Resource
| Id | Histone_ChIP-seq/ENCSR129NCV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR129NCV [biosample_summary="Homo sapiens stomach tissue male adult (34 years)" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (34 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN063GPO|/analyses/ENCAN063GPO/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF417COB|/files/ENCFF417COB/} processed by ChIP-seq ENCODE3 hg19 pipeline has 17858999 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 {ENCFF417COB|/files/ENCFF417COB/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF417COB|/files/ENCFF417COB/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.35. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR129NCV | float |
Histone_ChIP-seq_ENCSR129NCV |
Histone_ChIP-seq ENCSR129NCV [biosample_summary="Homo sapiens stomach tissue male adult (34 years)" and target="H3K4me3"]
|
 |
[1.78, 61] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 21257187 | 0.66% | 29093 |
| chr1 | 2069420 | 0.83% | 2785 |
| chr2 | 1439522 | 0.59% | 1980 |
| chr3 | 1169247 | 0.59% | 1519 |
| chr4 | 859238 | 0.45% | 1114 |
| chr5 | 1004052 | 0.55% | 1376 |
| chr6 | 1165195 | 0.68% | 1591 |
| chr7 | 1018982 | 0.64% | 1407 |
| chr8 | 821530 | 0.57% | 1117 |
| chr9 | 894384 | 0.65% | 1175 |
| chr10 | 877980 | 0.66% | 1238 |
| chr11 | 1191999 | 0.88% | 1611 |
| chr12 | 1051748 | 0.79% | 1415 |
| chr13 | 438979 | 0.38% | 625 |
| chr14 | 696405 | 0.65% | 949 |
| chr15 | 686673 | 0.67% | 917 |
| chr16 | 919370 | 1.02% | 1254 |
| chr17 | 1240700 | 1.49% | 1711 |
| chr18 | 365903 | 0.46% | 528 |
| chr19 | 1436233 | 2.45% | 2024 |
| chr20 | 575956 | 0.89% | 820 |
| chr21 | 224800 | 0.48% | 339 |
| chr22 | 512752 | 1.01% | 754 |
| chrM | 3523 | 21.26% | 7 |
| chrX | 567038 | 0.36% | 800 |
| chrY | 25558 | 0.04% | 37 |
| 3341 contigs with no values (129060516 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 29093 | 150 | 5034 | 730.66 | 577 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF651VPB.bed.gz | 738.0 KB | f3076ea64a26404ba17eaaa08de3b43c |
| ENCFF651VPB.tabix.bed.gz | 323.5 KB | 9b2a9357f07cece1eedbb924c235da1d |
| ENCFF651VPB.tabix.bed.gz.tbi | 158.31 KB | 730403b648230a9b030eb9093e1f6e8b |
| genomic_resource.yaml | 3.21 KB | 79a940e57209586d14240ee55476dbcc |
| statistics/ |