Resource
| Id | ATAC-seq/ENCSR404LLJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR404LLJ [biosample_summary="Homo sapiens transverse colon tissue female adult (53 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (53 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN680ZYC|/analyses/ENCAN680ZYC/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN680ZYC|/analyses/ENCAN680ZYC/} has in progress subobject document {c2efb293-2a58-4455-a528-da147246a17f|/documents/c2efb293-2a58-4455-a528-da147246a17f/} 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 {ENCFF413SRZ|/files/ENCFF413SRZ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.815462. 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 {ENCFF413SRZ|/files/ENCFF413SRZ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.83. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR404LLJ | float |
ATAC-seq_ENCSR404LLJ |
ATAC-seq ENCSR404LLJ [biosample_summary="Homo sapiens transverse colon tissue female adult (53 years)"]
|
 |
[1.28, 37.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 67220996 | 2.09% | 119795 |
| chr1 | 6469216 | 2.60% | 11315 |
| chr2 | 5446465 | 2.25% | 9947 |
| chr3 | 4134279 | 2.08% | 7539 |
| chr4 | 3052185 | 1.60% | 5677 |
| chr5 | 3419989 | 1.88% | 6258 |
| chr6 | 3905897 | 2.29% | 7036 |
| chr7 | 3420108 | 2.15% | 6173 |
| chr8 | 2855725 | 1.97% | 5179 |
| chr9 | 3020349 | 2.18% | 5404 |
| chr10 | 3310978 | 2.47% | 6061 |
| chr11 | 3481035 | 2.58% | 6117 |
| chr12 | 3274736 | 2.46% | 5793 |
| chr13 | 1565355 | 1.37% | 2864 |
| chr14 | 2117253 | 1.98% | 3775 |
| chr15 | 2257451 | 2.21% | 4038 |
| chr16 | 2447765 | 2.71% | 4232 |
| chr17 | 3249429 | 3.90% | 5494 |
| chr18 | 1388082 | 1.73% | 2587 |
| chr19 | 2561486 | 4.37% | 4059 |
| chr20 | 1828634 | 2.84% | 3266 |
| chr21 | 905253 | 1.94% | 1607 |
| chr22 | 1403389 | 2.76% | 2420 |
| chrX | 1705692 | 1.09% | 2953 |
| chrY | 245 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 119795 | 150 | 3140 | 561.13 | 463 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF563UYM.bed.gz | 4.74 MB | ed7656106467465e9b3813c7aa0eaab8 |
| ENCFF563UYM.tabix.bed.gz | 1.31 MB | 7981a84dc4b2cbe58b41fb6a2fbbd243 |
| ENCFF563UYM.tabix.bed.gz.tbi | 446.72 KB | db170fc6622e1b3d0cbc9a2eb2d6ad14 |
| genomic_resource.yaml | 2.8 KB | 7c7a5dd11262a006a5bb6a8455b3b7be |
| statistics/ |