Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection

Table 2

Mapping and coverage of the reads from the landraces to Nipponbare reference genome.

Landraces	indica 12	indica 13	indica 15	japonica 11	japonica 14
Total	129,251,696	112,867,645	151,576,754	133,602,832	161,141,384
# mapped	112,667,155	101,814,936	130,851,417	125,253,671	151,261,159
Mapped reads (%)	87.17%	90.21%	86.33%	93.75%	93.87%
# unmapped	16,584,541	11,052,709	20,725,337	8,349,161	9,880,225
Unmapped reads (%)	12.83%	9.79%	13.67%	6.25%	6.13%
Mean mapping	42.21	44.59	42.03	47.81	48.14
	91.30%	89.18%	92.56%	95.50%	96.49%
	29.94	27.09	34.74	33.46	40.41

raw reads in the FASTQ files. number of reads mapped to 12 chromosomes in the nucleus. number of unmapped reads to both nuclear and organellar genomes. error probability of read mapping scaled by Phred quality. breadth of coverage across the nuclear genome. sequencing depth of reads.