Resource
| Id | ATAC-seq/ENCSR812ZKP |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR812ZKP [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 (49 years) with amyotrophic lateral sclerosis output_type: replicated peaks audit_internal_action: Released analysis {ENCAN085JAW|/analyses/ENCAN085JAW/} 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 {ENCFF333UUT|/files/ENCFF333UUT/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.776902. 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 {ENCFF333UUT|/files/ENCFF333UUT/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.79. 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 {ENCFF379GTS|/files/ENCFF379GTS/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.779854. 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 {ENCFF379GTS|/files/ENCFF379GTS/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.80. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR812ZKP | float |
ATAC-seq_ENCSR812ZKP |
ATAC-seq ENCSR812ZKP [biosample_summary="Homo sapiens from a donor with amyotrophic lateral sclerosis; motor neuron"]
|
 |
[1.29, 40.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 112008583 | 3.48% | 163094 |
| chr1 | 10216258 | 4.10% | 14632 |
| chr2 | 9364474 | 3.87% | 13854 |
| chr3 | 7326454 | 3.69% | 10943 |
| chr4 | 5582632 | 2.93% | 8493 |
| chr5 | 6287246 | 3.46% | 9428 |
| chr6 | 6729672 | 3.94% | 9870 |
| chr7 | 5866562 | 3.68% | 8629 |
| chr8 | 5113676 | 3.52% | 7619 |
| chr9 | 4826045 | 3.49% | 6978 |
| chr10 | 5562245 | 4.16% | 8123 |
| chr11 | 5534818 | 4.10% | 7953 |
| chr12 | 5489203 | 4.12% | 7951 |
| chr13 | 2869165 | 2.51% | 4379 |
| chr14 | 3546384 | 3.31% | 5124 |
| chr15 | 3830676 | 3.76% | 5459 |
| chr16 | 3637257 | 4.03% | 5086 |
| chr17 | 4828773 | 5.80% | 6564 |
| chr18 | 2387491 | 2.97% | 3626 |
| chr19 | 3450858 | 5.89% | 4494 |
| chr20 | 3236392 | 5.02% | 4676 |
| chr21 | 1350941 | 2.89% | 1944 |
| chr22 | 2008133 | 3.95% | 2782 |
| chrX | 2798612 | 1.79% | 4209 |
| chrY | 164616 | 0.29% | 278 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 163094 | 150 | 4040 | 686.77 | 606 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF594FVI.bed.gz | 6.52 MB | b5477c5f27c85874a3b860b7e2933004 |
| ENCFF594FVI.tabix.bed.gz | 1.79 MB | 38d15ccc2be1303e9320766b6e6557de |
| ENCFF594FVI.tabix.bed.gz.tbi | 574.97 KB | e1a88cc22cace1f031cbf0d9fb3170cf |
| genomic_resource.yaml | 3.87 KB | bd3c481860415a5b02dc75dd4f6a54fa |
| statistics/ |