Resource
| Id | Histone_ChIP-seq/ENCSR385NUC |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR385NUC [biosample_summary="Homo sapiens muscle layer of colon tissue female adult (77 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (77 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN902NAO|/analyses/ENCAN902NAO/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF206RZP|/files/ENCFF206RZP/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline has 34086440 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 {ENCFF206RZP|/files/ENCFF206RZP/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.83. 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 {ENCFF206RZP|/files/ENCFF206RZP/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC2 value of 5.56. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR385NUC | float |
Histone_ChIP-seq_ENCSR385NUC |
Histone_ChIP-seq ENCSR385NUC [biosample_summary="Homo sapiens muscle layer of colon tissue female adult (77 years)" and target="H3K4me1"]
|
 |
[1.77, 15.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 114183899 | 3.55% | 107982 |
| chr1 | 11417500 | 4.59% | 10401 |
| chr2 | 9707744 | 4.01% | 9009 |
| chr3 | 8439005 | 4.26% | 7937 |
| chr4 | 5071206 | 2.67% | 5204 |
| chr5 | 5959313 | 3.28% | 5814 |
| chr6 | 5987984 | 3.51% | 6113 |
| chr7 | 5360281 | 3.36% | 5397 |
| chr8 | 4739426 | 3.27% | 4776 |
| chr9 | 5696314 | 4.12% | 5077 |
| chr10 | 6892649 | 5.15% | 6162 |
| chr11 | 6263750 | 4.64% | 5568 |
| chr12 | 5983152 | 4.49% | 5627 |
| chr13 | 2832403 | 2.48% | 2753 |
| chr14 | 3997356 | 3.73% | 3617 |
| chr15 | 4015899 | 3.94% | 3782 |
| chr16 | 3644438 | 4.03% | 3415 |
| chr17 | 5094103 | 6.12% | 4561 |
| chr18 | 2307062 | 2.87% | 2248 |
| chr19 | 3021767 | 5.16% | 2999 |
| chr20 | 3131182 | 4.86% | 2925 |
| chr21 | 1075193 | 2.30% | 1078 |
| chr22 | 2409100 | 4.74% | 2103 |
| chrX | 1137072 | 0.73% | 1416 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 107982 | 245 | 17018 | 1057.43 | 810 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF607YTO.bed.gz | 2.37 MB | a6f63e9684af3b98cb8bcce11f2e1682 |
| ENCFF607YTO.tabix.bed.gz | 1.11 MB | 4e3bf37993ec8d5d826136990fcc4aa1 |
| ENCFF607YTO.tabix.bed.gz.tbi | 307.29 KB | dc4708a963326876bfd73b9615f51a22 |
| genomic_resource.yaml | 3.33 KB | 1481acf10550ec91782f84f52034393a |
| statistics/ |