Zea mays vs Brachypodium distachyon LastZ results

Zea mays (Zea mays, B73_RefGen_v4) and Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. 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)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

ParameterZea maysBrachypodium 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 192,674 alignment blocks

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

Uncovered: 2,063,487,735 out of 2,135,083,061
Covered: 71,595,326 out of 2,135,083,061

Uncovered: 16,220,792 out of 48,442,923
Matches: 25,000,485 out of 48,442,923
Mismatches: 6,366,945 out of 48,442,923
Insertions: 854,701 out of 48,442,923
Identity over aligned base-pairs: 77.6%

Brachypodium distachyon

Uncovered: 212,442,663 out of 271,163,419
Covered: 58,720,756 out of 271,163,419

Uncovered: 8,361,328 out of 39,007,317
Matches: 23,340,855 out of 39,007,317
Mismatches: 6,506,651 out of 39,007,317
Insertions: 798,483 out of 39,007,317
Identity over aligned base-pairs: 76.2%

Block size distribution

Size range All 192,674 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,260
7.3 kb
10 bp - 100 bp
26,691
1.8 Mb
10,957
786.9 kb
100 bp - 1 kb
141,482
52.6 Mb
58,402
20.1 Mb
1 kb - 10 kb
23,237
38.3 Mb
19,496
50.8 Mb
10 kb - 100 kb
4
54.5 kb
794
15.4 Mb
100 kb - 1 Mb
25
5.6 Mb