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Mouse vs Northern American deer mouse LastZ results

Mouse (Mus musculus, GRCm39) and Northern American deer mouse (Peromyscus maniculatus bairdii, HU_Pman_2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 103. Mouse 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)3000
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
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

ParameterMouseNorthern American deer mouse
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 2,013,808 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Mouse

Uncovered: 1,008,978,431 out of 2,728,222,451
Covered: 1,719,244,020 out of 2,728,222,451

Uncovered: 440,673 out of 36,014,121
Matches: 31,285,087 out of 36,014,121
Mismatches: 4,135,811 out of 36,014,121
Insertions: 152,550 out of 36,014,121
Identity over aligned base-pairs: 87.9%

Northern American deer mouse

Uncovered: 892,677,534 out of 2,512,423,440
Covered: 1,619,745,906 out of 2,512,423,440

Uncovered: 1,345,985 out of 33,606,407
Matches: 28,920,326 out of 33,606,407
Mismatches: 3,234,634 out of 33,606,407
Insertions: 105,462 out of 33,606,407
Identity over aligned base-pairs: 89.6%

Block size distribution

Size range All 2,013,808 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
53,558
343.8 kb
10 bp - 100 bp
206,006
10.6 Mb
26,112
1.7 Mb
100 bp - 1 kb
1,142,744
515.7 Mb
89,141
31.5 Mb
1 kb - 10 kb
609,876
1.3 Gb
25,246
65.0 Mb
10 kb - 100 kb
1,617
22.9 Mb
2,605
50.9 Mb
100 kb - 1 Mb
7
942.3 kb
94
30.3 Mb
1 Mb - 10 Mb
69
258.1 Mb
10 Mb - 100 Mb
36
1.4 Gb