samtools pileup base quality

swapna

Junior Member

Join Date: Feb 2011

Posts: 2
- Share
- Tweet
#1

samtools pileup base quality

02-23-2011, 04:36 AM

Hello,

I would like to understand the pileup base quality scores for SNPs.

For example, I have this SNP call at one of the positions
T to Y (which is C or T).
The read depth is 61.
The base quality column is
C$C$C$.$C$C$CCC..CC.CC..C.CCC.CC.CCCCCC.....,,,,,,......,.......,,,

I suppose in this case . probably means 'same as the original base', which would be 'T' in this case. But I don't understand what the , and $ stand for.

What is the best way to determine the relative proportion of each base in case of ambiguous SNPs?

Can I just calculate the number of reads with the individual calls?

In the other calls I have come across the following symbols which I need help to interpret.
$ , . ~ ^ CAPITAL_LETTERS small_letters

Is there a parameter I can use in pileup to give me a score for the individual calls? I did not find anything helpful in the manual.

Apologies in case this question has already been asked/answered in the past. It would be great if somebody could direct me to the right thread.

Thanks!
Tags: base quality, pileup, samtools, snps

Previous template Next

Nine Things a Sample Prep Scientist Thinks About Before Sequencing

by SEQadmin2

I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

Here are nine questions we think about, in roughly the order they matter, before...
- Channel: Articles
06-18-2026, 07:11 AM
From Collection to Sequencing: Why Sample Preparation and Preservation Define Sequencing Data

by SEQadmin2

Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.

The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...
- Channel: Articles
06-02-2026, 10:05 AM
Single-Cell Sequencing at an Inflection Point: Early Impacts of New Platforms and Emerging Trends

by SEQadmin2

With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.

Introduction

Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...
- Channel: Articles
05-22-2026, 06:42 AM

Topics	Statistics	Last Post
Whole-Genome Sequencing Traces Faroe Islands Ancestry to a North Atlantic Founder Population by SEQadmin2 Started by SEQadmin2, 06-17-2026, 06:09 AM	0 responses 21 views 0 reactions	Last Post by SEQadmin2 06-17-2026, 06:09 AM
Sequencing the Two-Toed Sloth Genome Reveals Jumping Genes Tied to Its Extreme Metabolism by SEQadmin2 Started by SEQadmin2, 06-09-2026, 11:58 AM	0 responses 38 views 0 reactions	Last Post by SEQadmin2 06-09-2026, 11:58 AM
A New Method Makes Hantavirus Genome Analysis Faster and More Accessible by SEQadmin2 Started by SEQadmin2, 06-05-2026, 10:09 AM	0 responses 45 views 0 reactions	Last Post by SEQadmin2 06-05-2026, 10:09 AM
A New Single-Cell Method Maps DNA-Protein Interactions by SEQadmin2 Started by SEQadmin2, 06-04-2026, 08:59 AM	0 responses 49 views 0 reactions	Last Post by SEQadmin2 06-04-2026, 08:59 AM

Unconfigured Ad

samtools pileup base quality

Latest Articles

ad_right_rmr

News