In this section

Triticum aestivum vs Triticum aestivum Paragon LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Triticum aestivum Paragon (Triticum aestivum, GCA949126075v1) 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 aestivum Paragon
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,360,770 alignment blocks

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

Uncovered: 1,984,495,315 out of 14,547,261,565
Covered: 12,562,766,250 out of 14,547,261,565

Uncovered: 3,795,225 out of 133,674,966
Matches: 128,926,683 out of 133,674,966
Mismatches: 845,681 out of 133,674,966
Insertions: 107,377 out of 133,674,966
Identity over aligned base-pairs: 99.3%

Triticum aestivum Paragon

Uncovered: 1,934,527,593 out of 14,589,628,860
Covered: 12,655,101,267 out of 14,589,628,860

Uncovered: 4,338,444 out of 127,526,820
Matches: 121,983,912 out of 127,526,820
Mismatches: 1,107,079 out of 127,526,820
Insertions: 97,385 out of 127,526,820
Identity over aligned base-pairs: 99.0%

Block size distribution

Size range All 1,360,770 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
13,568
81.5 kb
10 bp - 100 bp
219,893
11.9 Mb
90,781
5.4 Mb
100 bp - 1 kb
475,713
178.5 Mb
222,503
79.0 Mb
1 kb - 10 kb
344,262
1.4 Gb
97,740
288.3 Mb
10 kb - 100 kb
293,451
9.5 Gb
6,704
126.9 Mb
100 kb - 1 Mb
13,883
1.8 Gb
355
136.4 Mb
1 Mb - 10 Mb
86
309.6 Mb
10 Mb - 100 Mb
23
530.0 Mb
100 Mb - 1 Gb
21
11.5 Gb