# Very low percentage of merged reads in DADA2 with 16S V4, 2×150 bp paired-end sequencing

**URL:** https://forum.qiime2.org/t/very-low-percentage-of-merged-reads-in-dada2-with-16s-v4-2x150-bp-paired-end-sequencing/34302
**Category:** User Support
**Tags:** dada2
**Created:** [August 28, 2026, 5:05am UTC](https://forum.qiime2.org/t/very-low-percentage-of-merged-reads-in-dada2-with-16s-v4-2x150-bp-paired-end-sequencing/34302 "2026-08-28T05:05:16Z")
**Posts on this page:** 1
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### Author: ![SoilRotifer](https://forum.qiime2.org/user_avatar/forum.qiime2.org/soilrotifer/32/21071_2.png) [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)
#### Post date: [August 28, 2026, 2:04pm UTC](https://forum.qiime2.org/t/very-low-percentage-of-merged-reads-in-dada2-with-16s-v4-2x150-bp-paired-end-sequencing/34302/2 "2026-08-28T14:04:53Z")

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Hi @Sergio

> [@Sergio](#):
>
> he expected V4 amplicon is approximately **250 bp** , so theoretically I should have around 50 bp of overlap between R1 and R2:
> 
> **150 + 150 − 250 ≈ 50 bp overlap**

I'd still look into truncating your reads a little, given the amount of overlap you have. That is, there is going to be in increase in the chance of mismatches with longer overlap, even with high-quality data. See this [thread](https://forum.qiime2.org/t/running-dada2-on-pre-processed-data/34195/4).

I also had a similar case in which I also had to trim a little from the 5' end, with similar scores. I assume these might be from the new score/binning methods used? If so, hopefully some one else can provide recommendations / insight.

-Cheers!

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