Genomic data

Each sample is uploaded with exactly one of two kinds of genomic data. In the submission form, the files go into the file categories named below.

Option 1: aligned reads

One BAM file per sample, in the file category Aligned reads (BAM). The reads must be:

• aligned to the Wuhan-Hu-1 reference only: the BAM header lists exactly one reference, MN908947.3 or NC_045512.2, with a length of 29903;
• primer-trimmed, e.g. with ivar trim;
• dehosted: human reads have been removed.

The SNV frequencies and the depth per site are derived from the reads during processing and published next to the BAM file.

Option 2: SNV frequencies and depth per site

Two files per sample. Both may be gzip-compressed.

SNV frequencies (VCF)

File category SNV frequencies (VCF). A VCF file with a #CHROM header line:

• records are on MN908947.3 or NC_045512.2, and positions start at 1;
• every record carries the allele frequency, a number between 0 and 1, as AF in the INFO column;
• the total depth at the position as DP in the INFO column is welcome.

Report all variants you called, including those at low frequency, e.g. LoFreq or iVar output without a frequency cutoff: lineage estimation relies on low-frequency variants.

Example record (columns separated by tabs) for the mutation A23403G, found in 98.2 % of the 1840 reads covering position 23403:

#CHROM       POS    ID  REF  ALT  QUAL  FILTER  INFO
MN908947.3   23403  .   A    G    .     PASS    DP=1840;AF=0.982

Depth per site (TSV)

File category Depth per site (TSV). A tab-separated text file with the header position<TAB>depth and then one line for each of the 29903 positions of the reference, in order: the position (starting at 1) and the number of reads covering it. Use the same alignment as for the VCF file.

position	depth
1	12
2	15
3	15