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Triticum aestivum vs Triticum urartu LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Triticum urartu (Triticum urartu, IGDB) 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)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 urartu
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,765,728 alignment blocks

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

Uncovered: 11,121,243,220 out of 14,547,261,565
Covered: 3,426,018,345 out of 14,547,261,565

Uncovered: 9,642,350 out of 133,674,966
Matches: 117,530,080 out of 133,674,966
Mismatches: 5,883,868 out of 133,674,966
Insertions: 618,668 out of 133,674,966
Identity over aligned base-pairs: 94.8%

Triticum urartu

Uncovered: 2,541,025,331 out of 4,851,895,022
Covered: 2,310,869,691 out of 4,851,895,022

Uncovered: 710,584 out of 41,813,638
Matches: 40,126,970 out of 41,813,638
Mismatches: 875,902 out of 41,813,638
Insertions: 100,182 out of 41,813,638
Identity over aligned base-pairs: 97.6%

Block size distribution

Size range All 2,765,728 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
35,189
204.4 kb
10 bp - 100 bp
521,048
29.1 Mb
190,576
11.4 Mb
100 bp - 1 kb
1,477,968
591.4 Mb
543,941
217.8 Mb
1 kb - 10 kb
656,791
1.8 Gb
335,083
976.8 Mb
10 kb - 100 kb
74,715
1.5 Gb
28,189
694.5 Mb
100 kb - 1 Mb
17
1.8 Mb
3,182
694.1 Mb
1 Mb - 10 Mb
156
373.5 Mb
10 Mb - 100 Mb
6
74.7 Mb
100 Mb - 1 Gb
6
870.1 Mb