Resource
| Id | Histone_ChIP-seq/ENCSR000ANR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000ANR [biosample_summary="Homo sapiens skeletal muscle myoblast male adult (22 years)" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (22 years) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN089BLT|/analyses/ENCAN089BLT/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed unfiltered alignments file {ENCFF224BPX|/files/ENCFF224BPX/} processed by ChIP-seq ENCODE3 hg19 pipeline has 17816104 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_not_compliant: Processed unfiltered alignments file {ENCFF436TOF|/files/ENCFF436TOF/} processed by ChIP-seq ENCODE3 hg19 pipeline has 31767549 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. 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 alignments file {ENCFF391OJZ|/files/ENCFF391OJZ/} 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 {ENCFF391OJZ|/files/ENCFF391OJZ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.39. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000ANR | float |
Histone_ChIP-seq_ENCSR000ANR |
Histone_ChIP-seq ENCSR000ANR [biosample_summary="Homo sapiens skeletal muscle myoblast male adult (22 years)" and target="H3K9me3"]
|
 |
[1.59, 10.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 2273280 | 0.07% | 8774 |
| chr1 | 141165 | 0.06% | 565 |
| chr2 | 134039 | 0.06% | 570 |
| chr3 | 92332 | 0.05% | 380 |
| chr4 | 109324 | 0.06% | 474 |
| chr5 | 128032 | 0.07% | 514 |
| chr6 | 78296 | 0.05% | 337 |
| chr7 | 118338 | 0.07% | 472 |
| chr8 | 109836 | 0.08% | 428 |
| chr9 | 78531 | 0.06% | 310 |
| chr10 | 94870 | 0.07% | 403 |
| chr11 | 61934 | 0.05% | 256 |
| chr12 | 104862 | 0.08% | 413 |
| chr13 | 53610 | 0.05% | 242 |
| chr14 | 53055 | 0.05% | 219 |
| chr15 | 90321 | 0.09% | 326 |
| chr16 | 91747 | 0.10% | 343 |
| chr17 | 54136 | 0.07% | 219 |
| chr18 | 52770 | 0.07% | 222 |
| chr19 | 444309 | 0.76% | 1361 |
| chr20 | 46835 | 0.07% | 182 |
| chr21 | 60914 | 0.13% | 236 |
| chr22 | 50801 | 0.10% | 204 |
| chrX | 10450 | 0.01% | 48 |
| chrY | 12773 | 0.02% | 50 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 8774 | 135 | 2215 | 259.09 | 215 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF111IAC.bed.gz | 157.88 KB | c81c5ef2c622db03c19cdbc28c562b51 |
| ENCFF111IAC.tabix.bed.gz | 85.66 KB | 73c42c6c9657e2a115ef96f98eda49f2 |
| ENCFF111IAC.tabix.bed.gz.tbi | 62.38 KB | 973dc27d1fa4019a15203a1373a8bc0f |
| genomic_resource.yaml | 3.73 KB | ccb8ae1acf02b9df0870af460b6d4712 |
| statistics/ |