Table 1.
Summary of NGS data obtained from each file separated with an indexed sequence
| ID | Bulk or cultivar | Indexed sequence | Total reads (M)a | Mapped pairs (M) | Ratio of mapped sequences | Average insert size (bp) | Standard deviation of insert size | Number of loci (K)a | Average depth | Median of depth | Mode of depth | Estimated genome coverage |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A01 | Early | TGACGCCA | 9.2 | 6.5 | 70.5% | 336.2 | 44.8 | 113.1 | 57.1 | 1 | 6 | 2.3% |
| A02 | Early | GGCTTA | 11.8 | 8.1 | 68.4% | 337.1 | 44.9 | 123.3 | 65.7 | 1 | 7 | 2.5% |
| A03 | Late | CTAAGCA | 9.7 | 6.9 | 71.3% | 336.6 | 44.8 | 120.1 | 57.7 | 1 | 6 | 2.4% |
| A04 | Fukuyutaka | GCCTACCT | 9.7 | 6.6 | 68.5% | 336.5 | 44.8 | 103.5 | 64.2 | 1 | 6 | 2.1% |
| B01 | Early | CAGATA | 8.6 | 6.0 | 69.4% | 335.4 | 44.9 | 120.8 | 49.7 | 1 | 6 | 2.4% |
| B02 | Early | AACGCACATT | 10.9 | 7.7 | 70.6% | 334.3 | 44.8 | 121.4 | 63.6 | 1 | 6 | 2.4% |
| B03 | Late | ATTAT | 12.3 | 8.4 | 68.2% | 333.4 | 45.1 | 125.5 | 66.6 | 1 | 7 | 2.5% |
| B04 | Fukuyutaka | CACCA | 9.5 | 6.6 | 68.9% | 338.4 | 44.7 | 108.5 | 60.5 | 1 | 6 | 2.2% |
| C01 | Early | GAAGTG | 8.9 | 6.5 | 72.5% | 337.2 | 44.8 | 124.9 | 51.6 | 1 | 6 | 2.5% |
| C02 | Early | GAGCGACAT | 11.7 | 8.2 | 69.7% | 335.7 | 44.7 | 121.4 | 67.3 | 1 | 6 | 2.4% |
| C03 | Late | GCGCTCA | 11.0 | 7.6 | 69.1% | 336.6 | 44.6 | 116.7 | 65.1 | 1 | 6 | 2.3% |
| C04 | Toyoshirome | AATTAG | 10.5 | 7.5 | 71.5% | 336.6 | 44.9 | 108.0 | 69.8 | 1 | 7 | 2.2% |
| D01 | Early | TAGCGGAT | 10.9 | 7.6 | 69.8% | 336.0 | 44.7 | 126.2 | 60.1 | 1 | 6 | 2.5% |
| D02 | Early | CCTTGCCATT | 8.2 | 5.8 | 70.5% | 334.5 | 44.8 | 119.3 | 48.2 | 1 | 6 | 2.4% |
| D03 | Late | ACTGCGAT | 12.8 | 8.4 | 65.4% | 335.7 | 44.8 | 124.6 | 67.1 | 1 | 7 | 2.5% |
| D04 | Toyoshirome | GGAACGA | 11.1 | 8.0 | 71.9% | 338.0 | 44.7 | 104.3 | 76.3 | 1 | 6 | 2.1% |
| E01 | Early | TATTCGCAT | 9.5 | 6.7 | 69.9% | 335.7 | 44.8 | 117.8 | 56.6 | 1 | 6 | 2.4% |
| E02 | Late | GGTATA | 9.4 | 6.6 | 69.9% | 334.9 | 45.0 | 113.0 | 58.4 | 1 | 6 | 2.3% |
| E03 | Late | TTCGTT | 10.3 | 6.6 | 64.4% | 336.3 | 44.8 | 117.9 | 56.3 | 1 | 6 | 2.4% |
| F01 | Early | ATAGAT | 8.5 | 6.0 | 70.3% | 334.2 | 45.0 | 121.2 | 49.5 | 1 | 6 | 2.4% |
| F02 | Late | TCTTGG | 10.0 | 7.1 | 71.0% | 338.3 | 44.7 | 119.5 | 59.2 | 1 | 6 | 2.4% |
| F03 | Late | ATATAA | 12.0 | 8.6 | 71.6% | 330.7 | 45.0 | 115.6 | 74.6 | 1 | 7 | 2.3% |
| G01 | Early | CCGAACA | 9.1 | 6.4 | 70.3% | 336.8 | 44.7 | 125.5 | 51.0 | 1 | 6 | 2.5% |
| G02 | Late | GGTGT | 16.1 | 10.9 | 67.4% | 338.5 | 44.8 | 121.5 | 89.5 | 1 | 6 | 2.4% |
| G03 | Late | TGGCAACAGA | 11.2 | 7.7 | 69.0% | 334.3 | 44.7 | 112.6 | 68.5 | 1 | 6 | 2.3% |
| H01 | Early | GGAAGACAT | 8.7 | 6.2 | 70.6% | 335.3 | 44.8 | 121.9 | 50.6 | 1 | 6 | 2.4% |
| H02 | Late | GGATA | 10.1 | 7.2 | 71.7% | 335.8 | 44.9 | 118.4 | 61.1 | 1 | 6 | 2.4% |
| H03 | Late | CTCGTCG | 4.5 | 3.0 | 66.5% | 337.1 | 44.7 | 89.7 | 33.1 | 1 | 4 | 1.8% |
|
| ||||||||||||
| ALL | 286.40 | 199.14 | 69.5% | N. C.b | N. C. | 284.4 | 677.6 | 1 | 13 | 5.7% | ||
a
M, million; K, thousand.
b
Not calculated.