Ancient rivers shaped the current genetic diversity of the wood mouse (Apodemus speciosus) on the islands of the Seto Inland Sea, Japan

Sato, Jun J.; Yasuda, Kouki

doi:10.1186/s40851-022-00193-3

Table 1 Samples and sequence reads examined in this study

From: Ancient rivers shaped the current genetic diversity of the wood mouse (Apodemus speciosus) on the islands of the Seto Inland Sea, Japan

Specimen code	Sampling locality	Collection data	Locality code^a	Reads^b	Filtered reads^c	Sequence^e
FACT11	Fukuyama University, East	2009.05.14	Fuk	610,605	464,378	3,192,959
FACT65	Fukuyama University, South	2011.05.18	Fuk	546,955	411,144	2,850,601
FACT68	Fukuyama University, West	2011.05.20	Fuk	523,769	394,501	2,610,847
FACT88	Fukuyama University, South	2011.07.27	Fuk	323,440	242,039	1,639,713
FACT89	Fukuyama University, South	2011.07.27	Fuk	403,307	302,261	2,204,778
FACT95	Fukuyama University, South	2011.10.04	Fuk	342,990	257,740	1,695,525
FACT96	Fukuyama University, South	2011.10.07	Fuk	173,663	131,241	950,228
FACT100	Fukuyama University, South	2011.11.01	Fuk	526,191	394,848	2,802,797
FACT120	Fukuyama University, South	2012.05.29	Fuk	460,987	349,220	2,208,359
FACT121	Fukuyama University, South	2012.05.29	Fuk	277,445	207,640	1,342,532
FACT134	Fukuyama University, South	2012.07.06	Fuk	582,717	437,018	3,029,354
FACT155	Fukuyama University, Central	2012.11.16	Fuk	408,609	304,913	2,031,635
YT2005-1-Ap1	Kurihara, Onomichi	2005.03.05	Ono	386,249	299,551	1,025,703
YT2005-1-Ap2	Kurihara, Onomichi	2005.03.05	Ono	1,145,627	882,220	4,580,390
YT2005-1-Ap4	Kurihara, Onomichi	2005.03.05	Ono	813,412	615,202	3,756,417
KKE2019-5^d	Kawajiri, Kure	2019.03.16	Kre	184,484	138,460	936,406
KKE2019-6^d	Kawajiri, Kure	2019.03.16	Kre	369,578	278,630	2,136,055
KKE2019-8^d	Kawajiri, Kure	2019.03.16	Kre	417,047	313,603	2,463,980
KKE2019-11^d	Kawajiri, Kure	2019.03.16	Kre	344,682	259,770	1,988,195
FACT110	Mukaishima 1	2012.03.19	Muk	443,391	330,374	2,213,708
FACT111	Mukaishima 1	2012.03.19	Muk	530,764	392,925	2,691,564
YT2004-Ap1	Mukaishima 3	2004.01.28	Muk	802,243	617,739	2,983,375
YT2004-Ap17	Mukaishima 3	2004.01.29	Muk	925,945	720,928	4,019,596
YT2004-Ap18	Mukaishima 3	2004.01.29	Muk	648,414	491,681	3,214,390
FACT24	Innnoshima 1	2009.08.25	Inn	601,395	447,827	3,297,068
FACT157	Innnoshima 1	2013.03.30	Inn	682,230	512,792	3,581,029
FACT158	Innnoshima 2	2013.03.30	Inn	444,213	329,269	2,423,674
YT2004-Ap2	Innnoshima 3	2004.01.28	Inn	590,038	448,767	3,062,029
YT2004-Ap9	Innnoshima 4	2004.01.28	Inn	340,931	259,071	1,751,508
FACT159	Ikuchijima 1	2013.04.23	Iku	337,184	253,724	1,838,443
FACT164	Ikuchijima 2	2013.04.30	Iku	365,148	273,741	2,018,363
FACT165	Ikuchijima 2	2013.04.30	Iku	296,847	222,520	1,689,762
FACT173	Ikuchijima 3	2013.05.07	Iku	407,486	308,867	2,325,840
FACT174	Ikuchijima 3	2013.05.07	Iku	890,895	680,129	3,855,503
FACT188	Ohmishima 1	2014.03.28	Ohm	609,670	459,241	3,148,761
FACT190	Ohmishima 2	2014.03.28	Ohm	542,077	406,988	3,022,620
FACT192	Ohmishima 3	2014.03.28	Ohm	428,164	320,154	2,521,039
FACT194	Ohmishima 3	2014.03.28	Ohm	347,202	260,088	2,111,406
YT2005-Ap43	Ohmishima 5	2005.12.16	Ohm	519,501	394,926	2,938,063
FACT203	Hakatajima 1	2014.04.19	Hak	431,393	321,996	2,471,386
FACT210	Hakatajima 3	2014.04.26	Hak	234,729	175,184	1,361,140
FACT215	Hakatajima 4	2014.05.01	Hak	362,459	273,737	2,207,141
FACT216	Hakatajima 4	2014.05.01	Hak	479,212	361,246	2,603,294
FACT217	Hakatajima 4	2014.05.01	Hak	540,473	409,670	3,039,106
FACT218	Ohshima 1	2014.05.17	Ohs	478,380	358,778	2,645,564
FACT228	Ohshima 1	2014.05.17	Ohs	351,081	262,959	2,070,297
FACT230	Ohshima 2	2014.05.17	Ohs	907,618	702,505	4,182,623
FACT231	Ohshima 2	2014.05.17	Ohs	343,885	258,180	2,060,732
YT2004-Ap65	Ohshima 3	2004.01.31	Ohs	824,801	624,690	3,319,858
YT2006-Ap12	Ohsakikamijima 1	2006.12.21	Osk	809,828	613,162	3,881,513
YT2006-Apo13	Ohsakikamijima 1	2006.12.21	Osk	638,800	493,364	3,340,137
YT2006-Apo14	Ohsakikamijima 1	2006.12.21	Osk	513,099	391,261	2,772,793
YT2006-Ap15	Ohsakikamijima 2	2006.12.21	Osk	624,672	482,994	3,389,840
YT2006-Apo16	Ohsakikamijima 2	2006.12.21	Osk	703,884	544,903	3,536,874
FACT296	Ohsakishimojima 1	2015.05.16	Oss	674,877	501,386	3,412,139
FACT298	Ohsakishimojima 1	2015.05.16	Oss	869,970	669,627	4,298,248
FACT299	Ohsakishimojima 1	2015.05.16	Oss	1,057,143	813,733	4,723,477
FACT337	Ohsakishimojima 2	2015.05.30	Oss	375,107	282,977	2,012,430
FACT338	Ohsakishimojima 2	2015.05.30	Oss	1,141,604	875,120	4,768,518
FACT301	Kamikamagarijima 1	2015.05.16	Kk	487,512	368,339	2,829,217
FACT304	Kamikamagarijima 1	2015.05.16	Kk	349,187	261,167	2,047,916
FACT347	Kamikamagarijima 2	2015.05.30	Kk	1,582,305	1,197,292	5,774,382
FACT348	Kamikamagarijima 2	2015.05.30	Kk	528,843	398,074	3,028,705
YT2006-Apo51	Kamikamagarijima 3	2006.12.23	Kk	850,356	654,643	3,181,260
FACT309	Shimokamagarijima 1	2015.05.16	Sk	562,118	424,020	3,035,563
FACT310	Shimokamagarijima 1	2015.05.16	Sk	652,773	498,554	3,406,747
FACT352	Shimokamagarijima 2	2015.05.30	Sk	528,294	398,328	3,002,296
FACT353	Shimokamagarijima 2	2015.05.30	Sk	630,449	475,138	3,241,963
YT2006-Ap91	Shimokamagarijima 3	2006.12.24	Sk	819,549	628,697	3,279,102
KKE2019-2^d	Kurahashijima 1	2019.03.16	Kra	412,653	308,736	2,401,222
KKE2019-15^d	Kurahashijima 1	2019.06.01	Kra	241,634	182,177	1,443,335
KKE2019-16^d	Kurahashijima 1	2019.06.01	Kra	272,576	205,352	1,588,854
KKE2019-17^d	Kurahashijima 1	2019.06.01	Kra	297,317	223,525	1,803,011
KKE2019-1^d	Etajima 1	2019.03.16	Eta	480,989	359,975	2,815,332
KKE2019-25^d	Etajima 1	2019.06.01	Eta	231,987	173,884	1,349,540
KKE2019-20^d	Etajima 2	2019.06.01	Eta	277,509	205,728	1,658,799
KKE2019-21^d	Etajima 2	2019.06.01	Eta	340,125	252,617	2,065,899
FACT265	Tamagawa, Imabari	2014.10.08	Ima	277,880	211,743	1,326,597
FACT266	Tamagawa, Imabari	2015.02.27	Ima	290,853	216,641	2,278,718
FACT268	Tamagawa, Imabari	2015.02.27	Ima	452,811	342,996	2,334,059
FACT269	Tamagawa, Imabari	2015.02.27	Ima	564,866	425,470	2,997,828
FACT270	Tamagawa, Imabari	2015.02.27	Ima	287,971	213,685	1,489,619
FACT271	Tamagawa, Imabari	2015.02.27	Ima	369,675	275,842	2,186,221
FACT273	Tamagawa, Imabari	2015.02.27	Ima	524,129	392,358	2,900,232
FACT276	Tamagawa, Imabari	2015.02.27	Ima	367,933	276,014	2,059,745
FACT284	Tamagawa, Imabari	2015.02.27	Ima	757,705	570,727	3,777,165
HS53	Saga, Kurose, Kochi	1984.11.12	Koc	288,082	215,310	1,512,866
HS310	Mt. Tsurugi, Tokushima	unknown	Tsu	545,818	409,244	2,996,747
HS2222	Mt. Tsurugi, Tokushima	unknown	Tsu	468,929	348,670	2,616,918
HS2223	Mt. Tsurugi, Tokushima	unknown	Tsu	938,752	700,751	4,372,891
HS2797	Mt. Tsurugi, Tokushima	unknown	Tsu	809,282	609,439	3,825,308
HS2798	Mt. Tsurugi, Tokushima	unknown	Tsu	430,746	323,737	2,447,166

^aThe locality codes are consistent with those in Fig. 1
^bTotal reads obtained from NGS
^cFiltered reads with more than Q30 quality and with length more than100 bp
^dSamples newly obtained in this study
^eSequences examined in STACKS for each sample (base pair)

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