Resource
| Id | Histone_ChIP-seq/ENCSR000APK |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000APK [biosample_summary="Homo sapiens osteoblast" and target="H3K4me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN631RME|/analyses/ENCAN631RME/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF204IFH|/files/ENCFF204IFH/} processed by ChIP-seq ENCODE3 hg19 pipeline has 8649672 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 {ENCFF939UEF|/files/ENCFF939UEF/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.88. 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 {ENCFF939UEF|/files/ENCFF939UEF/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.33. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000APK | float |
Histone_ChIP-seq_ENCSR000APK |
Histone_ChIP-seq ENCSR000APK [biosample_summary="Homo sapiens osteoblast" and target="H3K4me2"]
|
 |
[1.64, 61.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 102287358 | 3.18% | 102840 |
| chr1 | 9623812 | 3.87% | 9492 |
| chr2 | 8235332 | 3.40% | 8565 |
| chr3 | 6616261 | 3.34% | 6806 |
| chr4 | 5057773 | 2.66% | 5284 |
| chr5 | 5815855 | 3.20% | 5970 |
| chr6 | 6640322 | 3.89% | 6556 |
| chr7 | 5167174 | 3.24% | 5349 |
| chr8 | 4679933 | 3.22% | 4896 |
| chr9 | 4346784 | 3.14% | 4453 |
| chr10 | 4810570 | 3.60% | 4845 |
| chr11 | 5177646 | 3.83% | 5022 |
| chr12 | 5406973 | 4.06% | 5270 |
| chr13 | 2691969 | 2.35% | 2853 |
| chr14 | 3161324 | 2.95% | 3129 |
| chr15 | 3473965 | 3.41% | 3516 |
| chr16 | 3221379 | 3.57% | 3135 |
| chr17 | 4656646 | 5.59% | 4367 |
| chr18 | 2106068 | 2.62% | 2266 |
| chr19 | 3663165 | 6.25% | 3201 |
| chr20 | 2415946 | 3.75% | 2473 |
| chr21 | 1206899 | 2.58% | 1230 |
| chr22 | 1765811 | 3.47% | 1711 |
| chrX | 2345318 | 1.50% | 2450 |
| chrY | 433 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 102840 | 185 | 22049 | 994.63 | 727 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF605FCR.bed.gz | 2.55 MB | 03830ca2f3cf999cf3e34231be729e58 |
| ENCFF605FCR.tabix.bed.gz | 1.1 MB | 78ff5f4dbcfe5c574301d137b294a121 |
| ENCFF605FCR.tabix.bed.gz.tbi | 366.84 KB | b5ee97981b29b0a937cbeca574a54def |
| genomic_resource.yaml | 3.18 KB | a894b2fd58aa656ed41bd4c69d1ec1d0 |
| statistics/ |