Table A1.
Statistical summary of sequence preprocessing.
| ID * | Raw PE | Filtered Tags | Filtered Tags (%) | Merged Tags | Merged Tags (%) | Nonchimeric Tags | Effective Tags (%) |
|---|---|---|---|---|---|---|---|
| TF1.W4 | 123,903 | 79,394 | 64.08% | 72,872 | 58.81% | 64,776 | 52.28% |
| TF1.W5 | 86,941 | 55,172 | 63.46% | 50,744 | 58.37% | 45,633 | 52.49% |
| TF1.W6 | 101,821 | 65,428 | 64.26% | 58,992 | 57.94% | 54,234 | 53.26% |
| TF1.W7 | 138,003 | 88,307 | 63.99% | 80,465 | 58.31% | 73,880 | 53.54% |
| TF1.W8 | 98,923 | 61,695 | 62.37% | 55,449 | 56.05% | 50,946 | 51.50% |
| TF2.W4 | 117,882 | 75,321 | 63.90% | 69,764 | 59.18% | 62,166 | 52.74% |
| TF2.W5 | 112,773 | 66,447 | 58.92% | 61,495 | 54.53% | 55,681 | 49.37% |
| TF2.W6 | 105,421 | 65,833 | 62.45% | 59,271 | 56.22% | 54,147 | 51.36% |
| TF2.W7 | 118,204 | 76,548 | 64.76% | 71,142 | 60.19% | 66,869 | 56.57% |
| TF2.W8 | 88,600 | 55,839 | 63.02% | 50,175 | 56.63% | 45,956 | 51.87% |
| TF3.W4 | 112,476 | 72,692 | 64.63% | 66,330 | 58.97% | 58,931 | 52.39% |
| TF3.W5 | 95,308 | 60,193 | 63.16% | 55,567 | 58.30% | 50,921 | 53.43% |
| TF3.W6 | 102,185 | 64,955 | 63.57% | 58,532 | 57.28% | 52,719 | 51.59% |
| TF3.W7 | 92,117 | 56,548 | 61.39% | 51,256 | 55.64% | 47,089 | 51.12% |
| TF3.W8 | 89,963 | 58,077 | 64.56% | 52,419 | 58.27% | 48,176 | 53.55% |
| T1.W4 | 302,001 | 205,657 | 68.10% | 188,734 | 62.49% | 165,859 | 54.92% |
| T1.W5 | 112,046 | 68,051 | 60.73% | 62,878 | 56.12% | 57,506 | 51.32% |
| T1.W6 | 118,202 | 77,451 | 65.52% | 68,632 | 58.06% | 61,049 | 51.65% |
| T1.W7 | 94,575 | 53,614 | 56.69% | 48,405 | 51.18% | 46,262 | 48.92% |
| T1.W8 | 107,927 | 67,024 | 62.10% | 59,844 | 55.45% | 56,116 | 51.99% |
| T2.W4 | 132,767 | 83,571 | 62.95% | 76,393 | 57.54% | 69,621 | 52.44% |
| T2.W5 | 126,506 | 80,552 | 63.67% | 74,922 | 59.22% | 71,227 | 56.30% |
| T2.W6 | 124,477 | 79,001 | 63.47% | 70,664 | 56.77% | 64,270 | 51.63% |
| T2.W7 | 79,886 | 52,599 | 65.84% | 47,511 | 59.47% | 44,677 | 55.93% |
| T2.W8 | 105,825 | 69,527 | 65.70% | 62,486 | 59.05% | 57,150 | 54.00% |
| T3.W4 | 128,444 | 84,426 | 65.73% | 77,355 | 60.22% | 71,235 | 55.46% |
| T3.W5 | 108,635 | 68,023 | 62.62% | 62,412 | 57.45% | 59,490 | 54.76% |
| T3.W6 | 128,206 | 83,377 | 65.03% | 75,457 | 58.86% | 68,640 | 53.54% |
| T3.W7 | 76,829 | 46,952 | 61.11% | 42,923 | 55.87% | 41,842 | 54.46% |
| T3.W8 | 94,509 | 60,704 | 64.23% | 54,762 | 57.94% | 50,392 | 53.32% |
* Sample IDs consist of group, mouse ID, and sampling time. For example, TF1.W4 represents the sample collected from mouse #1 in the TF group in the 4th week, and F3.W8 represents the sample collected from mouse #3 in the T group in the 8th week.