Resource
| Id | Histone_ChIP-seq/ENCSR000APQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000APQ [biosample_summary="Homo sapiens fibroblast of dermis" and target="H3K4me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN410ANP|/analyses/ENCAN410ANP/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF439DMO|/files/ENCFF439DMO/} processed by ChIP-seq ENCODE3 hg19 pipeline has 8818655 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me2-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 {ENCFF516TKM|/files/ENCFF516TKM/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF516TKM|/files/ENCFF516TKM/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.24. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000APQ | float |
Histone_ChIP-seq_ENCSR000APQ |
Histone_ChIP-seq ENCSR000APQ [biosample_summary="Homo sapiens fibroblast of dermis" and target="H3K4me2"]
|
 |
[1.69, 31.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 57005612 | 1.77% | 88080 |
| chr1 | 5459743 | 2.19% | 8209 |
| chr2 | 4461671 | 1.84% | 7092 |
| chr3 | 3582685 | 1.81% | 5577 |
| chr4 | 2570118 | 1.35% | 3975 |
| chr5 | 3093589 | 1.70% | 4903 |
| chr6 | 3634864 | 2.13% | 5602 |
| chr7 | 2787935 | 1.75% | 4446 |
| chr8 | 2479514 | 1.71% | 3967 |
| chr9 | 2437127 | 1.76% | 3753 |
| chr10 | 2811708 | 2.10% | 4378 |
| chr11 | 2947347 | 2.18% | 4334 |
| chr12 | 3087733 | 2.32% | 4529 |
| chr13 | 1357938 | 1.19% | 2207 |
| chr14 | 1762305 | 1.65% | 2712 |
| chr15 | 1950801 | 1.91% | 3030 |
| chr16 | 1841976 | 2.04% | 2860 |
| chr17 | 2841528 | 3.41% | 4134 |
| chr18 | 1221020 | 1.52% | 1907 |
| chr19 | 2395089 | 4.09% | 3445 |
| chr20 | 1374757 | 2.13% | 2183 |
| chr21 | 644735 | 1.38% | 1062 |
| chr22 | 1092259 | 2.15% | 1678 |
| chrX | 1168956 | 0.75% | 2096 |
| chrY | 214 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 88080 | 155 | 18257 | 647.2 | 455 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF350PQN.bed.gz | 1.95 MB | c511531474e85ea473270d172753e7b6 |
| ENCFF350PQN.tabix.bed.gz | 932.38 KB | b9ae7be6a175ca373eed26b338a93243 |
| ENCFF350PQN.tabix.bed.gz.tbi | 306.05 KB | 4dc24c5796b7d88ee4429e980d9788f6 |
| genomic_resource.yaml | 3.3 KB | 3228c0d79bda3cbd2d0c3515aab394d8 |
| statistics/ |