Metadata

Filename	21C125_R1.fastq.gz
Filesize	0.45 GiB
Filename read 2	21C125_R2.fastq.gz
Filesize read 2	0.46 GiB
Sequali version	0.11.0
Report generated on	2024-08-09 17:14:52+0200

Read 1: Summary

Mean length	151.00
Length range (min-max)	151	151
Total reads	5,477,353
Q20 reads	5,147,175	93.97%
Total bases	827,080,303
Total GC bases	273,860,586	33.11%
Q20 bases	798,680,482	96.57%

Read 2: Summary

Mean length	151.00
Length range (min-max)	151	151
Total reads	5,477,353
Q20 reads	5,182,064	94.61%
Total bases	827,080,303
Total GC bases	273,545,195	33.07%
Q20 bases	797,522,582	96.43%

Read 1: Sequence length distribution

Read 2: Sequence length distribution

Read 1: Per position quality score distribution

Read 2: Per position quality score distribution

Read 1: Per position quality percentiles

Shows the mean for all bases and the means of the lowest and highest percentiles to indicate the spread. Since the graph is based on the sampled categories, rather than exact phreds, it is an approximation.

Read 2: Per position quality percentiles

Shows the mean for all bases and the means of the lowest and highest percentiles to indicate the spread. Since the graph is based on the sampled categories, rather than exact phreds, it is an approximation.

Read 1: Per sequence average quality scores

>=Q5	5,477,353	100.00%
>=Q7	5,477,352	100.00%
>=Q10	5,477,328	100.00%
>=Q12	5,477,287	100.00%
>=Q15	5,470,227	99.87%
>=Q20	5,147,175	93.97%
>=Q30	1,962,703	35.83%

Read 2: Per sequence average quality scores

>=Q5	5,477,353	100.00%
>=Q7	5,477,349	100.00%
>=Q10	5,477,286	100.00%
>=Q12	5,476,997	99.99%
>=Q15	5,461,081	99.70%
>=Q20	5,182,064	94.61%
>=Q30	1,537,904	28.08%

Read 1: Per position base content

Read 2: Per position base content

Read 1: Per position N content

Read 2: Per position N content

Read 1: Per sequence GC content

For short reads with fixed size (i.e. Illumina) the plot will look very spiky due to the GC content calculation: GC bases / all bases. For read lengths of 151, both 75 and 76 GC bases lead to a percentage of 50% (rounded) and 72 and 73 GC bases leads to 48% (rounded). Only 74 GC bases leads to 49%. As a result the even categories will be twice as high, which creates a spike. The smoothened plot is provided to give a clearer picture in this case.

Read 2: Per sequence GC content

For short reads with fixed size (i.e. Illumina) the plot will look very spiky due to the GC content calculation: GC bases / all bases. For read lengths of 151, both 75 and 76 GC bases lead to a percentage of 50% (rounded) and 72 and 73 GC bases leads to 48% (rounded). Only 74 GC bases leads to 49%. As a result the even categories will be twice as high, which creates a spike. The smoothened plot is provided to give a clearer picture in this case.

Adapter Content

By calculating the overlap between reads it is possible to determine where the adapter is.

Total reads	5,477,353	100.00%
Adapters in read 1	1,834,674	33.50%
Adapters in read 2	1,834,674	33.50%

Longest most frequent adapter	Adapter Sequence	Best match
Read 1	CTGTCTCTTATACACATCTCCGAGCCCACGA	gnl|uv|NGB00726.1:1-34 Illumina Nextera transposase sequence Read 2 (Oligonucleotide sequence copyright 2007-2012 Illumina, Inc. All rights reserved.)
Read 2	CTGTCTCTTATACACATCTGACGCTGCCGAC	gnl|uv|NGB00725.1:1-33 Illumina Nextera transposase sequence Read 1 (Oligonucleotide sequence copyright 2007-2012 Illumina, Inc. All rights reserved.)

Adapters read 1

Adapter	Count
C	21908
CT	22392
CTG	22566
CTGT	22406
CTGTC	22114
CTGTCT	22459
CTGTCTC	22067
CTGTCTCT	22882
CTGTCTCTT	22742
CTGTCTCTTA	22790
CTGTCTCTTAT	22434
CTGTCTCTTATA	22582
CTGTCTCTTATAC	22132
CTGTCTCTTATACA	22417
CTGTCTCTTATACAC	22842
CTGTCTCTTATACACA	22801
CTGTCTCTTATACACAT	22547
CTGTCTCTTATACACATC	22387
CTGTCTCTTATACACATCT	22785
CTGTCTCTTATACACATCTC	22647
CTGTCTCTTATACACATCTCC	22655
CTGTCTCTTATACACATCTCCG	21916
CTGTCTCTTATACACATCTCCGA	21661
CTGTCTCTTATACACATCTCCGAG	22071
CTGTCTCTTATACACATCTCCGAGC	22229
CTGTCTCTTATACACATCTCCGAGCC	22234
CTGTCTCTTATACACATCTCCGAGCCC	22728
CTGTCTCTTATACACATCTCCGAGCCCA	21942
CTGTCTCTTATACACATCTCCGAGCCCAC	22272
CTGTCTCTTATACACATCTCCGAGCCCACG	22093
CTGTCTCTTATACACATCTCCGAGCCCACGA	1049249

Adapters read 2

Adapter	Count
C	21351
CT	22003
CTG	22202
CTGT	22198
CTGTC	21694
CTGTCT	22182
CTGTCTC	21657
CTGTCTCT	22528
CTGTCTCTT	22440
CTGTCTCTTA	22510
CTGTCTCTTAT	22274
CTGTCTCTTATA	22421
CTGTCTCTTATAC	21408
CTGTCTCTTATACA	21996
CTGTCTCTTATACAC	22437
CTGTCTCTTATACACA	22327
CTGTCTCTTATACACAT	22121
CTGTCTCTTATACACATC	22027
CTGTCTCTTATACACATCT	22470
CTGTCTCTTATACACATCTG	22118
CTGTCTCTTATACACATCTGA	22460
CTGTCTCTTATACACATCTGAC	22209
CTGTCTCTTATACACATCTGACG	21792
CTGTCTCTTATACACATCTGACGC	21918
CTGTCTCTTATACACATCTGACGCT	22235
CTGTCTCTTATACACATCTGACGCTG	22269
CTGTCTCTTATACACATCTGACGCTGC	22964
CTGTCTCTTATACACATCTGACGCTGCC	22048
CTGTCTCTTATACACATCTGACGCTGCCG	22280
CTGTCTCTTATACACATCTGACGCTGCCGA	22053
CTGTCTCTTATACACATCTGACGCTGCCGAC	1063178

Insert Sizes

Insert sizes are calculated by taking the first and last 16 bp from read 2. These are searched for in read 1 while allowing at most 1 error. This method is very fast and reasonably accurate, but does not account for long poly-G cycles.

Total reads	5,477,353
Reads without overlap	1,552,343	28.34%

Read 1: Per tile quality

This graph shows the deviation of each tile on each position from the geometric mean of all tiles at that position. The scale is expressed in phred units. -10 is 10 times more errors than the average. -3 is ~2 times more errors than the average. Only points that deviate more than 2 phred units from the average are shown.

Tiles with more than 2 times the average error: 1142, 1549, 1569, 2113, 2136, 2150, 2231, 2256, 2264, 2273, 2548, 2550, 2619, 2671, 2676

Tiles with more than 10 times the average error: 2114, 2610, 2611, 2617, 2618

Read 2: Per tile quality

This graph shows the deviation of each tile on each position from the geometric mean of all tiles at that position. The scale is expressed in phred units. -10 is 10 times more errors than the average. -3 is ~2 times more errors than the average. Only points that deviate more than 2 phred units from the average are shown.

Tiles with more than 2 times the average error: 1444, 1540, 2278, 2373, 2669

Tiles with more than 10 times the average error:

Duplication percentages

Fingerprints are taken by taking a sample from the beginning and the end at an offset. The samples are combined and hashed while using the length as a seed. A subsample of these fingerprints is stored to estimate the duplication rate. See the documentation for a complete explanation.

Fingerprint front sequence length	8
Fingerprint front sequence offset	0
Fingerprint back sequence length	8
Fingerprint back sequence offset	0
Subsampled fingerprints	572,140
Estimated remaining sequences if deduplicated	83.47%

Read 1: Overrepresented sequences

A subsample of the sequences is analysed Sequences are cut into fragments of up to 31 bp. Fragments are stored and counted. When the maximum amount of unique fragments is reached, only fragments that are already stored are counted. The rest of the fragments is ignored. Fragments are stored in their canonical representation. That is either the sequence or the reverse complement, whichever has the lowest sort order. Both representations are shown in the table. See the documentation for a complete explanation. The sequence identity is calculated by $\frac{\mathrm{Number\; of\; matched\; nucleotides\; -\; gap\; sequences\; in\; query\; alignment}}{\mathrm{Length\; of\; query}}$.

The percentage shown is an estimate based on the number of occurences of the fragment in relation to the number of sampled sequences. Fragments are only counted once per sequence. Fragments that occur more than once in a sequence are counted as one.

Total sequences in file	5,477,353
Sampled sequences	684,670
Sampling rate	1 in 8
Total fragments sampled	5,475,263
Stored unique fragments	1,828,940
Maximum unique fragments	5,000,000
Fragment size	21

Read 2: Overrepresented sequences

A subsample of the sequences is analysed Sequences are cut into fragments of up to 31 bp. Fragments are stored and counted. When the maximum amount of unique fragments is reached, only fragments that are already stored are counted. The rest of the fragments is ignored. Fragments are stored in their canonical representation. That is either the sequence or the reverse complement, whichever has the lowest sort order. Both representations are shown in the table. See the documentation for a complete explanation. The sequence identity is calculated by $\frac{\mathrm{Number\; of\; matched\; nucleotides\; -\; gap\; sequences\; in\; query\; alignment}}{\mathrm{Length\; of\; query}}$.

The percentage shown is an estimate based on the number of occurences of the fragment in relation to the number of sampled sequences. Fragments are only counted once per sequence. Fragments that occur more than once in a sequence are counted as one.

Total sequences in file	5,477,353
Sampled sequences	684,670
Sampling rate	1 in 8
Total fragments sampled	5,476,939
Stored unique fragments	1,885,977
Maximum unique fragments	5,000,000
Fragment size	21

Nanopore time series

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