> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/instrumentation/miseq-i100-series/instrumentation-miseq-i100-series-reference_material-list/000009204.md).
# Specifications for the MiSeq i100 Series Instruments
**Output per flow cell for various read lengths**
Sequence read length refers to the length of each sequenced DNA fragment and whether it is sequenced from one end (single read) or both ends (paired-end reads). For example, a 2 × 150 bp run generates two reads (forward and reverse) of 150 base pairs each for a single DNA fragment. Longer read lengths have a better probability of spanning repeats in the DNA sequence, while shorter read lengths can be cost-effective for counting methodologies where broad genome coverage is not required.
**Table 1.** Yield Expectations Based on Read length.
1. Specifications based on Illumina PhiX control library at recommended loading concentration.
2. 5M and 25M flow cells available with platform release for both the MiSeq i100 and the MiSeq i100 Plus Systems.
3. 50M and 100M flow cells are available for the MiSeq i100 Plus System only.
**Reads passing filter per flow cell**
Reads Passing Filter (%PF) is the percentage of clusters passing chastity filtering, providing one read (single-end reads) or two reads (paired-end reads). Single-end runs involve sequencing DNA from only one end and offer an economical alternative. Paired-end runs sequence both DNA ends for easier analysis of rearrangements, novel transcripts, and more.
**Table 2.** Read Specifications
1. 5M and 25M flow cells available with platform release for both the MiSeq i100 and the MiSeq i100 Plus Systems.
2. 50M and 100M flow cells are available for the MiSeq i100 Plus System only.
**Quality scores**
A quality score, or Q score, is a prediction of the probability of an error in base calling. Higher Q scores indicate a smaller probability of error. A quality score of 30 represents an error rate of 1 in 1000 with a corresponding call accuracy of 99.9%.
**Table 3.** Q30 Score Specifications
**NOTE:** The percentage of bases ≥ Q30 is averaged across the entire sequencing run. Quality scores are based on MiSeq i100 Series reagents using an Illumina PhiX control library.
**Run time**
Sequencing run time includes cluster generation, onboard denaturation, sequencing, base calling, and quality scoring on the instrument.
**Table 4.** Run Time Estimates
1. 5M and 25M flow cells available with platform release for both the MiSeq i100 and the MiSeq i100 Plus Systems.
2. 50M and 100M flow cells are available for the MiSeq i100 Plus System only.
**Estimated sample throughput for key applications**
Sample throughput is the number of samples that can be sequenced in a single run per flow cell.
**Table 5.** Estimated sample throughput for key applications
1. Reads per sample and sample throughputs are estimates and highly variable, depending on the panel and desired coverage.
2. 5M and 25M flow cells available with platform release for both the MiSeq i100 and the MiSeq i100 Plus Systems.
3. 50M and 100M flow cells are available for the MiSeq i100 Plus System only.
4. Estimated reads per sample based on minimum 30× coverage of an average 5MB bacterial genome.
See the [MiSeq i100 Series Specifications page](https://www.illumina.com/systems/sequencing-platforms/miseq-i100/specifications.html) for more information.
\
\
\
| |
| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #9204), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009204%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |
---
# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.
## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.
Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:
```
GET https://knowledge.illumina.com/instrumentation/miseq-i100-series/instrumentation-miseq-i100-series-reference_material-list/000009204.md?ask=&goal=
```
`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.
Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.