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Triticum aestivum vs Triticum timopheevii LastZ results

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

Statistics over 2,679,637 alignment blocks

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

Uncovered: 10,408,171,871 out of 14,547,261,565
Covered: 4,139,089,694 out of 14,547,261,565

Uncovered: 49,104,499 out of 133,674,966
Matches: 81,913,717 out of 133,674,966
Mismatches: 2,388,795 out of 133,674,966
Insertions: 267,955 out of 133,674,966
Identity over aligned base-pairs: 96.9%

Triticum timopheevii

Uncovered: 5,256,359,892 out of 9,351,419,471
Covered: 4,095,059,579 out of 9,351,419,471

Uncovered: 28,635,282 out of 175,451,481
Matches: 139,554,423 out of 175,451,481
Mismatches: 6,469,693 out of 175,451,481
Insertions: 792,083 out of 175,451,481
Identity over aligned base-pairs: 95.1%

Block size distribution

Size range All 2,679,637 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
33,899
190.6 kb
10 bp - 100 bp
534,821
29.4 Mb
211,340
12.4 Mb
100 bp - 1 kb
1,295,844
513.9 Mb
523,910
202.9 Mb
1 kb - 10 kb
708,682
2.1 Gb
332,939
998.1 Mb
10 kb - 100 kb
106,283
2.2 Gb
16,907
275.9 Mb
100 kb - 1 Mb
108
12.7 Mb
531
164.7 Mb
1 Mb - 10 Mb
162
498.0 Mb
10 Mb - 100 Mb
20
612.5 Mb
100 Mb - 1 Gb
9
2.1 Gb