Segmental Phylogenetic Relationships of Inbred Mouse Strains Revealed by Fine-Scale Analysis of Sequence Variation Across 4.6 Mb of Mouse Genome

Table 1.

Characterization of the Phylogenetic Segments
All 15 strains
13 lab strains
Segment
Start
End
Length
Tiled bases
% tiled
SNPs
bp/SNP
SNPs
bp/SNP
A. NT_027761
    1 4775 60,623 55,848 39,942 72 178 224 27 1479
    2 60,624 96,289 35,665 29,995 84 261 115 44 682
    3 96,290 154,178 57,888 49,967 86 325 153 14 3569
    4 154,179 167,379 13,200 9983 76 78 128 11 908
    5 167,380 328,404 161,024 109,918 68 1070 103 453 243
    6 328,405 546,803 218,398 169,859 78 1330 128 163 1042
    7 546,804 561,088 14,284 9988 70 77 130 10 999
    8 561,089 672,407 111,318 86,567 78 533 162 10 8657
Entire contig 667,625 506,219 76 3852 131 732 692
B. NT_026540
    1 25 41,753 41,728 29,953 72 258 116 77 389
    2 41,754 55,130 13,376 10,012 75 96 103 18 556
    3 55,131 259,782 204,651 159,826 78 1282 125 333 480
    4 259,783 314,496 54,713 39,967 73 280 142 59 677
    5 314,497 343,919 29,422 9,986 34 95 105 22 454
    6 343,920 438,863 94,943 79,952 84 666 120 182 439
    7 438,864 452,944 14,080 9987 71 53 188 22 454
    8 452,945 480,192 27,247 19,997 73 146 137 45 444
    9 480,193 506,047 25,854 19,978 77 141 142 76 263
    10 506,048 532,543 26,495 19,975 75 79 253 28 713
    11 532,544 561,215 28,671 19,994 70 100 198 22 909
    12 561,216 585,089 23,873 19,984 84 82 244 12 1665
    13 585,090 617,308 32,218 29,539 92 84 352 17 1738
Entire contig 617,271 469,150 76 3362 140 913 514
C. NT_029829
    1 1221 411,323 410,102 259,556 63 1165 223 196 1324
    2 411,324 589,223 177,899 109,808 62 564 195 84 1307
    3 589,224 1,197,358 608,134 409,304 67 1886 217 39 10,495
    4 1,197,359 1,266,511 69,152 39,921 58 257 155 50 798
    5 1,266,512 1,300,811 34,299 19,953 58 151 132 26 767
    6 1,300,812 1,316,392 15,580 9978 64 78 128 18 554
    7 1,316,393 1,558,180 241,787 154,033 64 784 196 85 1812
Entire contig 1,556,953 1,002,553 64 4885 205 498 2013
D. Cytokine interval
    1 4290 41,519 37,229 29,961 80 104 288 45 666
    2 41,520 71,794 30,274 19,956 66 93 215 46 434
    3 71,795 168,876 97,081 64,490 66 80 806 13 4961
    4 168,877 367,752 198,875 139,833 70 1062 132 449 311
    5 367,753 453,442 85,689 59,923 70 328 183 87 689
    6 453,443 469,695 16,252 9,983 61 80 125 39 256
    7 469,696 496,748 27,052 19,966 74 149 134 63 317
    8 496,749 597,137 100,388 69,920 70 255 274 130 538
    9 597,138 609,095 11,957 9992 84 31 322 11 908
    10 609,096 663,488 54,392 39,992 74 179 223 94 425
    11 663,489 704,386 40,897 29,996 73 133 226 54 555
    12 704,387 734,769 30,382 19,968 66 116 172 67 298
    13 734,770 795,947 61,177 49,975 82 335 149 169 296
    14 795,948 917,066 121,118 98,423 81 544 181 211 466
Entire contig 912,763 662,378 73 3489 190 1478 448
E. NT_014989
    1 70 123,575 123,505 29,942 24 222 135 32 936
    2 123,576 358,931 235,355 109,949 47 788 140 22 4998
    3 358,932 502,615 143,683 69,952 49 511 137 63 1110
    4 502,616 540,102 37,486 30,003 80 388 77 165 182
    5 540,103 552,618 12,515 9993 80 129 77 57 175
    6 552,619 567,174 14,555 9993 69 102 98 38 263
    7 567,175 649,219 82,044 29,977 37 230 130 60 500
    8 649,220 821,887 172,667 71,558 41 408 175 7 10,223
Entire contig
821,810
361,367
44
2778
130
444
814

  • For each of the five contigs, the start nucleotide, end nucleotide, and length in base pairs of the phylogenetic segments are given. The number of unique base pairs synthesized onto the water (Tiled bases) and the percentage that this represents are indicated for each segment. The number of variable sites identified within each segment (SNPs) from all 15 strains (All 15 strains) and the SNP frequency (bp/SNP) calculated as the number of unique base pairs identified divided by the number of SNPs are given. The number of SNPs identified in each segmental block from the 13 classical strains (13 lab strains) excluding Mus. mus castaneus and Mus. spretus and the corresponding SNP frequencies are also given. Sequences at the beginning and end of each contig were not included in the analysis, and thus the indicated contig lengths and number of tiled bases is different from that stated in the Methods section.

This Article

  1. Genome Res. 14: 1493-1500

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  1. January 2026, 36 (1)
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