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Table 3 Summary of sequence variants identified in SR86

From: Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar – sea rice 86

Variation type Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9 Chr10 Chr11 Chr12
SNP 355,983 294,965 293,130 270,562 274,041 286,513 239,191 261,864 212,275 218,936 275,254 242,149
Ti/Tv 2.53 2.54 2.66 2.31 2.63 2.55 2.48 2.51 2.53 2.48 2.43 2.36
INDEL 18,270 15,194 14,895 12,741 13,111 14,261 12,475 12,831 10,956 11,113 13,305 12,228
Insertion 9356 7761 7496 6545 6698 7193 6502 6558 5649 5702 6911 6448
Deletion 8914 7433 7399 6196 6413 7068 5973 6273 5307 5411 6394 5780
Small insert 3 19 13 29 13 2 15 19 17 5 10 12
Large insert 23 84 15 11 16 79 11 37 22 52 18 139
Average insert 20 19 20 20 20 19 19 20 20 19 20 20
Small deletion 50 11 11 15 16 27 24 14 20 36 14 36
Large deletion 16 14 45 16 47 34 13 31 11 68 31 11
Average deletion 17 16 16 16 16 16 16 16 16 16 16 15
Structural variant 18 16 10 11 11 9 17 16 10 18 15 21
Structural insertion 5 5 0 3 5 2 3 6 4 4 8 10
Structural deletion 13 11 10 8 6 7 14 10 6 14 7 11
Multiple alterations 655 583 469 620 534 557 532 608 487 454 764 789
Total 424,146 349,943 347,169 318,172 320,667 336,769 282,385 307,495 248,844 257,257 322,081 285,209