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Prepare for public release on Gitea: simurgarray package names, community files, Gitea templates, pseudonymised P6 probe names
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kemal committed 2026-09-30 12:09:13 +01:00
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docs/validation/P6_gsa36_vs_gtc2vcf.json
+87 -86
View File
@@ -6,26 +6,26 @@
"probes_in_merged_records": 5000,
"probes_only_in_oracle": 22449,
"only_in_oracle_examples": [
"10:135332149_CNV_CYP2E1",
"10:135332539_CNV_CYP2E1",
"10:135332749_CNV_CYP2E1",
"10:135333169_CNV_CYP2E1",
"10:135333379_CNV_CYP2E1",
"10:135333589_CNV_CYP2E1",
"10:135333799_CNV_CYP2E1",
"10:135334009_CNV_CYP2E1",
"10:135334009_CNV_CYP2E1_ilmndup1",
"10:135334219_CNV_CYP2E1",
"10:135334429_CNV_CYP2E1",
"10:135334639_CNV_CYP2E1",
"10:135334849_CNV_CYP2E1",
"10:135335059_CNV_CYP2E1",
"10:135335569_CNV_CYP2E1",
"10:135335569_CNV_CYP2E1_ilmndup1",
"10:135335869_CNV_CYP2E1",
"10:135335869_CNV_CYP2E1_ilmndup1",
"10:135336079_CNV_CYP2E1",
"10:135336289_CNV_CYP2E1"
"locus_0001",
"locus_0002",
"locus_0003",
"locus_0004",
"locus_0005",
"locus_0006",
"locus_0007",
"locus_0008",
"locus_0009",
"locus_0010",
"locus_0011",
"locus_0012",
"locus_0013",
"locus_0014",
"locus_0015",
"locus_0016",
"locus_0017",
"locus_0018",
"locus_0019",
"locus_0020"
],
"categories": {
"grouping_differs": 6424,
@@ -39,7 +39,7 @@
"grouping_differs": [
[
"207895980019_R14C03",
"ilmnseq_rs2013249.2_F2BT",
"locus_0021",
[
"1",
"19287570",
@@ -57,7 +57,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs201615754.1_F2BT",
"locus_0022",
[
"1",
"97515784",
@@ -75,7 +75,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs201615754.2_F2BT",
"locus_0023",
[
"1",
"97515784",
@@ -93,7 +93,7 @@
],
[
"207895980019_R14C03",
"rs201615754",
"locus_0024",
[
"1",
"97515784",
@@ -111,7 +111,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs168107.1_ilmnrev_F2BT",
"locus_0025",
[
"1",
"108937356",
@@ -129,7 +129,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs168107.2_ilmnfwd_F2BT",
"locus_0026",
[
"1",
"108937356",
@@ -147,7 +147,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs168107.2_ilmnrev_F2BT",
"locus_0027",
[
"1",
"108937356",
@@ -165,7 +165,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs4648276.2_F2BT",
"locus_0028",
[
"1",
"186676356",
@@ -183,7 +183,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs4648276_ilmnfwd_F2BT",
"locus_0029",
[
"1",
"186676356",
@@ -201,7 +201,7 @@
],
[
"207895980019_R14C03",
"rs4648276",
"locus_0030",
[
"1",
"186676356",
@@ -219,7 +219,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs1819741.1_F2BT",
"locus_0031",
[
"1",
"192815708",
@@ -237,7 +237,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs2777511.1_ilmnfwd_F2BT",
"locus_0032",
[
"10",
"33785635",
@@ -255,7 +255,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs2777511.1_ilmnrev_F2BT",
"locus_0033",
[
"10",
"33785635",
@@ -273,7 +273,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs2777511.2_ilmnrev_F2BT",
"locus_0034",
[
"10",
"33785635",
@@ -291,7 +291,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs11819745.2_F2BT",
"locus_0035",
[
"10",
"37501484",
@@ -309,7 +309,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs7091672.2_F2BT",
"locus_0036",
[
"10",
"118836909",
@@ -327,7 +327,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs7091672.3_F2BT",
"locus_0037",
[
"10",
"118836909",
@@ -345,7 +345,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs7091672_ilmnfwd_F2BT",
"locus_0038",
[
"10",
"118836909",
@@ -363,7 +363,7 @@
],
[
"207895980019_R14C03",
"rs7091672",
"locus_0039",
[
"10",
"118836909",
@@ -381,7 +381,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs1219648.2_F2BT",
"locus_0040",
[
"10",
"121586676",
@@ -400,7 +400,7 @@
],
"representation_diff": [
[
"IlmnSeq_rs3215400",
"locus_0041",
[
"1",
"20589096",
@@ -415,7 +415,7 @@
]
],
[
"ilmnseq_rs3215400_ilmnrev",
"locus_0042",
[
"1",
"20589096",
@@ -430,7 +430,7 @@
]
],
[
"rs3215400",
"locus_0043",
[
"1",
"20589096",
@@ -445,7 +445,7 @@
]
],
[
"ilmnseq_rs61697860_ilmnfwd",
"locus_0044",
[
"1",
"78303099",
@@ -460,7 +460,7 @@
]
],
[
"ilmnseq_rs35219756_ilmnrev_F2BTindel",
"locus_0045",
[
"1",
"78392093",
@@ -475,7 +475,7 @@
]
],
[
"ilmnseq_rs35081652_ilmnfwd",
"locus_0046",
[
"1",
"78411336",
@@ -490,7 +490,7 @@
]
],
[
"IlmnSeq_rs72549303_IlmnFWD",
"locus_0047",
[
"1",
"97450065",
@@ -505,7 +505,7 @@
]
],
[
"IlmnSeq_rs72549303_IlmnREV",
"locus_0048",
[
"1",
"97450065",
@@ -520,7 +520,7 @@
]
],
[
"ilmnseq_rs72549303",
"locus_0049",
[
"1",
"97450065",
@@ -535,7 +535,7 @@
]
],
[
"ilmnseq_rs72549303_ilmndup1",
"locus_0050",
[
"1",
"97450065",
@@ -550,7 +550,7 @@
]
],
[
"ilmnseq_rs72549303_ilmnfwd_deg3a2b0",
"locus_0051",
[
"1",
"97450065",
@@ -565,7 +565,7 @@
]
],
[
"ilmnseq_rs72549303_ilmnrev_deg3a1b0",
"locus_0052",
[
"1",
"97450065",
@@ -580,7 +580,7 @@
]
],
[
"ilmnseq_rs1184321568",
"locus_0053",
[
"1",
"97593250",
@@ -595,7 +595,7 @@
]
],
[
"ilmnseq_rs1184321568_ilmnfwd",
"locus_0054",
[
"1",
"97593250",
@@ -610,7 +610,7 @@
]
],
[
"ilmnseq_rs1184321568_ilmnfwd_deg3a1b0",
"locus_0055",
[
"1",
"97593250",
@@ -625,7 +625,7 @@
]
],
[
"ilmnseq_rs1184321568_ilmnrev",
"locus_0056",
[
"1",
"97593250",
@@ -640,7 +640,7 @@
]
],
[
"ilmnseq_rs1184321568_ilmnrev_deg3a1b0",
"locus_0057",
[
"1",
"97593250",
@@ -655,7 +655,7 @@
]
],
[
"IlmnSeq_rs72549315_IlmnFWD",
"locus_0058",
[
"1",
"147208902",
@@ -670,7 +670,7 @@
]
],
[
"ilmnseq_rs72549315_ilmnfwd_ilmndup1",
"locus_0059",
[
"1",
"147208902",
@@ -685,7 +685,7 @@
]
],
[
"ilmnseq_rs72549315_ilmnfwd_ilmndup2",
"locus_0060",
[
"1",
"147208902",
@@ -703,7 +703,7 @@
"ours_missing_haploid_Y": [
[
"207895980019_R11C02",
"rs5018209",
"locus_0061",
[
"Y",
"19428214",
@@ -721,7 +721,7 @@
],
[
"207895980035_R10C01",
"rs186564287",
"locus_0062",
[
"Y",
"14081208",
@@ -739,7 +739,7 @@
],
[
"207895980019_R12C01",
"ilmnseq_rs538240449",
"locus_0063",
[
"Y",
"12030916",
@@ -757,7 +757,7 @@
],
[
"207895980019_R12C01",
"ilmnseq_rs537620655",
"locus_0064",
[
"Y",
"13331090",
@@ -775,7 +775,7 @@
],
[
"207895980035_R04C03",
"rs13304158",
"locus_0065",
[
"Y",
"9957467",
@@ -793,7 +793,7 @@
],
[
"207895980035_R04C03",
"exm1667692",
"locus_0066",
[
"Y",
"12816261",
@@ -811,7 +811,7 @@
],
[
"207895980019_R03C01",
"rs373082162",
"locus_0067",
[
"Y",
"19466559",
@@ -829,7 +829,7 @@
],
[
"207895980019_R04C01",
"rs4020596",
"locus_0068",
[
"Y",
"5680808",
@@ -847,7 +847,7 @@
],
[
"207895980019_R03C02",
"JHU_Y.14692226",
"locus_0069",
[
"Y",
"12580293",
@@ -867,7 +867,7 @@
"ours_missing_het_in_haploid": [
[
"207895980035_R13C03",
"rs5979572",
"locus_0070",
[
"X",
"7467632",
@@ -885,7 +885,7 @@
],
[
"207895980035_R13C03",
"rs7887088",
"locus_0071",
[
"X",
"7478861",
@@ -903,7 +903,7 @@
],
[
"207895980035_R13C03",
"rs146250304",
"locus_0072",
[
"X",
"68391913",
@@ -921,7 +921,7 @@
],
[
"207895980019_R06C01",
"rs138003892",
"locus_0073",
[
"X",
"33006670",
@@ -939,7 +939,7 @@
],
[
"207895980035_R09C03",
"rs28602676",
"locus_0074",
[
"MT",
"2690",
@@ -957,7 +957,7 @@
],
[
"207895980019_R15C02",
"rs1606778",
"locus_0075",
[
"X",
"79535086",
@@ -975,7 +975,7 @@
],
[
"207895980035_R14C01",
"rs104894858",
"locus_0076",
[
"X",
"120442599",
@@ -993,7 +993,7 @@
],
[
"207895980035_R03C03",
"JHU_X.22234615",
"locus_0077",
[
"X",
"22216499",
@@ -1011,7 +1011,7 @@
],
[
"207895980019_R09C03",
"rs9786566",
"locus_0078",
[
"Y",
"7044951",
@@ -1029,7 +1029,7 @@
],
[
"207895980035_R12C03",
"rs148519285",
"locus_0079",
[
"X",
"20830034",
@@ -1047,7 +1047,7 @@
],
[
"207895980035_R11C03",
"ilmnseq_rs111298280",
"locus_0080",
[
"X",
"91616889",
@@ -1065,7 +1065,7 @@
],
[
"207895980035_R11C03",
"ilmnseq_chrX:154532408_ilmnfwd_ilmndup3",
"locus_0081",
[
"X",
"154532408",
@@ -1083,7 +1083,7 @@
],
[
"207895980042_R15C02",
"ilmnseq_rs553518378",
"locus_0082",
[
"Y",
"15734824",
@@ -1101,7 +1101,7 @@
],
[
"207895980035_R05C03",
"rs12396137",
"locus_0083",
[
"X",
"7462384",
@@ -1119,7 +1119,7 @@
],
[
"207895980035_R05C03",
"rs4830772",
"locus_0084",
[
"X",
"7475195",
@@ -1137,7 +1137,7 @@
],
[
"207895980035_R05C03",
"rs146250304",
"locus_0072",
[
"X",
"68391913",
@@ -1155,5 +1155,6 @@
]
]
},
"unexplained": 0
"unexplained": 0,
"note": "Probe names from the vendor manifest are replaced by stable pseudonyms (locus_NNNN, shared by both oracle files); sample IDs, positions, alleles and all counts are unchanged."
}