Resource
| Id | ATAC-seq/ENCSR704VZY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR704VZY [biosample_summary="Homo sapiens from a donor with amyotrophic lateral sclerosis; motor neuron"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male child (6 years) with amyotrophic lateral sclerosis output_type: replicated peaks audit_internal_action: Released analysis {ENCAN326LEB|/analyses/ENCAN326LEB/} 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 {ENCFF577CYP|/files/ENCFF577CYP/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.70665. 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 {ENCFF577CYP|/files/ENCFF577CYP/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.73. 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 {ENCFF353HIF|/files/ENCFF353HIF/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.726472. 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 {ENCFF353HIF|/files/ENCFF353HIF/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.75. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR704VZY | float |
ATAC-seq_ENCSR704VZY |
ATAC-seq ENCSR704VZY [biosample_summary="Homo sapiens from a donor with amyotrophic lateral sclerosis; motor neuron"]
|
 |
[1.12, 40.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 97784568 | 3.04% | 156666 |
| chr1 | 10537267 | 4.23% | 16173 |
| chr2 | 7817020 | 3.23% | 12973 |
| chr3 | 5671719 | 2.86% | 9594 |
| chr4 | 4333708 | 2.28% | 7587 |
| chr5 | 5170287 | 2.85% | 8696 |
| chr6 | 5256704 | 3.08% | 8690 |
| chr7 | 4723312 | 2.96% | 7728 |
| chr8 | 4289889 | 2.96% | 7183 |
| chr9 | 4357188 | 3.15% | 6943 |
| chr10 | 4997892 | 3.74% | 8094 |
| chr11 | 5305682 | 3.93% | 8317 |
| chr12 | 4129972 | 3.10% | 6615 |
| chr13 | 2485556 | 2.17% | 4340 |
| chr14 | 2965682 | 2.77% | 4731 |
| chr15 | 3149914 | 3.09% | 4967 |
| chr16 | 3780625 | 4.18% | 5696 |
| chr17 | 4459477 | 5.36% | 6381 |
| chr18 | 2340484 | 2.91% | 3986 |
| chr19 | 3508591 | 5.99% | 4573 |
| chr20 | 2815804 | 4.37% | 4465 |
| chr21 | 1211458 | 2.59% | 1955 |
| chr22 | 2064420 | 4.06% | 3007 |
| chrX | 2311370 | 1.48% | 3769 |
| chrY | 100547 | 0.18% | 203 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 156666 | 150 | 3725 | 624.16 | 526 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF487GKW.bed.gz | 5.99 MB | 19137ffc81f8b769c080fef316f71d7f |
| ENCFF487GKW.tabix.bed.gz | 1.71 MB | 1d8306432acfa58618dc4fea80541471 |
| ENCFF487GKW.tabix.bed.gz.tbi | 570.31 KB | 1a895477f8485f3a30b6b5ea9c441b58 |
| genomic_resource.yaml | 3.87 KB | 51098bca25c7e66c433d92b00775753c |
| statistics/ |