Resource
| Id | Histone_ChIP-seq/ENCSR377QMP |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR377QMP [biosample_summary="Homo sapiens GM23248" and target="H3F3A"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN282IXK|/analyses/ENCAN282IXK/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF176WLX|/files/ENCFF176WLX/} processed by ChIP-seq ENCODE3 hg19 pipeline has 18996805 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3F3A-human and investigated as a broad histone mark is 20 million usable fragments. 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 {ENCFF984PKN|/files/ENCFF984PKN/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF984PKN|/files/ENCFF984PKN/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.87. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR377QMP | float |
Histone_ChIP-seq_ENCSR377QMP |
Histone_ChIP-seq ENCSR377QMP [biosample_summary="Homo sapiens GM23248" and target="H3F3A"]
|
 |
[1.44, 9.17] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 129755440 | 4.03% | 143452 |
| chr1 | 12872589 | 5.17% | 14144 |
| chr2 | 11695894 | 4.83% | 12413 |
| chr3 | 9378239 | 4.73% | 10320 |
| chr4 | 6322264 | 3.32% | 6972 |
| chr5 | 8160362 | 4.50% | 8544 |
| chr6 | 7957085 | 4.66% | 8798 |
| chr7 | 6317512 | 3.96% | 6955 |
| chr8 | 6435417 | 4.43% | 7046 |
| chr9 | 5859066 | 4.23% | 6412 |
| chr10 | 6533877 | 4.88% | 7219 |
| chr11 | 6783130 | 5.02% | 7320 |
| chr12 | 7377743 | 5.54% | 7978 |
| chr13 | 3274683 | 2.86% | 3730 |
| chr14 | 4267347 | 3.99% | 4720 |
| chr15 | 5011544 | 4.91% | 5130 |
| chr16 | 3242057 | 3.59% | 3877 |
| chr17 | 5101848 | 6.13% | 5844 |
| chr18 | 2544478 | 3.17% | 2896 |
| chr19 | 2585594 | 4.41% | 3333 |
| chr20 | 2947681 | 4.57% | 3425 |
| chr21 | 1442060 | 3.09% | 1608 |
| chr22 | 1924501 | 3.79% | 2192 |
| chrX | 1632344 | 1.05% | 2446 |
| chrY | 88125 | 0.15% | 130 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 143452 | 190 | 24379 | 904.52 | 672 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF921OQX.bed.gz | 3.46 MB | 9af97efbbfe462feed9d9d20d578c6e4 |
| ENCFF921OQX.tabix.bed.gz | 1.5 MB | df5605e8119cdcd856fc2a62f0aec620 |
| ENCFF921OQX.tabix.bed.gz.tbi | 333.47 KB | 6d33fbfa798620932e3c97b8a70af145 |
| genomic_resource.yaml | 3.16 KB | c34d97b58c030cd7dc4b1f43923da88a |
| statistics/ |