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Triticum aestivum vs Zea mays LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Zea mays (Zea mays, Zm-B73-REFERENCE-NAM-5.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 106. 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 aestivumZea mays
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 812,091 alignment blocks

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

Uncovered: 14,248,950,143 out of 14,547,261,565
Covered: 298,311,422 out of 14,547,261,565

Uncovered: 18,861,995 out of 133,674,966
Matches: 86,994,804 out of 133,674,966
Mismatches: 25,129,457 out of 133,674,966
Insertions: 2,688,710 out of 133,674,966
Identity over aligned base-pairs: 75.8%

Zea mays

Uncovered: 2,065,497,521 out of 2,182,075,994
Covered: 116,578,473 out of 2,182,075,994

Uncovered: 4,533,188 out of 43,681,835
Matches: 30,205,321 out of 43,681,835
Mismatches: 7,847,381 out of 43,681,835
Insertions: 1,095,945 out of 43,681,835
Identity over aligned base-pairs: 77.2%

Block size distribution

Size range All 812,091 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5,768
31.1 kb
10 bp - 100 bp
119,374
7.9 Mb
53,380
3.9 Mb
100 bp - 1 kb
593,774
217.3 Mb
287,613
102.4 Mb
1 kb - 10 kb
93,135
155.0 Mb
103,660
257.0 Mb
10 kb - 100 kb
40
541.8 kb
1,262
17.6 Mb