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Triticum aestivum vs Triticum spelta LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Triticum spelta (Triticum spelta, PGSBv2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 113. 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)5000
Threshold for gapped extension (L)5000
Threshold for alignments between gapped alignment blocks (H)3000
Masking count (M)10
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 aestivumTriticum spelta
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,468,354 alignment blocks

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

Uncovered: 2,340,062,721 out of 14,547,261,565
Covered: 12,207,198,844 out of 14,547,261,565

Uncovered: 4,147,007 out of 133,674,966
Matches: 128,284,961 out of 133,674,966
Mismatches: 1,117,517 out of 133,674,966
Insertions: 125,481 out of 133,674,966
Identity over aligned base-pairs: 99.0%

Triticum spelta

Uncovered: 1,806,177,662 out of 14,000,336,401
Covered: 12,194,158,739 out of 14,000,336,401

Uncovered: 1,355,245 out of 128,797,843
Matches: 126,576,667 out of 128,797,843
Mismatches: 800,798 out of 128,797,843
Insertions: 65,133 out of 128,797,843
Identity over aligned base-pairs: 99.3%

Block size distribution

Size range All 1,468,354 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
14,801
87.0 kb
10 bp - 100 bp
240,594
13.1 Mb
101,626
6.0 Mb
100 bp - 1 kb
511,065
193.1 Mb
236,034
84.9 Mb
1 kb - 10 kb
386,052
1.6 Gb
109,151
323.1 Mb
10 kb - 100 kb
305,510
9.5 Gb
6,080
109.2 Mb
100 kb - 1 Mb
10,332
1.3 Gb
342
133.2 Mb
1 Mb - 10 Mb
109
423.7 Mb
10 Mb - 100 Mb
20
465.4 Mb
100 Mb - 1 Gb
21
11.0 Gb