Resource
| Id | Histone_ChIP-seq/ENCSR000DUJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DUJ [biosample_summary="Homo sapiens foreskin fibroblast male newborn" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male newborn output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN328QXM|/analyses/ENCAN328QXM/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF023FMY|/files/ENCFF023FMY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 14629513 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 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 alignments file {ENCFF023FMY|/files/ENCFF023FMY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.81. 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 alignments file {ENCFF023FMY|/files/ENCFF023FMY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 5.59. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DUJ | float |
Histone_ChIP-seq_ENCSR000DUJ |
Histone_ChIP-seq ENCSR000DUJ [biosample_summary="Homo sapiens foreskin fibroblast male newborn" and target="H3K4me3"]
|
 |
[2.15, 137] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 39895567 | 1.24% | 26345 |
| chr1 | 3899628 | 1.57% | 2543 |
| chr2 | 2754839 | 1.14% | 1832 |
| chr3 | 2308153 | 1.16% | 1442 |
| chr4 | 1624575 | 0.85% | 1050 |
| chr5 | 1960467 | 1.08% | 1249 |
| chr6 | 2437291 | 1.43% | 1559 |
| chr7 | 1893431 | 1.19% | 1269 |
| chr8 | 1516724 | 1.05% | 994 |
| chr9 | 1626511 | 1.18% | 1139 |
| chr10 | 1677479 | 1.25% | 1126 |
| chr11 | 2146295 | 1.59% | 1352 |
| chr12 | 2207427 | 1.66% | 1353 |
| chr13 | 832197 | 0.73% | 586 |
| chr14 | 1268210 | 1.18% | 814 |
| chr15 | 1332374 | 1.31% | 872 |
| chr16 | 1535801 | 1.70% | 1055 |
| chr17 | 2229880 | 2.68% | 1515 |
| chr17_GL000205v2_random | 2237 | 1.21% | 2 |
| chr18 | 696952 | 0.87% | 508 |
| chr19 | 2421403 | 4.13% | 1697 |
| chr20 | 999912 | 1.55% | 695 |
| chr21 | 374884 | 0.80% | 259 |
| chr22 | 836356 | 1.65% | 561 |
| chr22_KI270733v1_random | 346 | 0.19% | 1 |
| chrUn_GL000195v1 | 320 | 0.17% | 1 |
| chrUn_GL000219v1 | 3253 | 1.82% | 3 |
| chrUn_GL000220v1 | 345 | 0.21% | 1 |
| chrX | 1263405 | 0.81% | 846 |
| chrY | 44872 | 0.08% | 21 |
| 3337 contigs with no values (128187826 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 26345 | 185 | 39207 | 1514.35 | 1167 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF385THT.bed.gz | 721.28 KB | efb82ec45cbb1fb14723964590495102 |
| ENCFF385THT.tabix.bed.gz | 305.61 KB | a5b44cc6918031d2fd010dd7174e053e |
| ENCFF385THT.tabix.bed.gz.tbi | 156.04 KB | f3f1b9b9f044d0e2b522c8efd1f3c08f |
| genomic_resource.yaml | 3.19 KB | 58771132aba5fb14a7d99c9ff94b417d |
| statistics/ |