Genome sequencing-based coverage analyses facilitate high-resolution detection of deletions linked to phenotypes of gamma-irradiated wheat mutants

Table 2 Summary of alignments and coverages of genome sequencing of wild-type and mutants of “Kitahonami”

Name	Total filtered reads (%)^a	Aligned reads (%)^b	Aligned reads after removal of PCR duplicate (%)^c	Reference bases covered (%)	Average depth-of-coverage
Kitahonami	2,724,430,844 (93.63%)	2,722,445,302 (99.93%)	2,323,699,205 (85.29%)	95.36	15.46
Kitahonami (5x)^d	881,408,040 (93.62%)	880,765,248 (99.93%)	832,372,258 (94.44%)	93.21	5.51
30579	2,172,729,570 (93.45%)	2,171,397,995 (99.94%)	1,956,235,087 (90.04%)	94.13	19.72
28511	2,393,917,360 (89.52%)	2,391,499,089 (99.90%)	2,159,808,051 (90.22%)	94.87	21.15
28511 (15x)^d	1,697,754,380 (89.52%)	1,696,038,607 (99.90%)	1,575,442,920 (92.80%)	94.58	15.43
28511 (10x)^d	1,131,807,308 (89.52%)	1,130,664,237 (99.90%)	1,075,319,384 (95.01%)	94.16	10.53
28511 (5x)^d	565,916,014 (89.52%)	565,343,556 (99.90%)	550,923,338 (97.35%)	92.76	5.39
28511 (2.5x)^d	282,949,706 (89.52%)	282,664,292 (99.90%)	278,932,625 (98.58%)	86.31	2.73

^aAn average base quality score per 4 bp > = 20
The filtered reads rate = Total filtered reads / Total reads × 100
^bThe aligned reads rate = Aligned reads / Total filtered reads × 100
^cThe filtered reads rate = Aligned reads after removing PCR duplicates / Total filtered reads × 100
^dThe sets of read data were used for the simulations. The number in the paratheses indicates approximate depth-of-coverage

ISSN: 1471-2164