Resource
| Id | Histone_ChIP-seq/ENCSR000ANZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000ANZ [biosample_summary="Homo sapiens myotube originated from skeletal muscle myoblast" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (22 years) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN984FTN|/analyses/ENCAN984FTN/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF031OJV|/files/ENCFF031OJV/} processed by ChIP-seq ENCODE3 hg19 pipeline has 7283193 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: Processed alignments file {ENCFF463DMW|/files/ENCFF463DMW/} processed by ChIP-seq ENCODE3 hg19 pipeline has 10620713 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 {ENCFF463DMW|/files/ENCFF463DMW/} 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 {ENCFF463DMW|/files/ENCFF463DMW/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.25. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000ANZ | float |
Histone_ChIP-seq_ENCSR000ANZ |
Histone_ChIP-seq ENCSR000ANZ [biosample_summary="Homo sapiens myotube originated from skeletal muscle myoblast" and target="H3K4me3"]
|
 |
[1.61, 61.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 39747012 | 1.24% | 36731 |
| chr1 | 3868293 | 1.55% | 3500 |
| chr2 | 2959955 | 1.22% | 2815 |
| chr3 | 2364160 | 1.19% | 2161 |
| chr4 | 1711792 | 0.90% | 1579 |
| chr5 | 1971760 | 1.09% | 1757 |
| chr6 | 2477579 | 1.45% | 2309 |
| chr7 | 1831817 | 1.15% | 1711 |
| chr8 | 1504760 | 1.04% | 1467 |
| chr9 | 1648654 | 1.19% | 1592 |
| chr10 | 1834717 | 1.37% | 1781 |
| chr11 | 2128681 | 1.58% | 1907 |
| chr12 | 2121355 | 1.59% | 1868 |
| chr13 | 928915 | 0.81% | 912 |
| chr14 | 1305479 | 1.22% | 1164 |
| chr15 | 1344390 | 1.32% | 1255 |
| chr16 | 1425997 | 1.58% | 1287 |
| chr17 | 2092065 | 2.51% | 1914 |
| chr18 | 710822 | 0.88% | 698 |
| chr19 | 2135107 | 3.64% | 1909 |
| chr20 | 926470 | 1.44% | 896 |
| chr21 | 453892 | 0.97% | 464 |
| chr22 | 837157 | 1.65% | 780 |
| chrX | 1125011 | 0.72% | 981 |
| chrY | 38184 | 0.07% | 24 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 36731 | 190 | 16461 | 1082.11 | 696 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF046FNE.bed.gz | 952.36 KB | 8ca5e2102c8440f917ba86c06c0b3177 |
| ENCFF046FNE.tabix.bed.gz | 413.13 KB | 87afd44d672ca4f18da5fab4c1918126 |
| ENCFF046FNE.tabix.bed.gz.tbi | 194.12 KB | 18b2415f6e632b12cfaed57de12fa467 |
| genomic_resource.yaml | 3.74 KB | e80db59b24877192435f13c94afbb704 |
| statistics/ |