Cell lines » Sample » Overview » SK-MEL-28 View in GRCh37 Archive

Note: In some web browsers, the Genome Browser may display a blank white content panel when switching back from another tab. If this happens please click and drag on the blank content panel, or click here to launch the Genome Browser in a new tab.

Loading sample Genome browser
This tab shows an overview of the sample data [more details]

Sample Information

Sample name
SK-MEL-28
Sample Id
COSS905954
Primary Site; Subtype1; Subtype 2; Subtype 3
Skin; NS; NS; NS
Primary Histology; Subtype1; Subtype 2; Subtype 3
Malignant melanoma; NS; NS; NS
Source
Cultured Sample( primary; cell-line )

Additional Information

Individual details

Age
51
Family
Unknown
Parents tested
Unknown
Normal tissue tested
No
Gender
Male

Supplier

Institute
Developmental Therapeutics Program
Address
National Cancer Institute,Frederick,MD 21701


Microsatellite Stability

BAT25 BAT26 D5S346 D2S123 D17S250
stable stable stable stable stable

STR Profile Data

AMEL CSF1PO D13S317 D16S539 D5S818 D7S820 TH01 TPOX vWA
ALLELE 1 X 10 11 9 11 10 7 8 16
ALLELE 2 Y 12 12 12 13 10 7 12 19
ADDITIONAL - - - - - - - - -



Sequence Statistics

These are the exome sequence statistics across the sample. [more details]
READ 0 READ 21 READ 41 Rpair Gbp Seq UM Pairs Gbp Map Mapped Gbp Uniq Unique
2.66 78.76 60.59 48885432 7.33 9.51 6.5 88.59 6.17 94.97

Download files

This tab shows the mutations observed in this sample [more details]
Gene Transcript Census Gene AA Mutation CDS Mutation Somatic status Zygosity Validated Type Position
This tab shows the mutations observed in this sample [more details]
GeneCDS Mutation Somatic status Zygosity Validated Type
This tab shows a circos diagram of the sample data [more details]
Circos image for 905954
This tab shows a candi diagram of the sample data [more details]
Candi image for 905954
This tab shows a heatmap diagram of the sample data [more details]
heatmap image for 905954
This tab shows the genes with no mutations in this sample (whole genome screen only) [more details]
Mutation ID (COST) Mutation Description Chromosome From Breakpoint From (GRCh38) Strand Chromosome To Breakpoint To (GRCh38) Strand Non Templated Inserted Seq
This tab shows the non-coding mutations in this sample (whole genome screen only) [more details]
Sample ID Sample Name ID NCV Annotation Zygosity Chromosome Genome start Genome stop Genome version Strand WT seq Mut seq
This tab shows the mutation spectrum observed in this sample [more details]
This tab shows the CNVs (copy number variants) for this sample. Only variants (classified as gain or loss) are listed. [more details]

Table Information

Hide

The average ploidy of the genome is 3.93. The table currently shows only high value (numeric) copy number data. Copy number segments are excluded if the total copy number and minor allele values are unknown.

Click here to include all copy number data. For more detailed information about copy number data and gain/loss definitions click here.

Gene Expression Expr Level (Z-Score)

Over Expressed; Z-Score > 2.0

Under Expressed; Z-Score < -2.0

Normal; Z-Score within the range -2.0 to 2.0

CN Type Minor Allele Copy Number CN Segment Posn. Average Ploidy

1. N/A represents cases where the average ploidy value is not available( mostly ICGC samples). For some TCGA samples where the minor allele information is not available the average ploidy value could not be calculated.

2. For TCGA samples, the ASCAT algorithm was used to calculate the average ploidy.

3. For CGP samples, the PICNIC algorithm was used to calculate the average ploidy.

Study CNV
This tab shows the methylation data for this sample. Only variants classified as 'High' (hypermethylation) or 'Low' (hypomethylation) are listed. [more details]
Gene Name Probe ID Probe Posn. Type

High (Hypermethylated); Beta-Value > 0.8 and differs from normal average by > 0.5

Low (Hypomethylated); Beta-Value < 0.2 and differs from normal average by > 0.5

Level (Beta-Value) Normal Average

Mutation Filters