|  | Trimmed | Genome Matched | cDNA Matched | |||
---|---|---|---|---|---|---|---|
Condition | ID# | Distincta | Totalb | Distinctc | Totald | Distincte | Totalf |
Brachypodium PARE | |||||||
 Root Bio#1 | BDI20 | 2,273,863 | 10,551,854 | 1,600,582 | 9,263,616 | 1,576,585 | 7,451,753 |
 Leaf Bio#1 | BDI21 | 1,226,270 | 13,696,309 | 682,819 | 12,251,858 | 658,393 | 9,549,413 |
 Stem Bio#1 | BDI23 | 3,499,449 | 16,005,365 | 1,416,469 | 12,416,968 | 1,350,442 | 11,930,438 |
 Panicle Bio#1 | BDI25 | 4,256,035 | 28,940,535 | 3,415,326 | 26,535,542 | 3,355,513 | 23,614,486 |
 Root Bio#2 | BDI381 | 14,892,253 | 71,328,838 | 10,909,520 | 64,296,408 | 10,072,279 | 62,003,648 |
 Leaf Bio#2 | BDI288 | 15,673,931 | 93,529,302 | 8,204,778 | 80,615,543 | 7,675,634 | 75,965,360 |
 Stem Bio#2 | BDI289 | 20,330,230 | 106,942,289 | 11,417,928 | 93,078,760 | 10,527,104 | 85,961,342 |
 Panicle Bio#2 | BDI287 | 13,605,701 | 70,071,025 | 10,619,657 | 64,290,369 | 10,165,770 | 53,396,674 |
 Control Bio#1 | BDI283 | 18,739,274 | 116,856,674 | 8,033,068 | 99,574,648 | 7,475,766 | 94,337,424 |
 Control Bio#2 | BDI490b | 11,609,931 | 57,136,919 | 9,220,303 | 51,975,771 | 8,871,646 | 44,558,561 |
 Cold Bio#1 | BDI507 | 14,094,807 | 71,335,970 | 10,300,680 | 63,667,922 | 9,476,866 | 60,202,779 |
 Cold Bio#2 | BDI542 | 5,954,379 | 26,243,974 | 4,873,635 | 23,735,487 | 4,626,612 | 23,513,295 |
 Drought Bio#1 | BDI284 | 16,895,332 | 110,043,868 | 8,551,529 | 94,797,698 | 7,833,753 | 70,824,614 |
 Drought Bio#2 | BDI514 | 6,549,245 | 30,377,458 | 4,954,837 | 27,533,267 | 4,509,215 | 21,352,193 |
 Heat Bio#1 | BDI491 | 9,064,716 | 36,739,900 | 7,008,303 | 32,960,526 | 6,557,997 | 24,894,799 |
 Heat Bio#2 | BDI544 | 12,502,104 | 71,856,374 | 10,147,454 | 65,621,210 | 9,309,732 | 64,252,301 |
 Submergence Bio#1 | BDI508 | 19,248,274 | 143,926,223 | 13,013,551 | 129,521,309 | 12,049,556 | 117,577,209 |
 Submergence Bio#2 | BDI493 | 11,085,014 | 47,501,130 | 8,186,439 | 42,683,558 | 7,802,211 | 38,304,004 |
Sorghum PARE | |||||||
 Root Bio#1 | SBI617 | 7,408,495 | 47,925,541 | 4,667,519 | 40,934,942 | 4,158,647 | 33,879,769 |
 Root Bio#2 | SBI620 | 7,471,715 | 37,774,801 | 4,059,238 | 30,725,474 | 3,799,122 | 13,074,749 |
 Leaf Bio#1 | SBI619 | 10,557,426 | 57,604,765 | 3,881,705 | 41,917,126 | 3,274,739 | 36,707,076 |
 Leaf Bio#2 | SBI615 | 6,473,759 | 40,090,222 | 4,233,698 | 34,957,079 | 3,841,772 | 29,383,910 |
 Panicle Bio#1 | SBI616 | 6,872,817 | 34,611,413 | 3,981,997 | 24,631,577 | 3,158,582 | 19,666,227 |
 Panicle Bio#2 | SBI618 | 12,386,838 | 49,631,535 | 8,261,402 | 41,607,791 | 7,172,569 | 36,467,170 |
 Control for Cold Bio#1 | SBI517 | 3,256,249 | 39,956,679 | 2,092,580 | 35,409,035 | 1,743,771 | 31,035,771 |
 Control for Cold Bio#2 | SBI519 | 3,885,061 | 39,822,428 | 2,579,391 | 35,514,462 | 2,183,104 | 31,347,460 |
 Cold Bio#1 | SBI518 | 3,197,687 | 47,188,888 | 2,294,992 | 44,114,986 | 1,957,618 | 30,508,940 |
 Cold Bio#2 | SBI520 | 3,420,185 | 36,488,885 | 2,324,259 | 33,101,913 | 1,795,310 | 22,262,865 |
Switchgrass PARE | |||||||
 Leaf Bio#1 | SWI352 | 18,119,798 | 66,514,735 | 7,302,551 | 29,289,132 | 6,684,352 | 27,261,224 |
 Leaf Bio#2 | SWI498 | 22,300,993 | 114,883,981 | 16,237,561 | 100,834,434 | 13,901,137 | 91,031,475 |
 Stem Bio#1 | SWI353 | 20,252,951 | 94,311,170 | 5,644,700 | 24,757,380 | 5,276,609 | 21,054,163 |
 Stem Bio#2 | SWI500 | 5,712,914 | 18,900,653 | 4,315,446 | 16,340,546 | 3,600,582 | 14,307,880 |
 Panicle Bio#1 | SWI382 | 23,916,903 | 96,013,301 | 15,181,789 | 80,968,945 | 13,320,327 | 76,420,288 |
 Panicle Bio#2 | SWI499 | 3,052,670 | 7,845,043 | 2,448,779 | 6,885,542 | 2,140,816 | 6,234,349 |
 Control for Cold Bio#1 | SWI521 | 10,188,795 | 62,673,164 | 7,125,183 | 55,462,967 | 6,454,159 | 50,607,577 |
 Control for Cold Bio#2 | SWI523 | 7,480,243 | 42,889,534 | 4,344,702 | 33,834,492 | 3,456,913 | 29,312,647 |
 Cold Bio#1 | SWI522 | 8,657,953 | 50,614,176 | 4,996,684 | 39,012,357 | 3,302,826 | 28,359,863 |
 Cold Bio#2 | SWI524 | 6,617,641 | 42,861,290 | 4,203,457 | 36,211,923 | 2,949,417 | 24,326,833 |
Switchgrass smRNA | |||||||
 Control for Cold | SWI560 | 5,575,102 | 33,117,391 | 4,036,929 | 29,240,850 | NA | NA |
 Cold | SWI559 | 10,477,573 | 74,342,226 | 7,231,085 | 64,406,974 | NA | NA |
 Control for Drought | SWI551 | 6,099,269 | 34,328,102 | 4,490,488 | 30,101,667 | NA | NA |
 Drought | SWI552 | 5,288,223 | 34,223,739 | 3,807,420 | 30,123,899 | NA | NA |
 Re-water | SWI553 | 5,202,390 | 30,490,652 | 3,728,694 | 26,891,552 | NA | NA |
 Leaf | SWI561 | 1,021,704 | 5,310,089 | 764,472 | 4,710,729 | NA | NA |
 Stem | SWI534 | 774,658 | 5,081,224 | 575,800 | 4,428,676 | NA | NA |
 Panicle | SWI562 | 1,798,117 | 3,221,179 | 1,472,871 | 2,807,413 | NA | NA |