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Zea mays vs Brachypodium distachyon LastZ results

Zea mays (Zea mays, Zm-B73-REFERENCE-NAM-5.0) and Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 106. Zea mays 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

ParameterZea maysBrachypodium distachyon
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 266,355 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Zea mays

Uncovered: 2,077,346,059 out of 2,182,075,994
Covered: 104,729,935 out of 2,182,075,994

Uncovered: 4,333,552 out of 43,681,835
Matches: 30,685,049 out of 43,681,835
Mismatches: 7,664,670 out of 43,681,835
Insertions: 998,564 out of 43,681,835
Identity over aligned base-pairs: 78.0%

Brachypodium distachyon

Uncovered: 207,938,873 out of 271,163,419
Covered: 63,224,546 out of 271,163,419

Uncovered: 6,902,511 out of 39,007,317
Matches: 24,650,582 out of 39,007,317
Mismatches: 6,637,915 out of 39,007,317
Insertions: 816,309 out of 39,007,317
Identity over aligned base-pairs: 76.8%

Block size distribution

Size range All 266,355 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,636
9.3 kb
10 bp - 100 bp
39,335
2.6 Mb
17,939
1.3 Mb
100 bp - 1 kb
195,259
71.4 Mb
90,462
31.3 Mb
1 kb - 10 kb
30,095
51.6 Mb
24,128
60.3 Mb
10 kb - 100 kb
30
472.3 kb
918
18.9 Mb
100 kb - 1 Mb
35
9.8 Mb
1 Mb - 10 Mb
4
4.6 Mb