Resource
| Id | ATAC-seq/ENCSR516YAD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR516YAD [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 (47 years) with amyotrophic lateral sclerosis output_type: replicated peaks audit_internal_action: Released analysis {ENCAN366NCA|/analyses/ENCAN366NCA/} 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 {ENCFF884SWM|/files/ENCFF884SWM/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.753647. 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 {ENCFF884SWM|/files/ENCFF884SWM/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.76. 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 {ENCFF367KMY|/files/ENCFF367KMY/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.757748. 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 {ENCFF367KMY|/files/ENCFF367KMY/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.77. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR516YAD | float |
ATAC-seq_ENCSR516YAD |
ATAC-seq ENCSR516YAD [biosample_summary="Homo sapiens from a donor with amyotrophic lateral sclerosis; motor neuron"]
|
 |
[1.21, 41.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 81958651 | 2.55% | 125362 |
| chr1 | 8907702 | 3.58% | 13160 |
| chr2 | 6424792 | 2.65% | 10187 |
| chr3 | 4643771 | 2.34% | 7505 |
| chr4 | 3421908 | 1.80% | 5606 |
| chr5 | 4260443 | 2.35% | 6792 |
| chr6 | 4530042 | 2.65% | 7105 |
| chr7 | 3873697 | 2.43% | 6052 |
| chr8 | 3635654 | 2.50% | 5829 |
| chr9 | 3532742 | 2.55% | 5386 |
| chr10 | 4186531 | 3.13% | 6495 |
| chr11 | 4434071 | 3.28% | 6698 |
| chr12 | 3460689 | 2.60% | 5206 |
| chr13 | 1996879 | 1.75% | 3311 |
| chr14 | 2427253 | 2.27% | 3714 |
| chr15 | 2631830 | 2.58% | 3931 |
| chr16 | 3288145 | 3.64% | 4824 |
| chr17 | 3923847 | 4.71% | 5418 |
| chr18 | 1955556 | 2.43% | 3151 |
| chr19 | 3162472 | 5.40% | 4107 |
| chr20 | 2359520 | 3.66% | 3580 |
| chr21 | 1020761 | 2.19% | 1577 |
| chr22 | 1845879 | 3.63% | 2617 |
| chrX | 1954044 | 1.25% | 2966 |
| chrY | 80423 | 0.14% | 145 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 125362 | 150 | 3928 | 653.78 | 563 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF415HUA.bed.gz | 4.98 MB | f01a69dbbe27fdcc9cfa9ae72666f475 |
| ENCFF415HUA.tabix.bed.gz | 1.38 MB | 8ac8c9134e610c50d10291d078988c5f |
| ENCFF415HUA.tabix.bed.gz.tbi | 491.85 KB | 69a07e35937570c3fa10ab51265a721a |
| genomic_resource.yaml | 3.87 KB | 0bf04253597fcdaac91f1a36895cbd50 |
| statistics/ |