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

Table 3 Summary of sequence variants identified in SR86

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

ISSN: 1471-2164