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Brachypodium distachyon vs Aegilops tauschii LastZ results

Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) and Aegilops tauschii (Aegilops tauschii subsp. strangulata, Aet_v4.0) 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 distachyonAegilops tauschii
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 801,048 alignment blocks

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

Uncovered: 155,031,446 out of 271,163,419
Covered: 116,131,973 out of 271,163,419

Uncovered: 2,992,705 out of 39,007,317
Matches: 29,194,870 out of 39,007,317
Mismatches: 5,948,692 out of 39,007,317
Insertions: 871,050 out of 39,007,317
Identity over aligned base-pairs: 81.1%

Aegilops tauschii

Uncovered: 3,928,206,844 out of 4,224,915,394
Covered: 296,708,550 out of 4,224,915,394

Uncovered: 5,013,787 out of 53,210,770
Matches: 38,486,786 out of 53,210,770
Mismatches: 8,435,615 out of 53,210,770
Insertions: 1,274,582 out of 53,210,770
Identity over aligned base-pairs: 79.9%

Block size distribution

Size range All 801,048 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5,354
29.9 kb
10 bp - 100 bp
155,294
10.1 Mb
102,609
6.9 Mb
100 bp - 1 kb
556,551
187.9 Mb
357,233
117.4 Mb
1 kb - 10 kb
83,745
146.7 Mb
74,284
175.0 Mb
10 kb - 100 kb
101
2.4 Mb
2,046
42.8 Mb
100 kb - 1 Mb
3
407.0 kb
29
5.5 Mb