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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 enhancer_promoter_interaction_HUVEC_test.csv.gz against train set enhancer_promoter_interaction_HUVEC_train.csv.gz
Data Leakage:!WarningHow a flag is decided →
gb-qc v1.0.0 · run 2026-09-15 22:31:12

Basic Descriptive Statistics

Filename enhancer_promoter_interaction_HUVEC_test.csv.gz enhancer_promoter_interaction_HUVEC_train.csv.gz
Number of sequences 2000 10000
Minimum length 5000 5000
Mean length 5000.00 5000.00
Maximum length 5000 5000

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 enhancer_promoter_interaction_HUVEC_test.csv.gz enhancer_promoter_interaction_HUVEC_train.csv.gz
Data Leakage (percentage) 1.75% 0.35%
Data Leakage (count) 35 35
Similarity Histogram
35 high-similarity alignments
Query (Q) Target (T) Q Cov. T Cov. % Identity % Similarity E-value Alignment
seq_700_test seq_4953_train 0.99 0.99 99.5 98.50 0.00e+00
seq_250_test seq_5346_train 0.99 0.99 99.5 98.50 0.00e+00
seq_1090_test seq_5473_train 0.99 0.99 99.5 98.50 0.00e+00
seq_244_test seq_7291_train 0.99 0.99 99.4 98.41 0.00e+00
seq_573_test seq_3266_train 0.99 0.99 99.4 98.41 0.00e+00
seq_245_test seq_6038_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1745_test seq_7352_train 0.99 0.99 99.4 98.41 0.00e+00
seq_682_test seq_9269_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1328_test seq_6415_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1106_test seq_9752_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1967_test seq_7755_train 0.99 0.99 99.4 98.41 0.00e+00
seq_188_test seq_6379_train 0.99 0.99 99.4 98.41 0.00e+00
seq_569_test seq_9313_train 0.99 0.99 99.4 98.41 0.00e+00
seq_21_test seq_4471_train 0.99 0.99 99.4 98.41 0.00e+00
seq_322_test seq_6797_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1486_test seq_4213_train 0.99 0.99 99.4 98.41 0.00e+00
seq_96_test seq_9288_train 0.99 0.99 99.4 98.41 0.00e+00
seq_628_test seq_5674_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1457_test seq_922_train 0.99 0.99 99.4 98.41 0.00e+00
seq_491_test seq_9646_train 0.99 0.99 99.4 98.41 0.00e+00
seq_507_test seq_5303_train 0.99 0.99 99.4 98.41 0.00e+00
seq_10_test seq_5652_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1754_test seq_3423_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1883_test seq_8948_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1410_test seq_3731_train 0.99 0.99 99.4 98.41 0.00e+00
seq_957_test seq_2818_train 0.99 0.99 99.4 98.41 0.00e+00
seq_24_test seq_4394_train 0.99 0.99 99.3 98.31 0.00e+00
seq_88_test seq_9187_train 0.99 0.99 99.3 98.31 0.00e+00
seq_1430_test seq_7455_train 0.99 0.99 99.3 98.31 0.00e+00
seq_84_test seq_1806_train 0.99 0.99 99.3 98.31 0.00e+00
seq_1531_test seq_4336_train 0.99 0.99 99.3 98.31 0.00e+00
seq_951_test seq_8834_train 0.99 0.99 99.3 98.31 0.00e+00
seq_1079_test seq_430_train 0.99 0.99 99.3 98.31 0.00e+00
seq_1289_test seq_9353_train 0.99 0.99 99.3 98.31 0.00e+00
seq_1156_test seq_7265_train 0.99 0.99 99.2 98.21 0.00e+00