Triticum aestivum vs Brachypodium distachyon LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Brachypodium distachyon (Brachypodium distachyon, Brachypodium_distachyon_v3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. Triticum aestivum 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

ParameterTriticum aestivumBrachypodium distachyon
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 2,227,317 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Triticum aestivum

Uncovered: 13,651,982,362 out of 14,547,261,565
Covered: 895,279,203 out of 14,547,261,565

Uncovered: 8,433,093 out of 136,655,258
Matches: 103,740,468 out of 136,655,258
Mismatches: 21,833,860 out of 136,655,258
Insertions: 2,647,837 out of 136,655,258
Identity over aligned base-pairs: 80.9%

Brachypodium distachyon

Uncovered: 145,247,128 out of 271,163,419
Covered: 125,916,291 out of 271,163,419

Uncovered: 2,592,219 out of 39,007,317
Matches: 29,466,875 out of 39,007,317
Mismatches: 6,028,796 out of 39,007,317
Insertions: 919,427 out of 39,007,317
Identity over aligned base-pairs: 80.9%

Block size distribution

Size range All 2,227,317 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15,172
84.8 kb
10 bp - 100 bp
408,693
26.5 Mb
261,669
17.8 Mb
100 bp - 1 kb
1,564,420
536.1 Mb
986,043
330.8 Mb
1 kb - 10 kb
239,011
422.6 Mb
211,414
511.9 Mb
10 kb - 100 kb
21
231.9 kb
5,950
113.9 Mb
100 kb - 1 Mb
59
11.2 Mb