Specifications for the MiSeq i100 Series Instruments

Output per flow cell for various read lengths

What is read length? 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 for each 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 supported cluster densities.

2. 5M and 25M flow cells available with platform release.

3. 50M and 100M flow cells will be available starting in 2025 for the MiSeq i100 Plus System only.

Reads passing filter per flow cell

What are reads passing filter(PF)? The percentage of clusters passing chastity filtering, with each passing filter cluster providing a read (single-end reads) or two reads (paired-end reads). Clusters pass filter if no more than one base call has a chastity value below 0.6 in the first 25 cycles. Chastity is defined as the ratio of the brightest base intensity divided by the sum of the brightest and second brightest base intensities. 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.

2. 50M and 100M flow cells will be available starting in 2025 for the MiSeq i100 Plus System only.

Quality scores

What is a quality score? 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

1. 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.

2. 5M and 25M flow cells available with platform release.

3. 50M and 100M flow cells will be available starting in 2025 for the MiSeq i100 Plus System only.

Run time

What is run time? Sequencing run time includes cluster generation, onboard denaturation, sequencing, base calling, and quality scoring on the instrument.

Table 4. Run Time Estimates

Estimated sample throughput for key applications

What is sample throughput? Sample throughput is the number of samples that can be sequenced in a single run per flow cell.

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.

3. 50M and 100M flow cells will be available starting in 2025 for the MiSeq i100 Plus System only.

4. Estimated reads per sample based on minimum 30× coverage of an average 5MB bacterial genome.

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