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Quast shows different reads count for the same fastq file?
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17 months ago
DanielC • 80
Canada

Dear Friends,

I ran quast to assess the quality of two contigs I assembled. I noticed that for both the contigs quast presents different "total reads": (the numbr of reads in fastq file is 2625009)

                   Contig1 Contig2

# contigs (>= 0 bp)     1   1
# contigs (>= 1000 bp)     1   1
# contigs (>= 5000 bp)     1   1
# contigs (>= 10000 bp)     1   1
# contigs (>= 25000 bp)     1   1
# contigs (>= 50000 bp)     1   1
Total length (>= 0 bp) 50406 88165
Total length (>= 1000 bp) 50406 88165
Total length (>= 5000 bp) 50406 88165
Total length (>= 10000 bp) 50406 88165
Total length (>= 25000 bp) 50406 88165
Total length (>= 50000 bp) 50406 88165
# contigs     1   1
Largest contig 50406 88165
Total length     50406 88165
GC (%)     45.62 38.98
N50     50406 88165
N75     50406 88165
L50 11
L75 11
# total reads     2683807 2625087
# left     0   0
# right     0   0
Mapped (%)     96.79   0.58
Properly paired (%)     0.0   0.0
Avg. coverage depth 14449     52
Coverage >= 1x (%) 100.0 100.0
# N's per 100 kbp     0.00   0.00

Could you please let me know what could be the reason here? Your comments will be highly appreciated.

Thanks, DK

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