Table 2.
Summary of sequencing data from 41 new soybean dwarf virus isolates
| GenBank accession no. | Isolate ID | Number of reads | No. of reads after trimming | No. of contigs after assembly | Contig length (nt) | Reads mapped (de novo) | Average coverage (de novo) | Reference | Number of reads mapped to reference | Average coverage (mapped) | Final length (nt) |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PP922804 | 6091 | 22,104,898 | 22,092,373 | 20,469 | 5,700 | 1,386,835 | 23,105 | NC003056 | 1,452,334 | 22,638 | 5,609 |
| PP922806 | 6694 | 20,628,914 | 20,613,554 | 20,115 | 5,926 | 207,565 | 3,408 | n/a | n/a | n/a | 5,609 |
| PP922807 | 6931 | 22,607,850 | 22,592,006 | 31,839 | 5,887 | 1,702,978 | 27,895 | n/a | n/a | n/a | 5,609 |
| PP922805 | 6692 | 19,395,142 | 19,383,697 | 21,324 | 5,878 | 1,314,610 | 21,560 | n/a | n/a | n/a | 5,609 |
| PP922800 | BC2020 | 53,522,120 | 53,522,098 | 25,478 | 5,831 | 1,173,236 | 19,004 | n/a | n/a | n/a | 5,604 |
| PP922801 | 3342 | 39,230,352 | 38,334,678 | 20,459 | 5,917 | 689,614 | 11,447 | n/a | n/a | n/a | 5,609 |
| PP922810 | KF20 | 41,097,054 | 40,365,759 | 27,674 | 3,748; 1,142 | 1,041,052; 548,224 | 27,295; 46,052 | LR584028 | 1,756,848 | 28,687 | 5,609 |
| PP922819 | WA8 | 57,384,178 | 55,951,527 | 30,772 | 5,950 | 552,795 | 9,146 | n/a | n/a | n/a | 5,609 |
| PP922820 | McG | 53,079,454 | 51,851,854 | 25,577 | 6,037 | 3,479,926 | 56,778 | n/a | n/a | n/a | 5,611 |
| PP922818 | SS1 | 48,673,758 | 45,577,214 | 22,218 | 5933 | 3,519,284 | 58,145 | n/a | n/a | n/a | 5,609 |
| PP922802 | 5432 | 62,076,358 | 60,037,094 | 32,357 | 5,108 | 2,608,915 | 50,176 | n/a | n/a | n/a | 5,609 |
| PP922787 | 5943 | 52,993,582 | 51,377,805 | 30,309 | 4,908; 1,096 | 3,401,863; 871,626 | 66,628; 74,596 | n/a | n/a | n/a | 5,459 |
| PP922809 | 5945 | 54,675,340 | 54,433,481 | 33,980 | 1,782; 1,202; 656; 737 | 1,928,006; 814,347; 146,719; 496,744 | 99,885; 65,075; 20,387; 58,227 | n/a | n/a | n/a | 5,697 |
| PP922808 | 5946 | 42,405,138 | 42,129,029 | 25,414 | 5,876 | 2,265,159 | 38,413 | n/a | n/a | n/a | 5,701 |
| PP922781 | 5433 | 46,109,438 | 45,908,319 | 22,653 | 5,190 | 5,680,097 | 108,557 | n/a | n/a | n/a | 5,459 |
| PP922786 | 5944 | 57,146,620 | 56,927,262 | 19,071 | 5,706 | 712,689 | 12,448 | n/a | n/a | n/a | 5,459 |
| PP922782 | 5434 | 47,162,646 | 46,922,166 | 23,475 | 5,756 | 5,187,565 | 89,779 | n/a | n/a | n/a | 5,459 |
| PP922803 | 5435 | 53,056,370 | 52,900,341 | 27,969 | 2,214; 5,950 | 95,844; 1,317,816 | 4,214; 22,001 | n/a | n/a | n/a | 5,609 |
| PP922783 | 5436 | 51,172,706 | 50,927,899 | 23,750 | 5,827 | 6,099,515 | 104,271 | n/a | n/a | n/a | 5,459 |
| PP922784 | 5481 | 71,168,032 | 70,928,034 | 19,809 | 5,749 | 48,487,240 | 840,894 | n/a | n/a | n/a | 5,459 |
| PP922785 | 5483 | 50,322,106 | 49,976,747 | 21,143 | 5,853 | 10,778,403 | 183,595 | n/a | n/a | n/a | 5,459 |
| PP922788 | L42 | 40,614,886 | 40,614,796 | 38,311 | 2966; 1723; 1091 | 624997; 308805; 117918 | 27301; 21971; 13950 | MF627965 | 1,245,669 | 29,738 | 5,459 |
| PP922789 | L43 | 34,250,078 | 34,249,989 | 27,449 | 1235; 4298 | 954; 2943 | 101; 93 | MF627965 | 4081 | 95 | 5,459 |
| PP922790 | L45 | 32,285,868 | 32,285,769 | 28,350 | 5,719 | 30,552 | 730 | n/a | n/a | n/a | 5,459 |
| PP922791 | L46 | 36,191,964 | 36,191,870 | 29,004 | 1415; 1388; 1094; 1163; 696 | 148405; 68970; 78667; 71214; 20253 | 14080; 6750; 9779; 8147; 3980 | MF627965 | 551,306 | 13,051 | 5,459 |
| PP922811 | L49 | 32,620,208 | 32,620,129 | 30,069 | 2814; 735; 550; 927 | 135428; 24610; 23075; 279 | 6234; 4284; 5060; 39 | LR584028 | 244,004 | 5,485 | 5,609 |
| PP922792 | L51 | 57,525,816 | 57,525,689 | 15,412 | 1271; 868; 1011; 1511; 715 | 18611; 3556; 12542; 24761; 10081 | 1819; 538; 1694; 2084; 1677 | MF627965 | 85,570 | 1,988 | 5,459 |
| PP922812 | L54 | 36,607,670 | 36,607,571 | 54,297 | 3896; 951; 1032; 618 | 18901; 856; 3798; 3646 | 636; 114; 482; 754 | LR584028 | 28,039 | 632 | 5,609 |
| PP922793 | L56 | 42,220,748 | 42,220,654 | 38,069 | 1827; 1119; 989; 772; 736; 764 | 153713; 86009; 23873; 22865; 7766; 42536 | 11449; 10175; 3207; 3663; 1332; 7555 | MF627965 | 443,643 | 10,573 | 5,459 |
| PP922799 | L59 | 34,097,278 | 34,097,190 | 29,816 | 1541; 687; 879; 664; 638 | 42035; 15556; 12163; 20023; 16201 | 3388; 3014; 1692; 3989; 3269 | MF627965 | 149,239 | 3,492 | 5,459 |
| PP922794 | L60 | 33,559,768 | 33,559,668 | 29,417 | 4445; 1078;1197 | 389872; 86205; 38284 | 11742; 10317; 3427 | MF627965 | 520,441 | 12,346 | 5,459 |
| PP922813 | L61 | 51,478,278 | 51,478,160 | 49,745 | 5,852 | 344,489 | 8,006 | NC003056 | 344,009 | 7,455 | 5,609 |
| PP922795 | L69 | 32,645,862 | 32,645,787 | 26,197 | 833; 845; 1083; 756; 546 | 23087; 47204; 78341; 53305; 28774 | 3680; 6762; 9650; 8625; 6739 | MF627965 | 321,165 | 21,526 | 5,459 |
| PP922814 | L70 | 42,457,582 | 42,457,486 | 33,471 | 1471; 1651; 892 | 218610; 164822; 85476 | 18993; 12947; 12790 | LR584028 | 657,403 | 15,227 | 5,609 |
| PP922780 | L71 | 37,889,610 | 37,889,513 | 27,161 | 1813; 686; 576; 620; 995; 571 | 143555; 34656; 39517; 6082; 3360; 4089 | 10244; 5222; 9180; 1119; 276; 602 | MF627965 | 404,881 | 9,414 | 5,456 |
| PP922796 | L72 | 64,673,360 | 54,673,190 | 49,915 | 1600; 980; 2579; 1506; 1491; 1173 | 115905; 27536; 268243; 98190; 36396; 1548 | 9601; 3708; 14223; 8841; 3188; 170 | MF627965 | 545,039 | 12,983 | 5,459 |
| PP922815 | L76 | 33,648,108 | 33,648,038 | 29,579 | 6,021 | 276,910 | 6,258 | n/a | n/a | n/a | 5,609 |
| PP922797 | L77 | 35,807,912 | 35,807,823 | 28,675 | 5,695 | 246,185 | 5,901 | n/a | n/a | n/a | 5,459 |
| PP922816 | L85 | 38,030,960 | 38,030,858 | 30,805 | 1729; 866; 932; 865; 701; 678 | 165881; 84164; 59107; 20979; 35343; 50424 | 12860; 12828; 7962; 3138; 6094; 9747 | LR584028 | 513,228 | 11,861 | 5,609 |
| PP922817 | L86 | 38,375,122 | 38,375,022 | 31,052 | 680; 840; 715; 1316; 1012; 699 | 62832; 40110; 10896; 68542; 40892; 12155 | 11677; 5778; 1821; 6840; 5238; 2120 | LR584028 | 291,276 | 6,936 | 5,609 |
| PP922798 | L87 | 28,236,728 | 28,236,652 | 21,438 | 2667; 853; 707; 675 | 101429; 11163; 2734; 18087 | 4844; 1686; 497; 3119 | MF627965 | 177,534 | 4,090 | 5,459 |