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Triticum dicoccoides vs Triticum aestivum LastZ results

Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) and Triticum aestivum (Triticum aestivum, IWGSC) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. Triticum dicoccoides 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 dicoccoidesTriticum aestivum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 1,497,407 alignment blocks

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

Uncovered: 2,434,228,557 out of 10,079,039,394
Covered: 7,644,810,837 out of 10,079,039,394

Uncovered: 12,403,620 out of 81,268,905
Matches: 67,719,060 out of 81,268,905
Mismatches: 1,025,922 out of 81,268,905
Insertions: 120,303 out of 81,268,905
Identity over aligned base-pairs: 98.3%

Triticum aestivum

Uncovered: 6,896,989,580 out of 14,547,261,565
Covered: 7,650,271,985 out of 14,547,261,565

Uncovered: 58,841,815 out of 133,674,966
Matches: 73,354,621 out of 133,674,966
Mismatches: 1,337,166 out of 133,674,966
Insertions: 141,364 out of 133,674,966
Identity over aligned base-pairs: 98.0%

Block size distribution

Size range All 1,497,407 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
16,395
96.6 kb
10 bp - 100 bp
256,769
13.8 Mb
105,856
6.2 Mb
100 bp - 1 kb
566,817
219.3 Mb
255,842
95.4 Mb
1 kb - 10 kb
429,070
1.6 Gb
132,500
400.2 Mb
10 kb - 100 kb
226,493
5.9 Gb
7,764
138.5 Mb
100 kb - 1 Mb
1,863
227.0 Mb
534
189.9 Mb
1 Mb - 10 Mb
164
541.4 Mb
10 Mb - 100 Mb
30
530.2 Mb
100 Mb - 1 Gb
14
6.1 Gb