Resource
| Id | ATAC-seq/ENCSR459PVP |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR459PVP [biosample_summary="Homo sapiens from a donor with amyotrophic lateral sclerosis; motor neuron"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (55 years) with amyotrophic lateral sclerosis output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN821PGU|/analyses/ENCAN821PGU/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} 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 {ENCFF742KHO|/files/ENCFF742KHO/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.766666. 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 {ENCFF742KHO|/files/ENCFF742KHO/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.78. 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 {ENCFF243CTN|/files/ENCFF243CTN/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.769549. 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 {ENCFF243CTN|/files/ENCFF243CTN/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.78. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR459PVP | float |
ATAC-seq_ENCSR459PVP |
ATAC-seq ENCSR459PVP [biosample_summary="Homo sapiens from a donor with amyotrophic lateral sclerosis; motor neuron"]
|
 |
[1.37, 42.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 130553381 | 4.06% | 180793 |
| chr1 | 12402438 | 4.98% | 16907 |
| chr2 | 10835401 | 4.47% | 15364 |
| chr3 | 8946958 | 4.51% | 12620 |
| chr4 | 6369742 | 3.35% | 9301 |
| chr5 | 7337732 | 4.04% | 10392 |
| chr6 | 7598999 | 4.45% | 10756 |
| chr7 | 6592869 | 4.14% | 9291 |
| chr8 | 6020648 | 4.15% | 8526 |
| chr9 | 5592943 | 4.04% | 7659 |
| chr10 | 6344339 | 4.74% | 8790 |
| chr11 | 6824292 | 5.05% | 9244 |
| chr12 | 6458287 | 4.85% | 8979 |
| chr13 | 3121132 | 2.73% | 4515 |
| chr14 | 3877287 | 3.62% | 5400 |
| chr15 | 4423637 | 4.34% | 6023 |
| chr16 | 4088072 | 4.53% | 5381 |
| chr17 | 5532937 | 6.65% | 7146 |
| chr18 | 3098737 | 3.86% | 4501 |
| chr19 | 3916001 | 6.68% | 4778 |
| chr20 | 3842316 | 5.96% | 5230 |
| chr21 | 1490699 | 3.19% | 2012 |
| chr22 | 2453821 | 4.83% | 3141 |
| chrX | 3181420 | 2.04% | 4511 |
| chrY | 202674 | 0.35% | 326 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 180793 | 150 | 5015 | 722.12 | 643 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF951DOQ.bed.gz | 7.04 MB | 2f0272b04c855d6fe58518d1b37372ac |
| ENCFF951DOQ.tabix.bed.gz | 2.0 MB | 3af27de863ae2aaaa855d25fc57d745b |
| ENCFF951DOQ.tabix.bed.gz.tbi | 595.29 KB | c1c6aa51ef2eb6a9f1ed28ef221da4ee |
| genomic_resource.yaml | 3.88 KB | d6c911303c1fe8daaa023f20f7569227 |
| statistics/ |