Table 2 Results of sequence quality filtering and mapping on the reference genome.

From: Population admixtures in medaka inferred by multiple arbitrary amplicon sequencing

Primer

Individual

Fastq

Quality check *1

Mapping *2

Raw reads (A)

Passed reads (B)

B/A

Properly paired

Uniquely mapped (C)

C/B

(C/A)

7-mer cocktail

Kun09

13,510,718

11,770,022

0.87

10,477,920

8,545,086

0.73

0.63

7-mer cocktail

Kun10

17,388,764

15,186,928

0.87

13,669,208

10,957,140

0.72

0.63

7-mer cocktail

Kun12

14,529,020

12,912,674

0.89

11,597,060

9,284,008

0.72

0.64

MIG-seq

Kun09

11,365,934

9,990,846

0.88

8,936,336

7,897,270

0.79

0.69

MIG-seq

Kun10

13,538,806

11,851,104

0.88

10,527,678

9,404,124

0.79

0.69

MIG-seq

Kun12

13,249,288

11,715,710

0.88

10,397,200

9,305,213

0.79

0.70

  1. *1: Primer sequences, Illumina adapters, and low-quality reads were trimmed. The phred score less than 15 for more than 40% bases, or a read with fewer than 15 bases. *2: Mapping on the reference genome was conducted using BWA mem. A summary of the mapped reads was obtained using SAMtools with the flagstat command.
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