Resource
| Id | Histone_ChIP-seq/ENCSR045QJH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR045QJH [biosample_summary="Homo sapiens common myeloid progenitor, CD34-positive" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN316MCW|/analyses/ENCAN316MCW/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF174ZXA|/files/ENCFF174ZXA/} processed by ChIP-seq ENCODE3 hg19 pipeline has 12353105 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 {ENCFF987LBK|/files/ENCFF987LBK/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.83. 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 {ENCFF987LBK|/files/ENCFF987LBK/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 5.93. 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 {ENCFF174ZXA|/files/ENCFF174ZXA/} 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 {ENCFF174ZXA|/files/ENCFF174ZXA/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.94. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR045QJH | float |
Histone_ChIP-seq_ENCSR045QJH |
Histone_ChIP-seq ENCSR045QJH [biosample_summary="Homo sapiens common myeloid progenitor, CD34-positive" and target="H3K4me3"]
|
 |
[1.5, 75.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 41849729 | 1.30% | 36077 |
| chr1 | 4164816 | 1.67% | 3597 |
| chr2 | 2898036 | 1.20% | 2492 |
| chr3 | 2458511 | 1.24% | 2092 |
| chr4 | 1650132 | 0.87% | 1364 |
| chr5 | 1971415 | 1.09% | 1608 |
| chr6 | 2474793 | 1.45% | 2045 |
| chr7 | 2039404 | 1.28% | 1843 |
| chr8 | 1522972 | 1.05% | 1337 |
| chr9 | 1723681 | 1.25% | 1511 |
| chr10 | 1778172 | 1.33% | 1587 |
| chr11 | 2185410 | 1.62% | 1811 |
| chr12 | 2299344 | 1.73% | 1939 |
| chr13 | 867998 | 0.76% | 765 |
| chr14 | 1386562 | 1.30% | 1154 |
| chr15 | 1391283 | 1.36% | 1243 |
| chr16 | 1641493 | 1.82% | 1461 |
| chr17 | 2383389 | 2.86% | 1988 |
| chr18 | 694748 | 0.86% | 655 |
| chr19 | 2618683 | 4.47% | 2288 |
| chr20 | 1083249 | 1.68% | 976 |
| chr21 | 502376 | 1.08% | 446 |
| chr22 | 919317 | 1.81% | 833 |
| chrX | 1193567 | 0.76% | 1041 |
| chrY | 378 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 36077 | 155 | 29033 | 1160.01 | 712 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF786UIZ.bed.gz | 916.07 KB | 5180a6e68ec5ebc470b06e19e45fbb73 |
| ENCFF786UIZ.tabix.bed.gz | 400.26 KB | e65745dc6158518121c0c29718d05e7f |
| ENCFF786UIZ.tabix.bed.gz.tbi | 178.97 KB | 6ed7dbb566a5c8b17853fb5967f38e88 |
| genomic_resource.yaml | 4.63 KB | 5c9981fbdf1f0228b010b4bb27d388ee |
| statistics/ |