium distachyon
Chunk size50,000,000100,100,000
Overlap0100,000
Group set size0100,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 108,532 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 93,675,392 out of 119,667,750
Covered: 25,992,358 out of 119,667,750

Uncovered: 14,393,303 out of 33,775,569
Matches: 12,552,135 out of 33,775,569
Mismatches: 6,440,411 out of 33,775,569
Insertions: 389,720 out of 33,775,569
Identity over aligned base-pairs: 64.8%

Brachypodium distachyon

Uncovered: 243,913,132 out of 271,163,419
Covered: 27,250,287 out of 271,163,419

Uncovered: 19,297,885 out of 39,007,317
Matches: 12,658,688 out of 39,007,317
Mismatches: 6,570,724 out of 39,007,317
Insertions: 480,020 out of 39,007,317
Identity over aligned base-pairs: 64.2%

Block size distribution

Size range All 108,532 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
785
4.1 kb
10 bp - 100 bp
16,858
1.2 Mb
2,831
201.3 kb
100 bp - 1 kb
84,639
28.1 Mb
20,343
8.6 Mb
1 kb - 10 kb
6,250
9.0 Mb
14,116
29.1 Mb
10 kb - 100 kb
34
406.0 kb