id stringlengths 21 21 | kind stringclasses 3
values | options listlengths 2 6 | target listlengths 2 6 | state stringlengths 161 241 | question stringclasses 7
values | domain stringclasses 1
value | family stringclasses 1
value | source stringclasses 1
value |
|---|---|---|---|---|---|---|---|---|
v3_751375abffebb75f_n | noul | [
"false",
"true"
] | [
0.6,
0.4
] | A rna-seq read set contains a stop codon mid-open-reading-frame; additionally has a consensus quality of Q20. Context: at 30x mean depth, under an active deadline. Reported by the review queue. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_9fffb325e1dca1c7_n | noul | [
"false",
"true"
] | [
0.73,
0.27
] | An amplicon sequence maps to two loci with equal coverage; additionally contains the known pseudo-gene region. Context: at 30x mean depth, during an external partner integration. Reported by the supervisor. | Is this scenario one where: the sequence supports the expected amplicon? | sequence_analysis | genomics | yuri_v3 |
v3_5a1a074e2b7a2c5e_n | noul | [
"false",
"true"
] | [
0.79,
0.21
] | An amplicon sequence has a 4bp insertion in the coding sequence; additionally reveals a premature poly-A signal. Context: with the long-read platform, under reduced staffing. Reported by the review queue. | Is this scenario one where: the sequence supports the expected amplicon? | sequence_analysis | genomics | yuri_v3 |
v3_fbf9b87f7247f2d1_c | choice | [
"valid",
"ambiguous",
"artifact",
"contaminated"
] | [
0.17,
0.28,
0.53,
0.02
] | An amplicon sequence shows strand bias at 4:1; additionally shows even coverage at 500x. Context: at 30x mean depth, immediately after go-live. Reported by the review queue. | Sequence verdict for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_62dc10ea7331352d_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.08,
0.27,
0.53,
0.1,
0.01
] | A rna-seq read set contains the known pseudo-gene region; additionally has a consensus quality of Q20. Context: against the latest reference, mid-incident. Reported by the on-call engineer. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_151e6db9210086a7_c | choice | [
"valid",
"ambiguous",
"artifact",
"contaminated"
] | [
0.1,
0.26,
0.61,
0.03
] | A rna-seq read set shows strand bias at 4:1; additionally contains the known pseudo-gene region. Context: at 30x mean depth, during normal operations. Reported by the review queue. | Sequence verdict for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_e6bcc1bf37f2da28_c | choice | [
"SNV",
"insertion",
"deletion",
"structural"
] | [
0,
0.9,
0,
0.1
] | A rna-seq read set maps to two loci with equal coverage; additionally has a 4bp insertion in the coding sequence. Context: against the latest reference, during a scheduled maintenance window. Reported by the operator. | Variant type for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_9207703ac918f00c_n | noul | [
"false",
"true"
] | [
0.62,
0.38
] | A contig assembly matches the expected amplicon size; additionally has a 4bp insertion in the coding sequence. Context: with the long-read platform, during normal operations. Reported by the review queue. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_e36af2ae959a202e_n | noul | [
"false",
"true"
] | [
0.57,
0.43
] | A contig assembly matches the expected amplicon size; additionally reveals a premature poly-A signal. Context: in the variant-calling pipeline, shortly after a software update. Reported by the on-call engineer. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_bfc02b582c93b066_c | choice | [
"SNV",
"insertion",
"deletion",
"structural"
] | [
0.85,
0.06,
0.05,
0.04
] | An amplicon sequence contains a stop codon mid-open-reading-frame; additionally shows 99.8% identity across the target region. Context: with the long-read platform, while on-call rotation changed. Reported by the review queue. | Variant type for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_47283396bbddcadb_n | noul | [
"false",
"true"
] | [
0.41,
0.59
] | A rna-seq read set reveals a premature poly-A signal; additionally shows even coverage at 500x. Context: in the variant-calling pipeline, as part of a compliance sweep. Reported by the monitoring system. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_9f41b3271de23d08_c | choice | [
"valid",
"ambiguous",
"artifact",
"contaminated"
] | [
0.9394,
0.0505,
0.0101,
0
] | An amplicon sequence has a consensus quality of Q20; additionally matches the expected amplicon size. Context: at 30x mean depth, during normal operations. Reported by the monitoring system. | Sequence verdict for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_94fd1cbdb1b4411f_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.03,
0.29,
0.61,
0.07,
0
] | An alignment result shows 99.8% identity across the target region; additionally maps to two loci with equal coverage. Context: in the variant-calling pipeline, while legacy systems are still active. Reported by the on-call engineer. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_b26e75b079c85242_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.02,
0.12,
0.42,
0.37,
0.06,
0.01
] | An amplicon sequence shows even coverage at 500x; additionally has a 4bp insertion in the coding sequence. Context: with the long-read platform, during the morning shift. Reported by the supervisor. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_6be377e727bfacd9_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.07,
0.35,
0.23,
0.28,
0.05,
0.02
] | A contig assembly shows even coverage at 500x; additionally contains the known pseudo-gene region. Context: with the long-read platform, while legacy systems are still active. Reported by the on-call engineer. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_bbf28e4a2b91225b_n | noul | [
"false",
"true"
] | [
0.15,
0.85
] | A contig assembly has a 4bp insertion in the coding sequence; additionally matches the expected amplicon size. Context: with the long-read platform, during the holiday freeze. Reported by the automated check. | Is this scenario one where: the sequence supports the expected amplicon? | sequence_analysis | genomics | yuri_v3 |
v3_aeb3f7e97173b00b_n | noul | [
"false",
"true"
] | [
0.59,
0.41
] | An amplicon sequence shows 99.8% identity across the target region; additionally contains a stop codon mid-open-reading-frame. Context: in the variant-calling pipeline, as part of a compliance sweep. Reported by the on-call engineer. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_18b66fc5d0156706_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.02,
0.06,
0.37,
0.5,
0.05,
0
] | An alignment result shows 99.8% identity across the target region; additionally maps to two loci with equal coverage. Context: in the variant-calling pipeline, during the morning shift. Reported by the monitoring system. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_ea869e4ee6c8cd06_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.07,
0.42,
0.42,
0.07,
0.01
] | An amplicon sequence has a 4bp insertion in the coding sequence; additionally matches the expected amplicon size. Context: with the long-read platform, mid-incident. Reported by the on-call engineer. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_280f4a3e51dbf4f7_n | noul | [
"false",
"true"
] | [
0.61,
0.39
] | A rna-seq read set contains a stop codon mid-open-reading-frame; additionally shows strand bias at 4:1. Context: at 30x mean depth, following a recent audit. Reported by the automated check. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_3b9d285cff738a39_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0,
0.02,
0.49,
0.46,
0.02
] | An alignment result has a 4bp insertion in the coding sequence; additionally reveals a premature poly-A signal. Context: with the long-read platform, while legacy systems are still active. Reported by the supervisor. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_76bc1d5a70812323_c | choice | [
"SNV",
"insertion",
"deletion",
"structural"
] | [
0.42,
0.08,
0.15,
0.35
] | A contig assembly reveals a premature poly-A signal; additionally shows 99.8% identity across the target region. Context: in the variant-calling pipeline, during the system migration. Reported by the operator. | Variant type for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_135c491edd05a8cb_c | choice | [
"SNV",
"insertion",
"deletion",
"structural"
] | [
0.13,
0,
0,
0.87
] | An alignment result maps to two loci with equal coverage; additionally shows 99.8% identity across the target region. Context: at 30x mean depth, during the holiday freeze. Reported by the on-call engineer. | Variant type for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_cf0f4f9904f391f7_n | noul | [
"false",
"true"
] | [
0.77,
0.23
] | A contig assembly matches the expected amplicon size; additionally has a consensus quality of Q20. Context: at 30x mean depth, during an external partner integration. Reported by the operator. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_bc6ee2952b5ff2d9_n | noul | [
"false",
"true"
] | [
0.66,
0.34
] | An amplicon sequence shows 99.8% identity across the target region; additionally shows strand bias at 4:1. Context: against the latest reference, with staffing at reduced levels. Reported by the monitoring system. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_ce928d6f32328150_n | noul | [
"false",
"true"
] | [
0.84,
0.16
] | An alignment result contains a stop codon mid-open-reading-frame; additionally shows strand bias at 4:1. Context: at 30x mean depth, during an external partner integration. Reported by the on-call engineer. | Is this scenario one where: the sequence supports the expected amplicon? | sequence_analysis | genomics | yuri_v3 |
v3_5dd0d6dccfaca477_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.05,
0.27,
0.47,
0.18,
0.03
] | A contig assembly reveals a premature poly-A signal; additionally shows 99.8% identity across the target region. Context: in the variant-calling pipeline, during an external partner integration. Reported by the automated check. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_f225a60377c8c3e1_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.0202,
0.3333,
0.4646,
0.1717,
0.0101
] | A rna-seq read set shows 99.8% identity across the target region; additionally reveals a premature poly-A signal. Context: in the variant-calling pipeline, under reduced staffing. Reported by the operator. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_ec8dd71585f6e78b_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.09,
0.34,
0.48,
0.08,
0.01
] | A contig assembly shows 99.8% identity across the target region; additionally has a 4bp insertion in the coding sequence. Context: at 30x mean depth, while on-call rotation changed. Reported by the operator. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_3a76c3bef8ba2687_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.02,
0.08,
0.29,
0.49,
0.11,
0.01
] | An amplicon sequence contains the known pseudo-gene region; additionally shows even coverage at 500x. Context: with the long-read platform, under reduced staffing. Reported by the on-call engineer. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_c94d0bc9ba8eb778_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.11,
0.14,
0.27,
0.34,
0.11,
0.03
] | A rna-seq read set reveals a premature poly-A signal; additionally shows even coverage at 500x. Context: at 30x mean depth, during the morning shift. Reported by the supervisor. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_f0efad800c0668a3_c | choice | [
"SNV",
"insertion",
"deletion",
"structural"
] | [
0.87,
0.05,
0.04,
0.04
] | A rna-seq read set shows even coverage at 500x; additionally contains a stop codon mid-open-reading-frame. Context: in the variant-calling pipeline, during the quarterly review. Reported by the supervisor. | Variant type for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_d4d63246e944dd42_n | noul | [
"false",
"true"
] | [
0.53,
0.47
] | An alignment result contains a stop codon mid-open-reading-frame; additionally contains the known pseudo-gene region. Context: in the variant-calling pipeline, during the quarterly review. Reported by the operator. | Is this scenario one where: re-sequencing is needed? | sequence_analysis | genomics | yuri_v3 |
v3_d9c85f1d5b83ba4e_n | noul | [
"false",
"true"
] | [
0.77,
0.23
] | An alignment result shows 99.8% identity across the target region; additionally has a consensus quality of Q20. Context: with the long-read platform, with a new vendor onboarded. Reported by the operator. | Is this scenario one where: re-sequencing is needed? | sequence_analysis | genomics | yuri_v3 |
v3_a21f9da6c534789a_n | noul | [
"false",
"true"
] | [
0.37,
0.63
] | An alignment result matches the expected amplicon size; additionally contains a stop codon mid-open-reading-frame. Context: at 30x mean depth, as part of a compliance sweep. Reported by the review queue. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_1759aad9ec903c0d_c | choice | [
"valid",
"ambiguous",
"artifact",
"contaminated"
] | [
0.55,
0.17,
0.22,
0.06
] | An amplicon sequence matches the expected amplicon size; additionally contains the known pseudo-gene region. Context: with the long-read platform, during the morning shift. Reported by the review queue. | Sequence verdict for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_9c5a222ffe80a1fd_n | noul | [
"false",
"true"
] | [
0.46,
0.54
] | An amplicon sequence shows 99.8% identity across the target region; additionally has a 4bp insertion in the coding sequence. Context: at 30x mean depth, under an active deadline. Reported by the operator. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_dc3b07b823e5980c_n | noul | [
"false",
"true"
] | [
0.71,
0.29
] | An alignment result has a consensus quality of Q20; additionally shows 99.8% identity across the target region. Context: in the variant-calling pipeline, immediately after go-live. Reported by the operator. | Is this scenario one where: re-sequencing is needed? | sequence_analysis | genomics | yuri_v3 |
v3_ffadcbfe8c732750_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.04,
0.23,
0.66,
0.07,
0
] | An amplicon sequence maps to two loci with equal coverage; additionally shows 99.8% identity across the target region. Context: against the latest reference, during the quarterly review. Reported by the supervisor. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_faa1ee7006d2b45a_n | noul | [
"false",
"true"
] | [
0.73,
0.27
] | An amplicon sequence contains the known pseudo-gene region; additionally reveals a premature poly-A signal. Context: in the variant-calling pipeline, shortly after a software update. Reported by the supervisor. | Is this scenario one where: the sequence supports the expected amplicon? | sequence_analysis | genomics | yuri_v3 |
v3_f8650c289b39bcc5_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.03,
0.33,
0.5,
0.12,
0.01
] | A rna-seq read set shows strand bias at 4:1; additionally shows even coverage at 500x. Context: with the long-read platform, during an external partner integration. Reported by the supervisor. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_91297a80393e2bdb_n | noul | [
"false",
"true"
] | [
0.47,
0.53
] | A contig assembly shows 99.8% identity across the target region; additionally has a 4bp insertion in the coding sequence. Context: against the latest reference, with staffing at reduced levels. Reported by the operator. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_cb28310779a62494_c | choice | [
"valid",
"ambiguous",
"artifact",
"contaminated"
] | [
0.01,
0.36,
0.34,
0.29
] | A contig assembly shows strand bias at 4:1; additionally maps to two loci with equal coverage. Context: against the latest reference, during normal operations. Reported by the supervisor. | Sequence verdict for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_dd093e043461db7a_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.19,
0.41,
0.34,
0.04,
0.01
] | An alignment result shows even coverage at 500x; additionally contains the known pseudo-gene region. Context: against the latest reference, during the system migration. Reported by the review queue. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_d52cd5850657c200_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.06,
0.03,
0.05,
0.68,
0.17,
0.01
] | An amplicon sequence reveals a premature poly-A signal; additionally has a 4bp insertion in the coding sequence. Context: at 30x mean depth, during normal operations. Reported by the supervisor. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_ea87bf9bda2b0eb2_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.05,
0.35,
0.54,
0.06,
0
] | An alignment result maps to two loci with equal coverage; additionally shows even coverage at 500x. Context: against the latest reference, during an external partner integration. Reported by the operator. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_c01ae9929cd66e7d_c | choice | [
"valid",
"ambiguous",
"artifact",
"contaminated"
] | [
0,
0.16,
0.82,
0.02
] | A contig assembly shows strand bias at 4:1; additionally contains a stop codon mid-open-reading-frame. Context: with the long-read platform, with a new vendor onboarded. Reported by the review queue. | Sequence verdict for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_c84f0da022194a63_n | noul | [
"false",
"true"
] | [
0.42,
0.58
] | An alignment result shows strand bias at 4:1; additionally has a 4bp insertion in the coding sequence. Context: against the latest reference, during an external partner integration. Reported by the automated check. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_0c19201691460115_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.04,
0.23,
0.16,
0.34,
0.16,
0.07
] | A contig assembly shows even coverage at 500x; additionally shows 99.8% identity across the target region. Context: in the variant-calling pipeline, shortly after a software update. Reported by the operator. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_2b67c7c94a1f9b38_n | noul | [
"false",
"true"
] | [
0.6,
0.4
] | A rna-seq read set shows even coverage at 500x; additionally contains a stop codon mid-open-reading-frame. Context: in the variant-calling pipeline, following a recent audit. Reported by the review queue. | Is this scenario one where: re-sequencing is needed? | sequence_analysis | genomics | yuri_v3 |
v3_4b2bf5613242a720_n | noul | [
"false",
"true"
] | [
0.38,
0.62
] | An amplicon sequence shows even coverage at 500x; additionally has a 4bp insertion in the coding sequence. Context: in the variant-calling pipeline, under an active deadline. Reported by the review queue. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_22c092c4f6211805_n | noul | [
"false",
"true"
] | [
0.68,
0.32
] | A contig assembly has a 4bp insertion in the coding sequence; additionally has a consensus quality of Q20. Context: with the long-read platform, under an active deadline. Reported by the monitoring system. | Is this scenario one where: the sequence supports the expected amplicon? | sequence_analysis | genomics | yuri_v3 |
v3_53141b060b2738f5_n | noul | [
"false",
"true"
] | [
0.39,
0.61
] | A rna-seq read set shows even coverage at 500x; additionally has a 4bp insertion in the coding sequence. Context: at 30x mean depth, mid-incident. Reported by the on-call engineer. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_4d773f30318e7176_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.01,
0.18,
0.32,
0.44,
0.05
] | An alignment result contains a stop codon mid-open-reading-frame; additionally shows 99.8% identity across the target region. Context: in the variant-calling pipeline, following a recent audit. Reported by the on-call engineer. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_e17f0dcb8d2b694c_n | noul | [
"false",
"true"
] | [
0.81,
0.19
] | A rna-seq read set has a 4bp insertion in the coding sequence; additionally contains a stop codon mid-open-reading-frame. Context: at 30x mean depth, mid-incident. Reported by the operator. | Is this scenario one where: the sequence supports the expected amplicon? | sequence_analysis | genomics | yuri_v3 |
v3_57a84c6c5a76e1c5_c | choice | [
"SNV",
"insertion",
"deletion",
"structural"
] | [
0.96,
0,
0,
0.04
] | A rna-seq read set shows strand bias at 4:1; additionally shows 99.8% identity across the target region. Context: in the variant-calling pipeline, following a recent audit. Reported by the supervisor. | Variant type for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_7024d7e4423790ff_c | choice | [
"SNV",
"insertion",
"deletion",
"structural"
] | [
0.2,
0.28,
0.12,
0.4
] | A contig assembly contains a stop codon mid-open-reading-frame; additionally has a consensus quality of Q20. Context: against the latest reference, during the morning shift. Reported by the review queue. | Variant type for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_52295b7d824100ef_c | choice | [
"valid",
"ambiguous",
"artifact",
"contaminated"
] | [
0.1,
0.36,
0.51,
0.03
] | An alignment result shows strand bias at 4:1; additionally shows 99.8% identity across the target region. Context: in the variant-calling pipeline, during the quarterly review. Reported by the supervisor. | Sequence verdict for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_01bc3f67e44e04ca_n | noul | [
"false",
"true"
] | [
0.53,
0.47
] | An alignment result reveals a premature poly-A signal; additionally maps to two loci with equal coverage. Context: at 30x mean depth, during an external partner integration. Reported by the operator. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_4a40cdc3cff8c49d_n | noul | [
"false",
"true"
] | [
0.78,
0.22
] | A contig assembly shows even coverage at 500x; additionally has a consensus quality of Q20. Context: with the long-read platform, with staffing at reduced levels. Reported by the automated check. | Is this scenario one where: re-sequencing is needed? | sequence_analysis | genomics | yuri_v3 |
v3_78fd84bdfba01373_n | noul | [
"false",
"true"
] | [
0.74,
0.26
] | An alignment result matches the expected amplicon size; additionally contains the known pseudo-gene region. Context: in the variant-calling pipeline, following a recent audit. Reported by the monitoring system. | Is this scenario one where: re-sequencing is needed? | sequence_analysis | genomics | yuri_v3 |
v3_8d67101df6881f9b_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.01,
0.05,
0.57,
0.35,
0.01
] | An alignment result contains a stop codon mid-open-reading-frame; additionally contains the known pseudo-gene region. Context: with the long-read platform, during peak load. Reported by the automated check. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_1c8e5a7fa5af4306_c | choice | [
"SNV",
"insertion",
"deletion",
"structural"
] | [
0.47,
0.01,
0.02,
0.5
] | A rna-seq read set shows strand bias at 4:1; additionally shows even coverage at 500x. Context: with the long-read platform, during the holiday freeze. Reported by the monitoring system. | Variant type for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_eb60b93df2d635b8_n | noul | [
"false",
"true"
] | [
0.68,
0.32
] | A contig assembly maps to two loci with equal coverage; additionally contains a stop codon mid-open-reading-frame. Context: with the long-read platform, during an external partner integration. Reported by the monitoring system. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_e9bfb50eca52c563_n | noul | [
"false",
"true"
] | [
0.4,
0.6
] | An amplicon sequence matches the expected amplicon size; additionally shows strand bias at 4:1. Context: against the latest reference, following a recent audit. Reported by the supervisor. | Is this scenario one where: re-sequencing is needed? | sequence_analysis | genomics | yuri_v3 |
v3_c60516c0bbfc131c_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.05,
0.23,
0.57,
0.14,
0
] | An alignment result contains the known pseudo-gene region; additionally has a 4bp insertion in the coding sequence. Context: against the latest reference, under an active deadline. Reported by the operator. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_fab8ec8be780b17c_n | noul | [
"false",
"true"
] | [
0.55,
0.45
] | A rna-seq read set matches the expected amplicon size; additionally has a 4bp insertion in the coding sequence. Context: in the variant-calling pipeline, with a new vendor onboarded. Reported by the monitoring system. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_0b701abe8fdc2fb6_c | choice | [
"SNV",
"insertion",
"deletion",
"structural"
] | [
0.17,
0.06,
0.03,
0.74
] | An alignment result contains a stop codon mid-open-reading-frame; additionally maps to two loci with equal coverage. Context: in the variant-calling pipeline, during the morning shift. Reported by the review queue. | Variant type for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_ea32604f9696454d_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.13,
0.52,
0.08,
0.17,
0.04,
0.06
] | An amplicon sequence matches the expected amplicon size; additionally shows 99.8% identity across the target region. Context: against the latest reference, during the morning shift. Reported by the review queue. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_52295b7d824100ef_n | noul | [
"false",
"true"
] | [
0.25,
0.75
] | An alignment result shows strand bias at 4:1; additionally shows 99.8% identity across the target region. Context: in the variant-calling pipeline, during the quarterly review. Reported by the supervisor. | Is this scenario one where: the sequence supports the expected amplicon? | sequence_analysis | genomics | yuri_v3 |
v3_c3ddaa76bc995aa1_n | noul | [
"false",
"true"
] | [
0.28,
0.72
] | An alignment result shows 99.8% identity across the target region; additionally contains the known pseudo-gene region. Context: with the long-read platform, at the end of the fiscal period. Reported by the on-call engineer. | Is this scenario one where: the sequence supports the expected amplicon? | sequence_analysis | genomics | yuri_v3 |
v3_3fded6adc7fa22ce_n | noul | [
"false",
"true"
] | [
0.78,
0.22
] | An alignment result maps to two loci with equal coverage; additionally contains a stop codon mid-open-reading-frame. Context: in the variant-calling pipeline, as part of a compliance sweep. Reported by the on-call engineer. | Is this scenario one where: the sequence supports the expected amplicon? | sequence_analysis | genomics | yuri_v3 |
v3_2c05d83607a50195_c | choice | [
"valid",
"ambiguous",
"artifact",
"contaminated"
] | [
0.01,
0.7,
0.25,
0.04
] | A rna-seq read set maps to two loci with equal coverage; additionally shows strand bias at 4:1. Context: against the latest reference, under an active deadline. Reported by the automated check. | Sequence verdict for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_8822d6627cf9d10f_n | noul | [
"false",
"true"
] | [
0.42,
0.58
] | A contig assembly contains the known pseudo-gene region; additionally reveals a premature poly-A signal. Context: at 30x mean depth, during the quarterly review. Reported by the automated check. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_0c0859d3cd7cac55_c | choice | [
"SNV",
"insertion",
"deletion",
"structural"
] | [
0.03,
0,
0,
0.97
] | An alignment result matches the expected amplicon size; additionally maps to two loci with equal coverage. Context: in the variant-calling pipeline, while legacy systems are still active. Reported by the supervisor. | Variant type for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_afa01b5290479999_n | noul | [
"false",
"true"
] | [
0.78,
0.22
] | A rna-seq read set shows even coverage at 500x; additionally contains a stop codon mid-open-reading-frame. Context: against the latest reference, under an active deadline. Reported by the automated check. | Is this scenario one where: the sequence supports the expected amplicon? | sequence_analysis | genomics | yuri_v3 |
v3_99316651cc285eba_n | noul | [
"false",
"true"
] | [
0.43,
0.57
] | An amplicon sequence shows even coverage at 500x; additionally reveals a premature poly-A signal. Context: at 30x mean depth, under an active deadline. Reported by the automated check. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_60bb6b83552c9542_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.01,
0.31,
0.55,
0.13,
0
] | A contig assembly shows 99.8% identity across the target region; additionally maps to two loci with equal coverage. Context: with the long-read platform, under an active deadline. Reported by the automated check. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_d3535c5ee9c28f9c_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.07,
0.29,
0.42,
0.19,
0.02
] | A rna-seq read set contains a stop codon mid-open-reading-frame; additionally shows even coverage at 500x. Context: in the variant-calling pipeline, mid-incident. Reported by the operator. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_ec245fecc78cea4f_c | choice | [
"valid",
"ambiguous",
"artifact",
"contaminated"
] | [
0.67,
0.21,
0.12,
0
] | A contig assembly shows even coverage at 500x; additionally has a consensus quality of Q20. Context: against the latest reference, during a scheduled maintenance window. Reported by the monitoring system. | Sequence verdict for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_160b1042e680d650_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.01,
0.3,
0.67,
0.02
] | A rna-seq read set contains a stop codon mid-open-reading-frame; additionally reveals a premature poly-A signal. Context: against the latest reference, during an external partner integration. Reported by the review queue. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_c564f15bb2ecb6dd_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.02,
0.1,
0.77,
0.11,
0
] | An alignment result contains the known pseudo-gene region; additionally maps to two loci with equal coverage. Context: at 30x mean depth, shortly after a software update. Reported by the monitoring system. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_bfb03dd92bae39c2_n | noul | [
"false",
"true"
] | [
0.34,
0.66
] | An alignment result shows strand bias at 4:1; additionally has a 4bp insertion in the coding sequence. Context: at 30x mean depth, mid-incident. Reported by the on-call engineer. | Is this scenario one where: re-sequencing is needed? | sequence_analysis | genomics | yuri_v3 |
v3_8a8ca8468e555d41_c | choice | [
"valid",
"ambiguous",
"artifact",
"contaminated"
] | [
0.42,
0.27,
0.28,
0.03
] | A rna-seq read set shows 99.8% identity across the target region; additionally shows even coverage at 500x. Context: against the latest reference, under reduced staffing. Reported by the review queue. | Sequence verdict for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_96a4c4c743f6fef1_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.13,
0.68,
0.18,
0.01,
0
] | A contig assembly matches the expected amplicon size; additionally shows strand bias at 4:1. Context: with the long-read platform, during the morning shift. Reported by the supervisor. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_792e121ce74117be_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.02,
0.02,
0.11,
0.58,
0.26,
0.01
] | An amplicon sequence contains the known pseudo-gene region; additionally reveals a premature poly-A signal. Context: with the long-read platform, with staffing at reduced levels. Reported by the monitoring system. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_9ea07acea5f63f70_n | noul | [
"false",
"true"
] | [
0.46,
0.54
] | An amplicon sequence contains a stop codon mid-open-reading-frame; additionally has a 4bp insertion in the coding sequence. Context: at 30x mean depth, during the holiday freeze. Reported by the automated check. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_d58c323e5ae9b28b_n | noul | [
"false",
"true"
] | [
0.72,
0.28
] | An alignment result contains a stop codon mid-open-reading-frame; additionally shows 99.8% identity across the target region. Context: with the long-read platform, during an external partner integration. Reported by the on-call engineer. | Is this scenario one where: the sequence supports the expected amplicon? | sequence_analysis | genomics | yuri_v3 |
v3_b6681c139924f7a8_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.03,
0.33,
0.55,
0.09,
0
] | An alignment result shows strand bias at 4:1; additionally shows 99.8% identity across the target region. Context: in the variant-calling pipeline, with a new vendor onboarded. Reported by the on-call engineer. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_0fd135d501ddd2fe_c | choice | [
"SNV",
"insertion",
"deletion",
"structural"
] | [
0.63,
0.04,
0.1,
0.23
] | An amplicon sequence reveals a premature poly-A signal; additionally contains a stop codon mid-open-reading-frame. Context: at 30x mean depth, as part of a compliance sweep. Reported by the supervisor. | Variant type for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_33ee1590c89fed90_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0,
0.17,
0.76,
0.07
] | An alignment result contains a stop codon mid-open-reading-frame; additionally reveals a premature poly-A signal. Context: against the latest reference, with a new vendor onboarded. Reported by the on-call engineer. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_a28d0fafdcbc5c51_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.03,
0.09,
0.14,
0.5,
0.22,
0.02
] | An amplicon sequence contains the known pseudo-gene region; additionally contains a stop codon mid-open-reading-frame. Context: with the long-read platform, during normal operations. Reported by the operator. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_8b3162c803700681_n | noul | [
"false",
"true"
] | [
0.88,
0.12
] | A contig assembly contains a stop codon mid-open-reading-frame; additionally maps to two loci with equal coverage. Context: in the variant-calling pipeline, mid-incident. Reported by the monitoring system. | Is this scenario one where: the sequence supports the expected amplicon? | sequence_analysis | genomics | yuri_v3 |
v3_2e7a62ac3d01c02b_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.02,
0.1,
0.78,
0.09,
0
] | An alignment result maps to two loci with equal coverage; additionally has a 4bp insertion in the coding sequence. Context: against the latest reference, during normal operations. Reported by the monitoring system. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_ee50dc33d559f477_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.01,
0.39,
0.59,
0.01
] | An alignment result shows strand bias at 4:1; additionally contains a stop codon mid-open-reading-frame. Context: at 30x mean depth, while on-call rotation changed. Reported by the operator. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_a88f29120786ab03_n | noul | [
"false",
"true"
] | [
0.77,
0.23
] | An amplicon sequence has a consensus quality of Q20; additionally matches the expected amplicon size. Context: at 30x mean depth, at the end of the fiscal period. Reported by the operator. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_e9a087b0da527fac_n | noul | [
"false",
"true"
] | [
0.62,
0.38
] | A rna-seq read set shows 99.8% identity across the target region; additionally contains a stop codon mid-open-reading-frame. Context: with the long-read platform, during the quarterly review. Reported by the review queue. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_085eacd7687860fd_n | noul | [
"false",
"true"
] | [
0.52,
0.48
] | A rna-seq read set maps to two loci with equal coverage; additionally shows 99.8% identity across the target region. Context: at 30x mean depth, during the holiday freeze. Reported by the review queue. | Is this scenario one where: re-sequencing is needed? | sequence_analysis | genomics | yuri_v3 |
v3_49f80ef3c0afb50a_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.07,
0.13,
0.14,
0.3,
0.25,
0.11
] | A rna-seq read set shows 99.8% identity across the target region; additionally shows even coverage at 500x. Context: with the long-read platform, at the end of the fiscal period. Reported by the review queue. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_590b3bfce74ff161_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.07,
0.34,
0.5,
0.08,
0
] | An amplicon sequence has a 4bp insertion in the coding sequence; additionally matches the expected amplicon size. Context: with the long-read platform, during the holiday freeze. Reported by the on-call engineer. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
End of preview. Expand in Data Studio
JEV corpus - sequence_analysis
7,870 typed calibrated decision rows from the jev-distill-corpus-v3 corpus (domain: sequence_analysis).
Each row is one typed decision: kind (noul / choice / score), a state, a question, options, and a target probability distribution over the options.
Part of the per-domain split of SargeDev/jev-distill-corpus-v3 - the full corpus in one repo.
Domains:
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