Resource
| Id | ATAC-seq/ENCSR042AWH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR042AWH [biosample_summary="Homo sapiens HepG2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN074ZCE|/analyses/ENCAN074ZCE/} has in progress subobject document {23706428-f8ac-4cfe-a00a-75c4fc032407|/documents/23706428-f8ac-4cfe-a00a-75c4fc032407/} audit_internal_action: Released analysis {ENCAN074ZCE|/analyses/ENCAN074ZCE/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_warning: Alignment file {ENCFF239RGZ|/files/ENCFF239RGZ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 23501715 usable fragments. According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline should have > 25 million usable fragments. 20-25 million is acceptable and < 15 million is not compliant. audit_warning: Alignment file {ENCFF394BBD|/files/ENCFF394BBD/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 23241010 usable fragments. According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline should have > 25 million usable fragments. 20-25 million is acceptable and < 15 million is not compliant. audit_warning: NRF (Non Redundant Fraction) is equal to the result of the division of the number of reads after duplicates removal by the total number of reads. An NRF value < 0.7 is poor complexity, between 0.7 and 0.9 is moderate complexity, and >= 0.9 high complexity. NRF value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF239RGZ|/files/ENCFF239RGZ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.80483. audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF239RGZ|/files/ENCFF239RGZ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.82. audit_warning: NRF (Non Redundant Fraction) is equal to the result of the division of the number of reads after duplicates removal by the total number of reads. An NRF value < 0.7 is poor complexity, between 0.7 and 0.9 is moderate complexity, and >= 0.9 high complexity. NRF value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF394BBD|/files/ENCFF394BBD/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.809794. audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF394BBD|/files/ENCFF394BBD/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.82. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR042AWH | float |
ATAC-seq_ENCSR042AWH |
ATAC-seq ENCSR042AWH [biosample_summary="Homo sapiens HepG2"]
|
 |
[1.42, 42.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 71845355 | 2.23% | 127218 |
| chr1 | 6129032 | 2.46% | 10654 |
| chr2 | 7864582 | 3.25% | 14305 |
| chr3 | 4118167 | 2.08% | 7449 |
| chr4 | 2871869 | 1.51% | 5249 |
| chr5 | 3325884 | 1.83% | 5991 |
| chr6 | 4931503 | 2.89% | 8872 |
| chr7 | 3533098 | 2.22% | 6293 |
| chr8 | 2841198 | 1.96% | 5122 |
| chr9 | 2821904 | 2.04% | 4979 |
| chr10 | 3236041 | 2.42% | 5808 |
| chr11 | 3395806 | 2.51% | 5983 |
| chr12 | 3023096 | 2.27% | 5252 |
| chr13 | 1557832 | 1.36% | 2802 |
| chr14 | 2713837 | 2.54% | 4739 |
| chr15 | 2083296 | 2.04% | 3634 |
| chr16 | 3269885 | 3.62% | 5611 |
| chr17 | 3566246 | 4.28% | 5983 |
| chr18 | 1406274 | 1.75% | 2642 |
| chr19 | 2455602 | 4.19% | 3996 |
| chr20 | 2864975 | 4.45% | 5191 |
| chr21 | 810394 | 1.73% | 1403 |
| chr22 | 1487646 | 2.93% | 2580 |
| chrX | 1453699 | 0.93% | 2532 |
| chrY | 83489 | 0.15% | 148 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 127218 | 150 | 4319 | 564.74 | 460 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF913MQB.bed.gz | 5.05 MB | 30b74a5eef3e616fe2a0ae4ee88481b2 |
| ENCFF913MQB.tabix.bed.gz | 1.39 MB | cfb118a612f4797962b454f18e979fff |
| ENCFF913MQB.tabix.bed.gz.tbi | 479.58 KB | 69b5eda99870620182454c755839e458 |
| genomic_resource.yaml | 4.65 KB | df6f997f6c467a0bcbec6e4181a638f2 |
| statistics/ |