Table 1.
Draft genome copy numbers and estimated copy numbers of repeated genes
| Annotation | No. Genome copies | No. Genome copies w. depth ≥ 100 reads | Avg. No. Estimated copies |
| trans-sialidase | 1430 | 725 | 24 |
| MASP | 1377 | 913 | 23 |
| RHS | 752 | 166 | 26 |
| TcMUCII | 728 | 708 | 38 |
| DGF-1 | 565 | 231 | 57 |
| GP63 | 425 | 158 | 27 |
| protein kinase | 311 | 38 | 36 |
| elongation factor 1-gamma | 178 | 13 | 18 |
| ATPase | 119 | 5 | 119 |
| ATP-dependent DEAD/H RNA helicase | 99 | 51 | 28 |
| UDP-Gal or UDP-GlcNac-dependent glycosyltransferase | 66 | 7 | 21 |
| beta galactofuranosyl glycosyltransferase | 66 | 52 | 27 |
| TcMUC | 59 | 44 | 44 |
| N-acetyltransferase complex ARD1 subunit | 58 | 52 | 28 |
| TcMUCI | 57 | 55 | 41 |
| serine/threonine protein kinase | 47 | 6 | 31 |
| glycine dehydrogenase | 37 | 36 | 27 |
| mucin-like glycoprotein | 28 | 9 | 23 |
| receptor-type adenylate cyclase | 25 | 2 | 17 |
| tryptophanyl-tRNA synthetase | 23 | 21 | 44 |
| amino acid transporter | 22 | 7 | 38 |
| histone H4 | 21 | 21 | 79 |
| casein kinase | 20 | 12 | 123 |
| histone H2A | 18 | 15 | 100 |
| DnaJ chaperone protein | 18 | 4 | 23 |
| heat shock protein 70 | 18 | 3 | 100 |
| metallopeptidase | 17 | 4 | 19 |
| expression site-associated gene (ESAG-like) | 16 | 7 | 16 |
| cation transporter | 16 | 6 | 55 |
| myosine heavy chain | 13 | 1 | 19 |
| mannosyl-oligosaccharide 1, 2-alpha mannosidase 1B | 13 | 9 | 20 |
| tyrosine aminotransferase | 13 | 9 | 38 |
| cystathionine beta-synthase | 12 | 12 | 63 |
| elongation factor 1-alpha | 12 | 10 | 39 |
| amastin | 12 | 6 | 19 |
| TcSMUGS | 11 | 11 | 39 |
| zinc finger protein | 11 | 1 | 16 |
| histone H3 | 11 | 9 | 42 |
| tuzin | 10 | 8 | 39 |
| DNA-directed RNA polymerase subunit | 10 | 7 | 14 |
| cysteine peptidase | 9 | 12 | 59 |
| helicase | 8 | 1 | 18 |
| flagellar calcium-binding protein | 8 | 8 | 66 |
| TcSMUGL | 8 | 8 | 61 |
| glutamamyl carboxypeptidase | 7 | 6 | 144 |
| hexose transporter | 7 | 6 | 35 |
| clathrin coat assembly protein AP19 | 7 | 2 | 76 |
| metacaspase | 6 | 4 | 25 |
| elongation factor 2 | 6 | 3 | 15 |
| chaperonin HSP60, mitochondrial precursor | 5 | 5 | 32 |
| calcium-binding protein | 5 | 3 | 74 |
| folate/pteridine transporter | 5 | 5 | 20 |
| heat shock protein 85 | 5 | 5 | 54 |
| serine carboxypeptidase (CBP1) | 5 | 5 | 31 |
| cruzipain precursor | 5 | 4 | 81 |
| kinase | 4 | 1 | 32 |
| histone H2B | 4 | 2 | 63 |
| tricohyaline | 4 | 1 | 16 |
| D-isomer specific 2-hydroxyacid dehydrogenase protein | 4 | 3 | 29 |
| membrane-bound acid phosphates | 3 | 1 | 20 |
| antigenic protein | 3 | 1 | 18 |
| prostaglandin F2-alpha synthase | 3 | 3 | 28 |
| mitochondrial RNA editing lipase 1 | 3 | 1 | 15 |
| mitotubule-associated protein Gb4 | 3 | 1 | 15 |
| oligosaccharyl transferase subunit | 3 | 1 | 19 |
| ubiquitine | 3 | 1 | 17 |
| 69 kDa paraflagellar rod protein | 2 | 2 | 16 |
| clathrin assembly protein | 2 | 2 | 76 |
| glucose transporter | 2 | 1 | 27 |
| pteridine reductase | 2 | 1 | 18 |
| L-threonine 3-dehydrogenase | 2 | 2 | 24 |
| TcMUCIII | 2 | 2 | 38 |
| U3 small nuclear ribonucloprotein snRNP | 2 | 2 | 25 |
| acetylornithine deacetylase | 1 | 1 | 153 |
| cytochrome oxidase assembly protein | 1 | 1 | 16 |
| heat shock protein 83 | 1 | 1 | 60 |
| monoglyceride lipase | 1 | 1 | 49 |
| paraxonemal rod protein PAR2 | 1 | 1 | 15 |
The table lists the 78 annotated genes with an average alignment depth of 100 or higher. The table does not include the hypothetical genes. The first column lists the name of the annotated gene. The second column lists the number of copies of that particular annotation in the draft genome. The third column lists the number of these annotated copies that have an average shotgun depth of 100 or higher, corresponding to an estimated copy number of 14 or higher. The fourth column lists the average estimated copy number of those annotated copies having an average shotgun depth of 100 or higher (listed in column three).