Summary

Basic Descriptive Statistics
✖ Data Leakage
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Automated quality control for genomic machine learning datasets: scores the biases, duplicates and data leakage a classifier could exploit before you train on it.
Searching test set transcription_factor_prediction_human_3_test.csv.gz against train set transcription_factor_prediction_human_3_train.csv.gz
Data Leakage:✖FailHow a flag is decided →
gb-qc v1.0.0 · run 2026-09-15 22:30:51

Basic Descriptive Statistics

Filename transcription_factor_prediction_human_3_test.csv.gz transcription_factor_prediction_human_3_train.csv.gz
Number of sequences 1000 27294
Minimum length 101 101
Mean length 101.00 101.00
Maximum length 101 101
✖

Data Leakage

Every test sequence searched against the train set with MMseqs2, and scored on its best hit. Similarity is min(query coverage, target coverage) × percent identity: how much of the shorter sequence the alignment spans, times how much of that matches. The histogram is the distribution of those best hits.

The flag is the percentage of test sequences at or above the threshold: Pass at 0%, Warning below 2%, Fail at 2% or more. A test sequence that near-duplicates a training one is one the model has already seen, so the accuracy it earns there is not evidence. What to do about it →

The panel under the histogram lists those alignments, up to the first 100; every one of them, listed or not, is exported to mmseqs/mmseqs2_search_result.tsv beside this report. Its columns are:

Query (Q)
Identifier of the test sequence: seq_<i>_test, where i is its 0-based position in the input test file.
Target (T)
Identifier of the train sequence: seq_<i>_train, where i is its 0-based position in the input train file.
Q Cov.
Fraction of the query sequence covered by the alignment (0–1).
T Cov.
Fraction of the target sequence covered by the alignment (0–1).
% Identity
Percent identical aligned positions in the aligned region.
% Similarity
Similarity score used for leakage detection, calculated as min(Q Cov., T Cov.) × % Identity.
E-value
MMseqs2 E-value (lower is more "significant").
Alignment
Click “Show” to expand the alignment visualisation for a row.
Filename transcription_factor_prediction_human_3_test.csv.gz transcription_factor_prediction_human_3_train.csv.gz
Data Leakage (percentage) 2.40% 0.13%
Data Leakage (count) 24 35
Similarity Histogram
35 high-similarity alignments
Query (Q) Target (T) Q Cov. T Cov. % Identity % Similarity E-value Alignment
seq_672_test seq_12901_train 1.00 1.00 100.0 100.00 3.52e-52
seq_877_test seq_19628_train 0.99 0.99 100.0 99.00 1.71e-51
seq_643_test seq_2093_train 0.98 0.98 100.0 98.00 8.25e-51
seq_877_test seq_15542_train 0.98 0.98 100.0 98.00 8.25e-51
seq_659_test seq_8091_train 0.98 0.98 100.0 98.00 8.25e-51
seq_817_test seq_17842_train 0.98 0.98 100.0 98.00 8.25e-51
seq_830_test seq_24861_train 0.97 0.97 100.0 97.00 3.97e-50
seq_859_test seq_4305_train 0.97 0.97 100.0 97.00 3.97e-50
seq_704_test seq_1275_train 0.97 0.97 100.0 97.00 3.97e-50
seq_632_test seq_21807_train 0.97 0.97 100.0 97.00 3.97e-50
seq_849_test seq_12602_train 0.96 0.96 100.0 96.00 1.90e-49
seq_704_test seq_15342_train 0.96 0.96 100.0 96.00 1.90e-49
seq_659_test seq_22760_train 0.95 0.95 100.0 95.00 9.05e-49
seq_691_test seq_5920_train 0.95 0.95 100.0 95.00 9.05e-49
seq_897_test seq_15348_train 0.95 0.95 100.0 95.00 9.05e-49
seq_859_test seq_14725_train 0.95 0.95 100.0 95.00 9.05e-49
seq_512_test seq_22652_train 0.94 0.94 100.0 94.10 4.30e-48
seq_817_test seq_2282_train 0.94 0.94 100.0 94.10 4.30e-48
seq_719_test seq_3417_train 0.97 0.98 96.9 93.99 2.08e-44
seq_630_test seq_11099_train 0.93 0.93 100.0 93.10 2.03e-47
seq_969_test seq_22298_train 0.93 0.93 100.0 93.10 2.03e-47
seq_640_test seq_26260_train 0.93 0.93 100.0 93.10 2.03e-47
seq_743_test seq_17539_train 0.96 0.97 96.9 93.02 9.56e-44
seq_775_test seq_12436_train 1.00 1.00 93.0 93.00 1.82e-40
seq_630_test seq_6280_train 0.92 0.92 100.0 92.10 9.55e-47
seq_673_test seq_9579_train 0.93 0.93 98.9 92.08 9.66e-46
seq_775_test seq_11487_train 1.00 0.99 93.0 92.07 3.58e-39
seq_966_test seq_6211_train 0.91 0.91 100.0 91.10 4.47e-46
seq_877_test seq_22474_train 0.91 0.91 100.0 91.10 4.47e-46
seq_941_test seq_8273_train 0.91 0.91 100.0 91.10 4.47e-46
seq_704_test seq_1817_train 0.91 0.91 100.0 91.10 4.47e-46
seq_803_test seq_27198_train 1.00 1.00 91.0 91.00 2.99e-37
seq_613_test seq_2509_train 0.90 0.90 100.0 90.10 2.08e-45
seq_803_test seq_26747_train 0.99 0.99 91.0 90.09 1.29e-36
seq_775_test seq_12980_train 0.99 0.99 91.0 90.09 1.29e-36