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_mouse_1_test.csv.gz against train set transcription_factor_prediction_mouse_1_train.csv.gz
Data Leakage:!WarningHow a flag is decided →
gb-qc v1.0.0 · run 2026-09-15 22:30:51

Basic Descriptive Statistics

Filename transcription_factor_prediction_mouse_1_test.csv.gz transcription_factor_prediction_mouse_1_train.csv.gz
Number of sequences 6745 53952
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_mouse_1_test.csv.gz transcription_factor_prediction_mouse_1_train.csv.gz
Data Leakage (percentage) 0.19% 0.05%
Data Leakage (count) 13 28
Similarity Histogram
30 high-similarity alignments
Query (Q) Target (T) Q Cov. T Cov. % Identity % Similarity E-value Alignment
seq_5913_test seq_45821_train 1.00 1.00 98.0 98.00 1.79e-48
seq_683_test seq_36302_train 0.99 1.00 98.0 97.02 4.01e-47
seq_5539_test seq_21467_train 0.99 0.98 97.0 95.06 8.87e-45
seq_1395_test seq_8280_train 0.98 0.98 96.9 94.96 1.91e-45
seq_691_test seq_32037_train 0.99 0.99 95.0 94.05 8.65e-43
seq_1395_test seq_49500_train 0.97 0.99 96.0 93.12 1.89e-43
seq_5539_test seq_6573_train 0.99 0.98 95.0 93.10 1.78e-41
seq_5597_test seq_43317_train 0.99 0.99 94.0 93.06 3.79e-41
seq_5913_test seq_32488_train 0.99 0.99 94.0 93.06 3.79e-41
seq_2628_test seq_34494_train 0.96 0.96 96.9 93.02 4.10e-44
seq_1846_test seq_37636_train 0.96 0.96 96.9 93.02 4.10e-44
seq_1846_test seq_27773_train 0.98 0.98 94.9 93.00 3.94e-42
seq_3771_test seq_49531_train 0.98 0.98 94.9 93.00 3.94e-42
seq_1103_test seq_21467_train 0.98 1.00 94.0 92.12 8.03e-41
seq_5913_test seq_8250_train 1.00 0.99 93.0 92.07 7.08e-39
seq_5539_test seq_20139_train 0.96 0.95 96.9 92.06 8.65e-43
seq_1395_test seq_33086_train 0.98 0.98 93.9 92.02 1.70e-40
seq_2264_test seq_12871_train 1.00 1.00 92.0 92.00 1.49e-38
seq_1103_test seq_20139_train 0.96 0.98 94.9 91.10 3.79e-41
seq_2628_test seq_24830_train 0.94 0.94 96.8 91.09 8.65e-43
seq_5539_test seq_36430_train 0.98 0.97 93.9 91.08 3.37e-39
seq_1395_test seq_44490_train 0.98 0.98 92.9 91.04 7.08e-39
seq_1395_test seq_49905_train 0.98 0.98 92.9 91.04 7.08e-39
seq_1395_test seq_13558_train 0.96 0.95 95.8 91.01 3.79e-41
seq_2074_test seq_22045_train 0.96 0.96 94.8 91.01 8.03e-41
seq_1846_test seq_2666_train 0.97 0.97 93.8 90.99 7.59e-40
seq_5539_test seq_31577_train 0.98 0.97 92.9 90.11 1.36e-37
seq_5539_test seq_40505_train 1.00 0.99 91.0 90.09 1.09e-35
seq_5539_test seq_47572_train 0.97 0.96 93.8 90.05 1.49e-38
seq_2404_test seq_46989_train 0.96 0.96 93.8 90.05 3.37e-39