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 demo_coding_vs_intergenomic_seqs_test.csv.gz against train set demo_coding_vs_intergenomic_seqs_train.csv.gz
Data Leakage:✖FailHow a flag is decided →
gb-qc v1.0.0 · run 2026-09-15 22:31:11

Basic Descriptive Statistics

Filename demo_coding_vs_intergenomic_seqs_test.csv.gz demo_coding_vs_intergenomic_seqs_train.csv.gz
Number of sequences 25000 75000
Minimum length 200 200
Mean length 200.00 200.00
Maximum length 200 200
✖

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 demo_coding_vs_intergenomic_seqs_test.csv.gz demo_coding_vs_intergenomic_seqs_train.csv.gz
Data Leakage (percentage) 6.86% 3.20%
Data Leakage (count) 1716 2403
Similarity Histogram
3294 high-similarity alignments (first 100 shown)
Query (Q) Target (T) Q Cov. T Cov. % Identity % Similarity E-value Alignment
seq_13024_test seq_54098_train 1.00 1.00 100.0 100.00 1.68e-107
seq_15219_test seq_60583_train 1.00 1.00 100.0 100.00 1.68e-107
seq_14606_test seq_54746_train 1.00 1.00 100.0 100.00 1.68e-107
seq_17256_test seq_57702_train 1.00 1.00 100.0 100.00 1.68e-107
seq_17257_test seq_74951_train 1.00 1.00 100.0 100.00 1.68e-107
seq_18470_test seq_44434_train 1.00 1.00 100.0 100.00 1.68e-107
seq_21793_test seq_38987_train 1.00 1.00 100.0 100.00 1.68e-107
seq_16616_test seq_39493_train 1.00 1.00 100.0 100.00 1.68e-107
seq_1144_test seq_2972_train 1.00 1.00 100.0 100.00 1.68e-107
seq_14963_test seq_67860_train 1.00 1.00 100.0 100.00 1.68e-107
seq_18132_test seq_67608_train 1.00 1.00 100.0 100.00 1.68e-107
seq_15975_test seq_43490_train 1.00 1.00 100.0 100.00 1.68e-107
seq_12708_test seq_48151_train 1.00 1.00 100.0 100.00 1.68e-107
seq_15440_test seq_46978_train 1.00 1.00 100.0 100.00 1.68e-107
seq_20492_test seq_54163_train 1.00 1.00 100.0 100.00 1.68e-107
seq_15244_test seq_45313_train 1.00 1.00 100.0 100.00 1.68e-107
seq_12578_test seq_66205_train 1.00 1.00 100.0 100.00 1.68e-107
seq_18483_test seq_40136_train 1.00 1.00 100.0 100.00 1.68e-107
seq_10942_test seq_32090_train 1.00 1.00 100.0 100.00 1.68e-107
seq_23978_test seq_45555_train 1.00 1.00 100.0 100.00 1.68e-107
seq_22248_test seq_72794_train 1.00 1.00 100.0 100.00 1.68e-107
seq_19680_test seq_74253_train 1.00 1.00 100.0 100.00 1.68e-107
seq_12881_test seq_38229_train 1.00 1.00 100.0 100.00 1.68e-107
seq_18653_test seq_54247_train 1.00 1.00 100.0 100.00 1.68e-107
seq_9205_test seq_17149_train 1.00 1.00 100.0 100.00 1.68e-107
seq_23256_test seq_70619_train 1.00 1.00 100.0 100.00 1.68e-107
seq_24487_test seq_38559_train 1.00 1.00 100.0 100.00 1.68e-107
seq_22809_test seq_46690_train 1.00 1.00 100.0 100.00 1.68e-107
seq_22149_test seq_48174_train 1.00 1.00 100.0 100.00 1.68e-107
seq_15138_test seq_44006_train 1.00 1.00 100.0 100.00 1.68e-107
seq_21116_test seq_49234_train 1.00 1.00 100.0 100.00 1.68e-107
seq_14807_test seq_67673_train 1.00 1.00 100.0 100.00 1.68e-107
seq_20796_test seq_70275_train 1.00 1.00 100.0 100.00 1.68e-107
seq_18151_test seq_38646_train 1.00 1.00 100.0 100.00 1.68e-107
seq_17361_test seq_72283_train 0.99 0.99 100.0 99.50 8.03e-107
seq_9334_test seq_25868_train 0.99 0.99 100.0 99.50 8.03e-107
seq_348_test seq_20254_train 0.99 0.99 100.0 99.50 8.03e-107
seq_20723_test seq_70603_train 0.99 0.99 100.0 99.50 8.03e-107
seq_20462_test seq_42515_train 0.99 0.99 100.0 99.50 8.03e-107
seq_13079_test seq_43434_train 0.99 0.99 100.0 99.50 8.03e-107
seq_21870_test seq_57738_train 0.99 0.99 100.0 99.50 8.03e-107
seq_23130_test seq_45209_train 0.99 0.99 100.0 99.50 8.03e-107
seq_18470_test seq_49813_train 0.99 0.99 100.0 99.50 8.03e-107
seq_18470_test seq_57851_train 0.99 0.99 100.0 99.50 8.03e-107
seq_18285_test seq_45763_train 0.99 0.99 100.0 99.50 8.03e-107
seq_19945_test seq_64276_train 0.99 0.99 100.0 99.50 8.03e-107
seq_23765_test seq_54780_train 1.00 1.00 99.5 99.50 8.34e-106
seq_14555_test seq_48746_train 0.99 0.99 100.0 99.50 8.03e-107
seq_14190_test seq_45385_train 0.99 0.99 100.0 99.50 8.03e-107
seq_19285_test seq_60773_train 0.99 0.99 100.0 99.50 8.03e-107
seq_5952_test seq_12258_train 0.99 0.99 100.0 99.50 8.03e-107
seq_22161_test seq_71976_train 0.99 0.99 100.0 99.50 8.03e-107
seq_17242_test seq_49502_train 0.99 0.99 100.0 99.50 8.03e-107
seq_20936_test seq_51916_train 0.99 0.99 100.0 99.50 8.03e-107
seq_13961_test seq_73165_train 0.99 0.99 100.0 99.50 8.03e-107
seq_5104_test seq_27432_train 0.99 0.99 100.0 99.50 8.03e-107
seq_13840_test seq_52340_train 0.99 0.99 100.0 99.50 8.03e-107
seq_20734_test seq_46083_train 0.99 0.99 100.0 99.50 8.03e-107
seq_18077_test seq_70462_train 0.99 0.99 100.0 99.50 8.03e-107
seq_18586_test seq_72015_train 0.99 0.99 100.0 99.50 8.03e-107
seq_19435_test seq_67502_train 0.99 0.99 100.0 99.50 8.03e-107
seq_2882_test seq_10355_train 0.99 0.99 100.0 99.50 8.03e-107
seq_21624_test seq_57877_train 0.99 0.99 100.0 99.50 8.03e-107
seq_4600_test seq_24185_train 1.00 1.00 99.5 99.50 8.34e-106
seq_15353_test seq_61509_train 0.99 0.99 100.0 99.50 8.03e-107
seq_15385_test seq_45050_train 0.99 0.99 100.0 99.50 8.03e-107
seq_19640_test seq_74402_train 0.99 0.99 100.0 99.50 8.03e-107
seq_21324_test seq_41951_train 0.99 0.99 100.0 99.50 8.03e-107
seq_18239_test seq_62787_train 0.99 0.99 100.0 99.50 8.03e-107
seq_7920_test seq_11818_train 0.99 0.99 100.0 99.50 8.03e-107
seq_19719_test seq_55864_train 0.99 0.99 100.0 99.50 8.03e-107
seq_18665_test seq_57560_train 0.99 0.99 100.0 99.50 8.03e-107
seq_10001_test seq_34640_train 0.99 0.99 100.0 99.50 8.03e-107
seq_15805_test seq_68518_train 0.99 0.99 100.0 99.50 8.03e-107
seq_6918_test seq_37254_train 0.99 0.99 100.0 99.50 8.03e-107
seq_14748_test seq_71711_train 0.99 0.99 100.0 99.50 8.03e-107
seq_22529_test seq_39502_train 0.99 0.99 100.0 99.50 8.03e-107
seq_9752_test seq_37143_train 0.99 0.99 100.0 99.50 8.03e-107
seq_16710_test seq_38838_train 0.99 0.99 100.0 99.50 8.03e-107
seq_15246_test seq_64919_train 0.99 0.99 100.0 99.50 8.03e-107
seq_13494_test seq_57794_train 0.99 0.99 100.0 99.50 8.03e-107
seq_13590_test seq_49011_train 0.99 0.99 100.0 99.50 8.03e-107
seq_19552_test seq_64999_train 0.99 0.99 100.0 99.50 8.03e-107
seq_14426_test seq_55067_train 0.99 0.99 100.0 99.50 8.03e-107
seq_24927_test seq_37730_train 0.99 0.99 100.0 99.50 8.03e-107
seq_20623_test seq_70890_train 0.99 0.99 100.0 99.50 8.03e-107
seq_17611_test seq_69987_train 0.99 0.99 100.0 99.50 8.03e-107
seq_23000_test seq_42075_train 0.99 0.99 100.0 99.50 8.03e-107
seq_17755_test seq_57247_train 0.99 0.99 100.0 99.50 8.03e-107
seq_15704_test seq_64730_train 0.99 0.99 100.0 99.50 8.03e-107
seq_24955_test seq_66024_train 0.99 0.99 100.0 99.50 8.03e-107
seq_24707_test seq_44793_train 0.99 0.99 100.0 99.50 8.03e-107
seq_19373_test seq_43025_train 0.99 0.99 100.0 99.50 8.03e-107
seq_23156_test seq_47015_train 0.99 0.99 100.0 99.50 8.03e-107
seq_16730_test seq_38571_train 0.99 0.99 100.0 99.50 8.03e-107
seq_2329_test seq_12180_train 1.00 1.00 99.5 99.50 8.34e-106
seq_16156_test seq_46131_train 0.99 0.99 100.0 99.50 8.03e-107
seq_2602_test seq_9765_train 0.99 0.99 100.0 99.00 3.82e-106
seq_7048_test seq_30234_train 1.00 1.00 99.0 99.00 4.07e-104
seq_15495_test seq_62008_train 0.99 0.99 100.0 99.00 3.82e-106