Resource
| Id | Histone_ChIP-seq/ENCSR366QMB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR366QMB [biosample_summary="Homo sapiens SK-N-SH" and target="H2AFZ"] |
| Description |
status: archived biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN150FBW|/analyses/ENCAN150FBW/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF441RNP|/files/ENCFF441RNP/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 12505929 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H2AFZ-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 {ENCFF441RNP|/files/ENCFF441RNP/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF441RNP|/files/ENCFF441RNP/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.79. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR366QMB | float |
Histone_ChIP-seq_ENCSR366QMB |
Histone_ChIP-seq ENCSR366QMB [biosample_summary="Homo sapiens SK-N-SH" and target="H2AFZ"]
|
 |
[1.65, 19.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 59420552 | 1.85% | 90885 |
| chr1 | 5695978 | 2.29% | 8620 |
| chr1_KI270708v1_random | 882 | 0.69% | 1 |
| chr1_KI270712v1_random | 535 | 0.30% | 2 |
| chr1_KI270713v1_random | 464 | 1.14% | 2 |
| chr2 | 5035012 | 2.08% | 7823 |
| chr3 | 3968084 | 2.00% | 6140 |
| chr4 | 4005009 | 2.11% | 6351 |
| chr4_GL000008v2_random | 333 | 0.16% | 1 |
| chr5 | 3844138 | 2.12% | 6014 |
| chr6 | 4152323 | 2.43% | 6192 |
| chr7 | 3674994 | 2.31% | 5632 |
| chr8 | 2745005 | 1.89% | 4295 |
| chr9 | 2195214 | 1.59% | 3426 |
| chr9_KI270719v1_random | 2510 | 1.42% | 4 |
| chr10 | 2418215 | 1.81% | 3635 |
| chr11 | 2644328 | 1.96% | 4026 |
| chr12 | 3100933 | 2.33% | 4726 |
| chr13 | 1964808 | 1.72% | 3211 |
| chr14 | 1693039 | 1.58% | 2487 |
| chr14_GL000009v2_random | 740 | 0.37% | 2 |
| chr14_GL000194v1_random | 319 | 0.17% | 1 |
| chr14_KI270722v1_random | 1274 | 0.66% | 1 |
| chr14_KI270723v1_random | 259 | 0.68% | 1 |
| chr14_KI270724v1_random | 910 | 2.30% | 1 |
| chr15 | 1623364 | 1.59% | 2342 |
| chr16 | 1363693 | 1.51% | 2009 |
| chr17 | 2187073 | 2.63% | 3114 |
| chr17_GL000205v2_random | 2753 | 1.48% | 4 |
| chr18 | 1391652 | 1.73% | 2239 |
| chr19 | 1768471 | 3.02% | 2465 |
| chr20 | 1195265 | 1.85% | 1788 |
| chr21 | 705094 | 1.51% | 1166 |
| chr22 | 571056 | 1.12% | 863 |
| chr22_KI270733v1_random | 960 | 0.53% | 3 |
| chrUn_GL000195v1 | 3370 | 1.84% | 7 |
| chrUn_GL000218v1 | 282 | 0.17% | 1 |
| chrUn_GL000219v1 | 4237 | 2.36% | 7 |
| chrUn_KI270337v1 | 201 | 17.93% | 1 |
| chrUn_KI270442v1 | 3325 | 0.85% | 6 |
| chrUn_KI270466v1 | 347 | 28.14% | 1 |
| chrUn_KI270467v1 | 1178 | 30.05% | 2 |
| chrUn_KI270519v1 | 224 | 0.16% | 1 |
| chrUn_KI270744v1 | 210 | 0.12% | 1 |
| chrUn_KI270750v1 | 905 | 0.61% | 2 |
| chrX | 1451586 | 0.93% | 2269 |
| 3321 contigs with no values (183166191 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 90885 | 185 | 6887 | 653.8 | 522 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF066ZAG.bed.gz | 2.15 MB | 26d5793b41fd139fdab50ea793f5f8fb |
| ENCFF066ZAG.tabix.bed.gz | 976.54 KB | 3a0868e45422496425c4e9f94af210a6 |
| ENCFF066ZAG.tabix.bed.gz.tbi | 358.74 KB | 5a806378e08484a0d1e66cfd67b30e71 |
| genomic_resource.yaml | 3.16 KB | e8cc85471c8d3fcdebd11dc8f459308f |
| statistics/ |