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Triticum aestivum vs Triticum aestivum Landmark LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Triticum aestivum Landmark (Triticum aestivum, PGSBv2.1) 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 aestivum Landmark
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,521,551 alignment blocks

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

Uncovered: 2,214,015,100 out of 14,547,261,565
Covered: 12,333,246,465 out of 14,547,261,565

Uncovered: 3,794,783 out of 133,674,966
Matches: 128,763,115 out of 133,674,966
Mismatches: 1,017,451 out of 133,674,966
Insertions: 99,617 out of 133,674,966
Identity over aligned base-pairs: 99.1%

Triticum aestivum Landmark

Uncovered: 2,091,687,251 out of 14,433,190,783
Covered: 12,341,503,532 out of 14,433,190,783

Uncovered: 7,860,449 out of 174,056,595
Matches: 164,745,437 out of 174,056,595
Mismatches: 1,322,678 out of 174,056,595
Insertions: 128,031 out of 174,056,595
Identity over aligned base-pairs: 99.1%

Block size distribution

Size range All 1,521,551 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
14,993
90.7 kb
10 bp - 100 bp
238,653
12.9 Mb
95,562
5.8 Mb
100 bp - 1 kb
499,854
186.0 Mb
239,423
84.1 Mb
1 kb - 10 kb
423,783
1.8 Gb
94,196
275.0 Mb
10 kb - 100 kb
337,254
9.8 Gb
5,072
92.8 Mb
100 kb - 1 Mb
7,014
880.3 Mb
480
186.8 Mb
1 Mb - 10 Mb
216
649.0 Mb
10 Mb - 100 Mb
24
531.6 Mb
100 Mb - 1 Gb
21
10.8 Gb