TABLE 2.
Details for samples used in this study
| MiSeq | Age (mo) | Sample date (day-mo-yr) | Group | Length (nt)a | Coverageb | Present in G setc | Present in F setd | GenBank no.e | ENA no.f |
|---|---|---|---|---|---|---|---|---|---|
| 10028_10 | 0 | 07-Jan-02 | A | 9,346 | 6,401 | Yes | KP317918 | ERR323212 | |
| 10028_11 | 6 | 27-Apr-02 | A | 7,091 | 10,370 | KP317940 | ERR323213 | ||
| 10028_12 | 6 | 28-Jan-03 | A | 9,776 | 5,692 | Yes | KP317955 | ERR323214 | |
| 11866_65 | 5 | 13-Feb-03 | A | 12,151 | 7,347 | Yes | Yes | KP317949 | ERR438932 |
| 11865_75 | 8 | 24-Mar-04 | A | 14,985 | 12,283 | Yes | Yes | KP317956 | ERR438910 |
| 10891_50 | 6 | 21-Jan-05 | A | 5,396 | 3,554 | Yes | Yes | KP317948 | ERR376407 |
| 10891_56 | 0 | 02-Feb-05 | A | 5,396 | 2,369 | Yes | Yes | KP317924 | ERR376413 |
| 9696_45 | 14 | 20-Feb-06 | A | 14,778 | 3,830 | Yes | Yes | KP317944 | ERR303303 |
| 10891_57 | 1 | 23-Feb-06 | A | 14,841 | 4,640 | Yes | Yes | KP317942 | ERR376414 |
| 10891_58 | 0 | 29-Mar-06 | A | 8,864 | 6,016 | KP317943 | ERR376415 | ||
| 10891_59 | 3 | 04-Jan-07 | A | 11,496 | 5,316 | Yes | KP317937 | ERR376416 | |
| 10891_60 | 1 | 05-Jan-07 | A | 14,791 | 4,454 | Yes | Yes | KP317926 | ERR376417 |
| 10891_51 | 0 | 07-Mar-08 | A | 14,967 | 4,882 | Yes | Yes | KP317933 | ERR376408 |
| 10891_52 | 11 | 17-Mar-08 | A | 5,636 | 1,201 | Yes | KP317931 | ERR376409 | |
| 10899_38 | 1 | 22-Feb-09 | A | 14,854 | 8,478 | Yes | Yes | KP317950 | ERR381723 |
| 10899_40 | 4 | 26-Jan-10 | A | 10,113 | 13,351 | Yes | KP317916 | ERR381725 | |
| 10899_41 | 18 | 10-Feb-10 | A | 14,713 | 12,405 | Yes | Yes | KP317935 | ERR381726 |
| 11864_54 | 3 | 29-Apr-10 | A | 14,716 | 7,071 | Yes | Yes | KP317936 | ERR438905 |
| 11862_33 | 3 | 26-Aug-10 | A | 14,719 | 8,961 | Yes | Yes | KP317921 | ERR438868 |
| 11864_53 | 1 | 25-Mar-11 | A | 14,735 | 6,891 | Yes | Yes | KP317951 | ERR438904 |
| 11862_28 | 28 | 13-Apr-11 | A | 15,214 | 10,434 | Yes | Yes | KP317920 | ERR438864 |
| 11862_29 | 4 | 23-Mar-12 | A | 14,950 | 12,922 | Yes | Yes | KP317953 | ERR438865 |
| 11862_32 | 14 | 30-Apr-12 | A | 7,197 | 6,180 | KP317947 | ERR438867 | ||
| 9697_16 | 10 | 06-Jul-02 | B | 15,040 | 5,419 | Yes | Yes | KP317939 | ERR303322 |
| 9697_10 | 8 | 13-Jan-03 | B | 9,790 | 6,853 | Yes | KP317930 | ERR303316 | |
| 10140_1 | 46 | 02-Apr-04 | B | 12,034 | 12,174 | Yes | Yes | KP317919 | ERR331021 |
| 9697_7 | 10 | 22-Dec-04 | B | 15,080 | 4,480 | Yes | Yes | KP317925 | ERR303313 |
| 9697_6 | 2 | 25-Dec-04 | B | 14,998 | 6,523 | Yes | Yes | KP317954 | ERR303312 |
| 9697_5 | 1 | 27-Jan-06 | B | 15,234 | 3,682 | Yes | Yes | KP317917 | ERR303311 |
| 9465_10 | 23 | 27-Feb-09 | B | 14,995 | 16,190 | Yes | Yes | KP317938 | ERR303268 |
| 9465_11 | 31 | 13-Feb-10 | B | 15,004 | 11,722 | Yes | Yes | KP317941 | ERR303269 |
| 9465_12 | 22 | 06-Apr-10 | B | 15,260 | 14,855 | Yes | Yes | KP317932 | ERR303270 |
| 9465_6 | 17 | 09-May-10 | B | 15,333 | 13,719 | Yes | Yes | KP317952 | ERR303264 |
| 9465_7 | 3 | 01-Feb-11 | B | 15,233 | 14,182 | Yes | Yes | KP317927 | ERR303265 |
| 9465_8 | 2 | 14-Apr-11 | B | 15,323 | 15,367 | Yes | Yes | KP317945 | ERR303266 |
| 9465_9 | 1 | 08-Jul-11 | B | 15,237 | 14,709 | Yes | Yes | KP317928 | ERR303267 |
| 9465_3 | 8 | 14-Jan-12 | B | 14,995 | 12,378 | Yes | Yes | KP317946 | ERR303261 |
| 9465_1 | 19 | 13-Feb-12 | B | 15,233 | 12,994 | Yes | Yes | KP317934 | ERR303259 |
| 9465_4 | 14 | 01-Mar-12 | B | 15,179 | 14,802 | Yes | Yes | KP317923 | ERR303262 |
| 10911_9 | 1 | 23-Mar-12 | B | 14,977 | 12,504 | Yes | Yes | KP317929 | ERR376442 |
| 9465_2 | 5 | 16-May-12 | B | 14,941 | 12,906 | Yes | Yes | KP317922 | ERR303260 |
a
Final sequence length obtained from de novo assembly of short read data (see Materials and Methods).
b
Coverage calculated by mapping all reads to final assembled contig. Coverage was calculated as the number of mapped reads/(length of the genome fragment/129).
c
Samples yielding sufficient sequence for G region analysis (Fig. 5).
d
Samples yielding sufficient sequence for F region analysis (Fig. 5).
e
The final genome data were deposited in GenBank with the indicated accession numbers.
f
Short-read data available at European Nucleotide Archive (http://www.ebi.ac.uk/ena).