Resource
| Id | ATAC-seq/ENCSR065CER |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR065CER [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 {ENCAN739IWP|/analyses/ENCAN739IWP/} 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 {ENCFF199OKA|/files/ENCFF199OKA/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.78308. 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 {ENCFF199OKA|/files/ENCFF199OKA/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with a PBC1 value of 0.80. 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 {ENCFF896PIT|/files/ENCFF896PIT/} processed by ATAC-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with NRF value of 0.762309. 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 {ENCFF896PIT|/files/ENCFF896PIT/} 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_ENCSR065CER | float |
ATAC-seq_ENCSR065CER |
ATAC-seq ENCSR065CER [biosample_summary="Homo sapiens from a donor with amyotrophic lateral sclerosis; motor neuron"]
|
 |
[1.24, 41.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 85882235 | 2.67% | 136493 |
| chr1 | 7843894 | 3.15% | 12045 |
| chr2 | 6908497 | 2.85% | 11380 |
| chr3 | 5048114 | 2.55% | 8432 |
| chr4 | 3817356 | 2.01% | 6545 |
| chr5 | 4649946 | 2.56% | 7720 |
| chr6 | 4707255 | 2.76% | 7710 |
| chr7 | 4346591 | 2.73% | 7042 |
| chr8 | 3916596 | 2.70% | 6511 |
| chr9 | 3830795 | 2.77% | 6035 |
| chr10 | 4333748 | 3.24% | 6982 |
| chr11 | 4630692 | 3.43% | 7149 |
| chr12 | 3919704 | 2.94% | 6150 |
| chr13 | 2205434 | 1.93% | 3788 |
| chr14 | 2625381 | 2.45% | 4151 |
| chr15 | 2758973 | 2.71% | 4309 |
| chr16 | 3289563 | 3.64% | 4960 |
| chr17 | 4079934 | 4.90% | 5874 |
| chr18 | 2054578 | 2.56% | 3471 |
| chr19 | 3244288 | 5.53% | 4331 |
| chr20 | 2393109 | 3.71% | 3740 |
| chr21 | 1068206 | 2.29% | 1721 |
| chr22 | 2061924 | 4.06% | 3021 |
| chrX | 2106019 | 1.35% | 3355 |
| chrY | 41638 | 0.07% | 71 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 136493 | 150 | 3693 | 629.21 | 537 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF974XTQ.bed.gz | 5.39 MB | a015fc7f7e4defa835a2827b30903291 |
| ENCFF974XTQ.tabix.bed.gz | 1.49 MB | 0b7f35f46f5b8b317a607c499dc75cdf |
| ENCFF974XTQ.tabix.bed.gz.tbi | 521.76 KB | de4d68bc7f1a0b01760fa9e5b7fb48d0 |
| genomic_resource.yaml | 3.87 KB | bdc2e4297da08da7a0cfb1c57db6dfa5 |
| statistics/ |