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 H3K36me3_test.csv.gz against train set H3K36me3_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 H3K36me3_test.csv.gz H3K36me3_train.csv.gz
Number of sequences 3000 30000
Minimum length 1000 1000
Mean length 1000.00 1000.00
Maximum length 1000 1000
!

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 H3K36me3_test.csv.gz H3K36me3_train.csv.gz
Data Leakage (percentage) 0.87% 0.16%
Data Leakage (count) 26 49
Similarity Histogram
66 high-similarity alignments
Query (Q) Target (T) Q Cov. T Cov. % Identity % Similarity E-value Alignment
seq_2457_test seq_22879_train 0.99 1.00 97.0 96.52 0.00e+00
seq_943_test seq_12104_train 0.99 0.99 96.7 96.12 0.00e+00
seq_209_test seq_13832_train 0.98 0.98 97.5 95.65 0.00e+00
seq_209_test seq_6709_train 0.98 0.98 97.3 95.65 0.00e+00
seq_1456_test seq_8490_train 0.99 0.99 96.2 95.53 0.00e+00
seq_1963_test seq_8490_train 0.99 0.99 96.3 95.43 0.00e+00
seq_209_test seq_7336_train 0.97 0.97 97.7 94.96 0.00e+00
seq_2696_test seq_19326_train 0.98 0.98 96.9 94.77 0.00e+00
seq_1506_test seq_24878_train 0.97 0.97 96.9 94.48 0.00e+00
seq_2657_test seq_12083_train 0.97 0.97 97.3 94.19 0.00e+00
seq_274_test seq_1048_train 0.98 0.98 96.3 94.09 0.00e+00
seq_1515_test seq_6486_train 0.96 0.97 97.3 93.89 0.00e+00
seq_2696_test seq_29326_train 0.97 0.97 97.1 93.80 0.00e+00
seq_1486_test seq_10113_train 0.99 0.99 94.8 93.47 0.00e+00
seq_2419_test seq_12766_train 0.97 0.97 96.3 93.41 0.00e+00
seq_2696_test seq_10093_train 0.97 0.97 96.5 93.22 0.00e+00
seq_1406_test seq_29672_train 0.99 0.99 93.9 93.15 0.00e+00
seq_1665_test seq_13034_train 0.98 0.98 94.9 93.10 0.00e+00
seq_2197_test seq_1568_train 0.96 0.96 97.0 92.93 0.00e+00
seq_1465_test seq_29656_train 0.98 0.98 94.7 92.90 0.00e+00
seq_2417_test seq_10113_train 0.98 0.98 94.6 92.80 0.00e+00
seq_704_test seq_12083_train 0.96 0.96 96.5 92.64 0.00e+00
seq_2548_test seq_8490_train 0.96 0.96 96.5 92.64 0.00e+00
seq_274_test seq_29656_train 0.99 0.99 93.7 92.58 0.00e+00
seq_943_test seq_1977_train 0.95 0.95 97.4 92.53 0.00e+00
seq_1465_test seq_47_train 0.98 0.99 94.1 92.41 0.00e+00
seq_1841_test seq_19056_train 0.94 0.94 98.0 92.32 0.00e+00
seq_45_test seq_6486_train 0.98 0.98 93.8 92.30 0.00e+00
seq_2417_test seq_4108_train 0.95 0.95 96.9 92.25 0.00e+00
seq_2612_test seq_5056_train 0.97 0.97 94.8 92.24 0.00e+00
seq_2612_test seq_15643_train 0.96 0.96 96.2 92.16 0.00e+00
seq_274_test seq_25707_train 0.96 0.96 96.4 92.16 0.00e+00
seq_274_test seq_29922_train 0.97 0.97 95.4 92.16 0.00e+00
seq_1963_test seq_10457_train 0.95 0.95 97.1 92.15 0.00e+00
seq_2696_test seq_7588_train 0.95 0.95 97.1 92.05 0.00e+00
seq_1456_test seq_10457_train 0.95 0.95 96.5 91.96 0.00e+00
seq_943_test seq_17651_train 0.95 0.95 96.7 91.96 0.00e+00
seq_1486_test seq_4108_train 0.95 0.95 97.0 91.86 0.00e+00
seq_2457_test seq_10707_train 0.94 0.95 97.4 91.75 0.00e+00
seq_1515_test seq_29859_train 0.98 0.98 93.7 91.73 0.00e+00
seq_2678_test seq_29326_train 0.96 0.96 95.4 91.68 0.00e+00
seq_2873_test seq_12083_train 0.95 0.95 96.0 91.49 0.00e+00
seq_2696_test seq_17070_train 0.94 0.94 97.4 91.46 0.00e+00
seq_2678_test seq_26905_train 0.98 0.98 93.5 91.44 0.00e+00
seq_2417_test seq_20068_train 0.95 0.95 96.1 91.39 0.00e+00
seq_1486_test seq_20068_train 0.95 0.95 96.6 91.38 0.00e+00
seq_943_test seq_15307_train 0.94 0.94 97.0 91.37 0.00e+00
seq_2678_test seq_10093_train 0.96 0.96 95.0 91.30 0.00e+00
seq_1665_test seq_6540_train 0.95 0.95 96.5 91.29 0.00e+00
seq_2612_test seq_15664_train 0.99 0.99 92.3 91.19 0.00e+00
seq_1456_test seq_19189_train 0.94 0.94 96.6 91.00 0.00e+00
seq_1841_test seq_3399_train 0.98 0.97 93.2 90.78 0.00e+00
seq_1841_test seq_27270_train 0.99 0.99 91.8 90.61 0.00e+00
seq_1515_test seq_14333_train 0.93 0.94 96.9 90.50 0.00e+00
seq_1017_test seq_14268_train 0.99 0.99 91.1 90.46 0.00e+00
seq_45_test seq_29859_train 1.00 0.99 91.4 90.39 0.00e+00
seq_1963_test seq_19189_train 0.94 0.94 96.0 90.24 0.00e+00
seq_1017_test seq_11969_train 1.00 1.00 90.6 90.24 0.00e+00
seq_1017_test seq_27866_train 1.00 1.00 90.6 90.24 0.00e+00
seq_45_test seq_29210_train 0.97 0.97 92.6 90.19 0.00e+00
seq_1841_test seq_27491_train 0.94 0.94 95.4 90.15 0.00e+00
seq_1406_test seq_5056_train 0.97 0.97 92.9 90.11 0.00e+00
seq_2243_test seq_7684_train 0.98 0.97 92.5 90.09 0.00e+00
seq_1465_test seq_1048_train 0.95 0.95 95.0 90.06 0.00e+00
seq_2419_test seq_21154_train 0.96 0.96 94.1 90.05 0.00e+00
seq_2612_test seq_29672_train 0.94 0.94 96.2 90.04 0.00e+00