Resource
| Id | Histone_ChIP-seq/ENCSR631BPS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR631BPS [biosample_summary="Homo sapiens CD8-positive, alpha-beta T cell" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN249QTZ|/analyses/ENCAN249QTZ/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF908RAR|/files/ENCFF908RAR/} processed by ChIP-seq ENCODE3 hg19 pipeline has 17814667 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_not_compliant: Processed redacted alignments file {ENCFF873LDM|/files/ENCFF873LDM/} processed by ChIP-seq ENCODE3 hg19 pipeline has 19485453 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) 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 > 0.8 is acceptable. ENCODE processed redacted alignments file {ENCFF908RAR|/files/ENCFF908RAR/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.87. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed redacted alignments file {ENCFF908RAR|/files/ENCFF908RAR/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.75. 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 > 0.8 is acceptable. ENCODE processed redacted alignments file {ENCFF873LDM|/files/ENCFF873LDM/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.87. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed redacted alignments file {ENCFF873LDM|/files/ENCFF873LDM/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.82. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR631BPS | float |
Histone_ChIP-seq_ENCSR631BPS |
Histone_ChIP-seq ENCSR631BPS [biosample_summary="Homo sapiens CD8-positive, alpha-beta T cell" and target="H3K4me1"]
|
 |
[1.58, 23.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 94032052 | 2.92% | 93045 |
| chr1 | 9388646 | 3.77% | 9035 |
| chr2 | 7934172 | 3.28% | 7564 |
| chr3 | 5673214 | 2.86% | 5791 |
| chr4 | 3222495 | 1.69% | 3360 |
| chr5 | 4517799 | 2.49% | 4459 |
| chr6 | 5685951 | 3.33% | 5718 |
| chr7 | 4167372 | 2.62% | 4273 |
| chr8 | 3508191 | 2.42% | 3579 |
| chr9 | 3593909 | 2.60% | 3572 |
| chr10 | 4285717 | 3.20% | 4282 |
| chr11 | 4905597 | 3.63% | 4554 |
| chr12 | 4804609 | 3.61% | 4917 |
| chr13 | 2172160 | 1.90% | 2173 |
| chr14 | 3770658 | 3.52% | 3456 |
| chr15 | 3277635 | 3.21% | 3194 |
| chr16 | 3462301 | 3.83% | 3397 |
| chr17 | 5354145 | 6.43% | 5100 |
| chr18 | 1551992 | 1.93% | 1617 |
| chr19 | 4147437 | 7.08% | 4349 |
| chr20 | 2668353 | 4.14% | 2612 |
| chr21 | 1293435 | 2.77% | 1203 |
| chr22 | 2316887 | 4.56% | 2167 |
| chrX | 2186627 | 1.40% | 2486 |
| chrY | 142750 | 0.25% | 187 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 93045 | 210 | 28965 | 1010.61 | 718 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF661YCD.bed.gz | 2.18 MB | d36ce01c68e708a334b5a8a9ec14fb6a |
| ENCFF661YCD.tabix.bed.gz | 992.01 KB | 22c9fa5de4c560b4ceeb5682864e2d0f |
| ENCFF661YCD.tabix.bed.gz.tbi | 226.25 KB | e82c9cc58ae3fd13c0736dbb5daa6a8d |
| genomic_resource.yaml | 5.16 KB | 52b08bb7300db34e2d223952fb3ee6dc |
| statistics/ |