Resource
| Id | Histone_ChIP-seq/ENCSR214NMO |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR214NMO [biosample_summary="Homo sapiens SJSA1" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN521QBP|/analyses/ENCAN521QBP/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} 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 {ENCFF660SFB|/files/ENCFF660SFB/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF660SFB|/files/ENCFF660SFB/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.73. 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 {ENCFF656NBV|/files/ENCFF656NBV/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 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 {ENCFF656NBV|/files/ENCFF656NBV/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.45. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR214NMO | float |
Histone_ChIP-seq_ENCSR214NMO |
Histone_ChIP-seq ENCSR214NMO [biosample_summary="Homo sapiens SJSA1" and target="H3K4me3"]
|
 |
[1.32, 293] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 31986206 | 0.99% | 20210 |
| chr1 | 3162335 | 1.27% | 1981 |
| chr2 | 2221956 | 0.92% | 1439 |
| chr3 | 1788576 | 0.90% | 1108 |
| chr4 | 1258876 | 0.66% | 817 |
| chr5 | 1540566 | 0.85% | 951 |
| chr6 | 1984048 | 1.16% | 1219 |
| chr7 | 1537491 | 0.96% | 958 |
| chr8 | 1212697 | 0.84% | 801 |
| chr9 | 1248411 | 0.90% | 812 |
| chr10 | 1358675 | 1.02% | 878 |
| chr11 | 1616273 | 1.20% | 1011 |
| chr12 | 1710905 | 1.28% | 1039 |
| chr13 | 677823 | 0.59% | 440 |
| chr14 | 1024330 | 0.96% | 620 |
| chr15 | 1068484 | 1.05% | 676 |
| chr16 | 1318914 | 1.46% | 807 |
| chr17 | 1863925 | 2.24% | 1183 |
| chr18 | 563895 | 0.70% | 363 |
| chr19 | 1930511 | 3.29% | 1261 |
| chr20 | 809198 | 1.26% | 510 |
| chr21 | 342724 | 0.73% | 233 |
| chr22 | 710833 | 1.40% | 442 |
| chrX | 1003100 | 0.64% | 644 |
| chrY | 31660 | 0.06% | 17 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 20210 | 238 | 19940 | 1582.69 | 1463 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF870NJQ.bed.gz | 604.09 KB | 37e6d783769752667e374c943c9f207d |
| ENCFF870NJQ.tabix.bed.gz | 245.95 KB | 77283cb9dd6cb15b24ec1f9cf5a29be3 |
| ENCFF870NJQ.tabix.bed.gz.tbi | 143.28 KB | b0c109889dfc076464afe6df48b087b7 |
| genomic_resource.yaml | 4.0 KB | 630672b79f2a98d6f6c54c9cacab3af2 |
| statistics/ |