Whole-genome sequencing of Puccinia striiformis f. sp. tritici mutant isolates identifies avirulence gene candidates

Table 2 Numbers of deleterious SNPs, Indels and corresponded genes in mutant isolates of Puccinia striiformis f. sp. tritici detected from the primary scaffolds of isolate 11–281

Mutant Isolate	Deleterious SNPs^a	Deleterious SNPs on genes^b	Deleterious Indels^c	Deleterious indels on genes	Deleterious SNPs and Indels on genes
M11-Yr36–1	1821	682	217	121	716
M11-Yr21	1820	664	254	123	698
M11-YrTr1	1612	641	271	125	682
M11-Yr24–1	1722	650	201	106	678
M11-Yr9–2	1695	651	218	117	688
M11-Yr17	1528	609	164	92	640
M11-Yr39	1371	544	120	77	582
M11-Yr10	1280	492	120	85	522
M11-YrA+	1273	509	128	76	537
M11-Yr9–1	1295	501	144	74	529
M11-Fielder	1317	503	176	91	532
M11-Yr6	1280	499	170	95	532
M11-Yr9–4	1134	491	152	98	543
M11-Yr1–2	1132	505	173	109	566
M11-Yr1–3	972	426	163	101	482
M11-YrSP-1	988	425	192	115	486
M11-Yr2–1	981	426	202	114	491
M11-Yr76–2	970	423	198	114	488
M11-YrExp2	965	424	190	120	492
M11-Yr2–2	971	421	187	111	484
M11-Paha	943	416	189	113	480
M11-Yr36–2	952	419	216	121	490
M11-YrSP-2	960	421	171	105	483
M11-Yr76–1	844	323	112	69	357
M11-Yr76–3	838	318	109	64	349
M11-Yr43	391	217	93	56	247
M11-Yr44	142	81	78	36	100
M11-Yr1–1	151	77	58	31	99
M11-Yr8	133	66	40	28	83
M11-Yr31	133	72	54	32	88
Total^d	4217	1042	1122	412	1135

^aAssociated deleterious SNPs were selected based on the types of variants annotated using the SnpEff program. SNPs with moderate and high effects were considered as deleterious SNPs
^bAssociated genes were deduced from the annotated file generated using the SnpEff program. Multiple SNPs can occur in one gene
^cAssociated deleterious indels were selected based on the types of variants annotated using the SnpEff program. Indels with moderate and high effects were considered as deleterious Indels
^dSNPs, Indels and genes can be shared in different mutant isolates, so the total number is not equal to summation of individuals

ISSN: 1471-2164