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Triticum aestivum vs Triticum aestivum Norin61 LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Triticum aestivum Norin61 (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 Norin61
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,317,967 alignment blocks

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

Uncovered: 1,535,004,492 out of 14,547,261,565
Covered: 13,012,257,073 out of 14,547,261,565

Uncovered: 1,767,418 out of 133,674,966
Matches: 130,953,481 out of 133,674,966
Mismatches: 863,794 out of 133,674,966
Insertions: 90,273 out of 133,674,966
Identity over aligned base-pairs: 99.3%

Triticum aestivum Norin61

Uncovered: 1,875,601,938 out of 14,910,390,598
Covered: 13,034,788,660 out of 14,910,390,598

Uncovered: 9,581,195 out of 180,930,939
Matches: 170,021,171 out of 180,930,939
Mismatches: 1,227,435 out of 180,930,939
Insertions: 101,138 out of 180,930,939
Identity over aligned base-pairs: 99.2%

Block size distribution

Size range All 1,317,967 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
12,106
72.6 kb
10 bp - 100 bp
203,845
11.2 Mb
84,605
5.1 Mb
100 bp - 1 kb
438,724
164.4 Mb
214,804
77.7 Mb
1 kb - 10 kb
335,978
1.4 Gb
93,524
266.2 Mb
10 kb - 100 kb
314,737
10.1 Gb
4,936
94.6 Mb
100 kb - 1 Mb
12,577
1.6 Gb
344
139.1 Mb
1 Mb - 10 Mb
115
381.8 Mb
10 Mb - 100 Mb
19
401.6 Mb
100 Mb - 1 Gb
21
12.0 Gb