# Poor quality of Forward vs Reverse reads
**URL:** https://forum.qiime2.org/t/poor-quality-of-forward-vs-reverse-reads/18444
**Category:** User Support
**Tags:** import
**Created:** [February 10, 2021, 9:44am UTC](https://forum.qiime2.org/t/poor-quality-of-forward-vs-reverse-reads/18444 "2021-02-10T09:44:28Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@Nicheca1](https://forum.qiime2.org/u/Nicheca1)
#### Post date: [February 10, 2021, 9:44am UTC](https://forum.qiime2.org/t/poor-quality-of-forward-vs-reverse-reads/18444/1 "2021-02-10T09:44:28Z")
Hello,
I imported pair-ends reads (PE300, Illumina HiSeq 4000 PE100, fastq files with quality at 33bp) with the manifest option reporting R1 as Forward and R2 as Reverse reads in 2 separeted column on top of the sample-id column.
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path manifest.tsv
--output-path demux-paired-end.qza
--input-format PairedEndFastqManifestPhred33V2
Manifest:
When I look at the demux-summay, I end it up with better quality of my reverse compared to forward reads. Any idea why? Should not be the contrary ?
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### Author:  [@lukasbeule](https://forum.qiime2.org/u/lukasbeule)
#### Post date: [February 10, 2021, 2:18pm UTC](https://forum.qiime2.org/t/poor-quality-of-forward-vs-reverse-reads/18444/2 "2021-02-10T14:18:40Z")
Hi @Nicheca1,
this may be anecdotal but I receive very similar quality plots for my sequence reads when I analyse mixed orientation sequences.
Cheers,
Lukas
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### Author:  [@Nicheca1](https://forum.qiime2.org/u/Nicheca1)
#### Post date: [February 11, 2021, 11:14am UTC](https://forum.qiime2.org/t/poor-quality-of-forward-vs-reverse-reads/18444/3 "2021-02-11T11:14:23Z")
Interesting @lukasbeule , is it maybe something not abnormal - But how explain?
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### Author:  [@lukasbeule](https://forum.qiime2.org/u/lukasbeule)
#### Post date: [February 11, 2021, 4:09pm UTC](https://forum.qiime2.org/t/poor-quality-of-forward-vs-reverse-reads/18444/4 "2021-02-11T16:09:55Z")
🤔 I don't know why the quality behaves like this. Maybe someone else in the forum knows the answer to it?!
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### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [February 11, 2021, 4:16pm UTC](https://forum.qiime2.org/t/poor-quality-of-forward-vs-reverse-reads/18444/5 "2021-02-11T16:16:33Z")
> [@Nicheca1](#):
>
> When I look at the demux-summay, I end it up with better quality of my reverse compared to forward reads. Any idea why? Should not be the contrary ?
I would not worry about it... it's true that reverse reads typically have lower quality than forward, but this is not a rule 🤷♂️
Someone on this forum (can't find the post) recently reported that their sequencing company mislabeled the forward and reverse reads, so it's also possible 🤷♂️ worth quickly inspecting the reads before importing to see if the orientations are clearly reversed (e.g., if primers are still in the reads or if there are other patterns to search for)
Good luck!
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### Author:  [@Nicheca1](https://forum.qiime2.org/u/Nicheca1)
#### Post date: [February 18, 2021, 8:33am UTC](https://forum.qiime2.org/t/poor-quality-of-forward-vs-reverse-reads/18444/6 "2021-02-18T08:33:45Z")
Hi @Nicholas_Bokulich, many thanks for your reply.
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [March 21, 2021, 2:33pm UTC](https://forum.qiime2.org/t/poor-quality-of-forward-vs-reverse-reads/18444/7 "2021-03-21T14:33:48Z")
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