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Table 3 The number of SNPs and indels detected in each transcript-read pairing of 12 Ae. umbellulata accessions

From: RNA-seq analysis reveals considerable genetic diversity and provides genetic markers saturating all chromosomes in the diploid wild wheat relative Aegilops umbellulata

Transcript model Read total NR SNPs and indels
KU-
4017
KU-
4026
KU-
4035
KU-
4043
KU-
4052
KU-
4103
KU-
5934
KU-
5954
KU-
12,180
KU-
12,198
KU-
8–5
KU-
8–7
KU-   2925 16,611 11,171 12,091 5316 24,975 14,064 29,726 23,244 13,400 24,601 85,758
4017   77 524 348 381 169 854 401 869 648 443 846 3284
KU- 10,754   16,535 11,666 12,869 5428 19,463 11,889 23,915 17,452 11,478 20,185 63,233
4026 350   612 429 420 153 762 405 787 565 412 754 2645
KU- 9069 3639   11,969 13,141 5372 25,450 14,991 30,925 23,575 13,356 25,797 89,369
4035 274 94   426 423 167 889 387 901 651 396 847 3303
KU- 9748 2959 17,571   11,772 5325 24,871 15,017 30,191 22,942 13,557 26,117 85,656
4043 287 83 611   404 155 867 423 883 662 459 809 3398
KU- 10,355 3393 20,370 11,585   5172 25,332 14,713 30,020 23,340 14,824 26,197 88,716
4052 347 92 665 408   153 848 406 951 716 493 872 3525
KU- 11,611 3811 19,020 13,758 13,022   21,807 13,405 25,741 19,851 14,038 21,764 71,071
4103 348 99 672 462 429   827 417 786 605 474 732 2932
KU- 14,265 3465 25,574 16,432 16,766 6131   13,619 31,109 23,359 15,968 25,591 89,344
5934 443 97 854 582 527 187   385 932 663 540 855 3489
KU- 15,032 3585 28,423 18,003 18,391 6424 25,505   30,219 22,205 17,868 25,394 91,059
5954 433 89 909 572 560 174 859   942 650 563 872 3723
KU- 24,232 6057 44,751 27,569 29,176 9695 42,984 27,022   24,142 30,721 34,445 99,411
12,180 698 163 1389 901 896 296 1384 768   719 935 1140 4246
KU- 21,096 5282 40,683 24,658 25,784 9259 39,208 22,641 26,570   27,036 31,815 100,683
12,198 614 117 1311 777 805 246 1263 627 809   813 1022 4085
KU- 12,822 3444 23,775 15,520 16,626 5893 24,993 15,271 30,526 23,495   25,746 91,080
8–5 375 100 784 558 577 164 907 439 952 689   860 3635
KU- 17,577 5041 33,501 20,936 21,374 7235 32,035 18,925 30,559 24,589 21,646   94,187
8–7 530 128 1068 694 650 227 1057 557 924 716 670   3728
  1. Upper and lower numbers at each comparison indicate SNPs and indels, respectively. NR non-redundant