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Table 3 Regions of low sequence-coverage

From: Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia

Locus tag Starta Enda Product description Pacbio coverage (×b) 454 Coverage (×) Illumina coverage (×) 454 Hybrid contig coveragec Draft assembly contig coverage
CAETHG_0145 156117 156914 Methionine synthase 87 26 62 Complete Partial
CAETHG_0152 161167 161292 Hypothetical protein 94 16 55 Complete Partial
CAETHG_0153 161313 161963 Dihydropteroate synthase DHPS 93 22 46 Complete Partial
CAETHG_0433 472649 474331 Transcriptional regulator, PucR family 110 25 57 Complete Partial
CAETHG_0601 661798 663339 Citrate lyase, alpha subunit 109 25 64 Partial Partial
CAETHG_0602 663332 664234 Citrate lyase, beta subunit 111 29 65 None None
CAETHG_0603 664234 664530 Citrate lyase acyl carrier protein 107 29 63 None None
CAETHG_0604 664553 665587 Citrate lyase ligase 109 23 63 None Partial
CAETHG_0605 665628 666806 Malic protein NAD-binding protein 101 27 69 None None
Intergenic 827340 827520 NA 106 30 53 None None
CAETHG_0774 832108 833028 SufBD protein 109 23 65 Complete Partial
CAETHG_0814 873533 874333 Hypothetical protein 106 23 69 Complete None
CAETHG_0815 874375 874953 Hypothetical protein 102 23 55 Complete None
rRNA 885055 887942 23s_rRNA 87 77 147 None None
rRNA 888206 889703 16s_rRNA 102 56 165 None None
CAETHG_0871 940541 941353 3-dehydroquinate dehydratase 109 27 59 Complete Partial
CAETHG_1038 1116305 1121431 Cell wall binding repeat 2-containing protein 127 27 69 Partial None
CAETHG_1052 1136476 1138017 Citrate lyase, alpha subunit 107 22 53 Partial None
CAETHG_1053 1138010 1138912 Citrate lyase, beta subunit 106 29 75 Complete None
CAETHG_1054 1138912 1139208 Citrate lyase acyl carrier protein 109 37 70 Complete None
CAETHG_1055 1139370 1140533 Malic protein NAD-binding protein 107 27 51 Partial Partial
Intergenic 1148600 1148780 NA 131 16 63 Complete None
CAETHG_1100 1186843 1187643 Hypothetical protein 118 23 68 Complete None
CAETHG_1101 1187685 1188263 Hypothetical protein 105 28 59 Complete None
CAETHG_1630 1752229 1753149 SufBD protein 118 26 79 Complete Partial
CAETHG_1634 1755642 1756505 modD protein 115 22 69 Complete Partial
CAETHG_1708 1841018 1841572 Lumazine-binding 132 23 66 Complete Complete
CAETHG_1816 1956238 1956534 Microcompartments protein 138 35 76 Complete Partial
CAETHG_1817 1956609 1956899 Microcompartments protein 139 19 81 Complete None
CAETHG_1818 1956948 1957598 Propanediol utilization protein 144 24 74 Complete None
CAETHG_1819 1957600 1959153 Acetaldehyde dehydrogenase (acetylating) 153 25 67 Complete None
CAETHG_1826 1963196 1964038 Ethanolamine utilization protein EutJ family protein 161 34 73 Complete Partial
CAETHG_1827 1964020 1964790 Hypothetical protein 162 22 68 Complete Partial
CAETHG_1949 2079078 2080271 Hypothetical protein 161 30 79 Complete Partial
CAETHG_1963 2095013 2096206 Hypothetical protein 128 36 97 Complete Partial
tRNA 2113813 2113886 tRNA_Met 128 15 61 None Complete
rRNA 2114155 2117042 23s_rRNA 122 81 161 None None
rRNA 2117334 2118831 16s_rRNA 118 66 128 None None
tRNA 2135117 2135189 tRNA_Met 132 22 64 Complete None
tRNA 2135201 2135286 tRNA_Leu 133 16 59 Complete None
tRNA 2135301 2135374 tRNA_Met 133 17 57 Complete None
tRNA 2135394 2136466 tRNA_Met 139 35 74 Complete None
tRNA 2135478 2135563 tRNA_Leu 140 30 62 Complete None
CAETHG_2076 2220169 2221506 Sigma54 specific transcriptional regulator, Fis family 122 32 85 Partial Partial
CAETHG_2077 2221658 2221885 Transcriptional regulator, Fis family 126 21 92 Partial None
CAETHG_2078 2222014 2222994 Putative sigma54 specific transcriptional regulator 135 30 77 Partial Partial
rRNA 2271738 2273235 16s_rRNA 165 10 26 None None
rRNA 2273527 2276414 23s_rRNA 158 10 26 None None
tRNA 2276744 2276817 tRNA_Met 153 28 70 None Complete
rRNA 2355334 2356831 16s_rRNA 145 11 24 None None
rRNA 2357123 2360010 23s_rRNA 136 13 23 None None
tRNA 2360340 2360412 tRNA_Lys 122 15 65 Complete Partial
rRNA 2372238 2373735 16s_rRNA 128 13 21 None None
rRNA 2374027 2376914 23s_rRNA 126 14 19 None None
rRNA 2392702 2394199 16s_rRNA 134 12 20 None None
rRNA 2394596 2397483 23s_rRNA 142 11 21 None None
CAETHG_2238 2397706 2397882 Hypothetical protein 138 23 57 Partial Complete
CAETHG_2268 2424703 2425503 Integrase catalytic region 115 26 61 Complete None
CAETHG_2269 2425545 2426123 Hypothetical protein 124 26 56 Complete None
Intergenic 2666300 2666515 NA 145 25 69 Complete None
Intergenic 2710650 2710840 NA 124 36 71 Complete None
CAETHG_2526 2714747 2715550 Hypothetical protein 133 28 74 Complete Partial
Intergenic 2769840 2769880 NA 124 23 67 Complete None
CAETHG_2620 2822788 2823741 Transposase IS66 124 30 59 Partial Complete
CAETHG_2621 2823723 2824328 Transposase IS66 127 30 52 Partial Partial
rRNA 2935186 2936683 16s_rRNA 127 14 27 None None
tRNA 2936973 2937045 tRNA_Ala 125 19 51 None None
tRNA 2937053 2937126 tRNA_Ile 125 26 58 None None
rRNA 2937443 2940330 23s_rRNA 117 14 28 None None
rRNA 2966992 2968489 16s_rRNA 126 11 20 None None
tRNA 2968779 2968851 tRNA_Ala 132 20 50 None None
tRNA 2968859 2968932 tRNA_Ile 131 23 70 None None
rRNA 2969222 2972109 23s_rRNA 128 10 19 None None
CAETHG_2843 3078642 3079445 Dihydropteroate synthase DHPS 152 30 66 Complete Partial
CAETHG_2844 3079499 3080131 Hypothetical protein 148 32 71 Complete Partial
CAETHG_2848 3085939 3086742 Dihydropteroate synthase DHPS 146 27 66 Complete Partial
CAETHG_2849 3086796 3087428 Hypothetical protein 139 31 75 Complete Partial
CAETHG_3037 3301321 3302088 MCP methyltransferase, CheR-type 149 23 65 Complete Partial
CAETHG_3075 3342748 3343524 Transposase IS66 112 39 74 Complete Partial
CAETHG_3281 3537107 3537880 Hypothetical protein 109 27 55 Complete Partial
CAETHG_3282 3537862 3538704 Ethanolamine utilization protein 107 30 62 Complete None
CAETHG_3283 3538721 3539026 Microcompartments protein 103 20 65 Complete None
CAETHG_3284 3539020 3539286 Ethanolamine utilization protein EutN/carboxysome structural protein Ccml 106 25 55 Complete None
CAETHG_3285 3539304 3539975 Ethanolamine utilization EutQ family protein 110 29 63 Complete None
CAETHG_3286 3540008 3540784 Microcompartments protein 106 30 61 Complete None
CAETHG_3287 3540833 3542350 Acetaldehyde dehydrogenase (acetylating) 111 27 61 Complete Partial
Intergenic 3848150 3848350 NA 126 34 39 Complete None
rRNA 3872016 3873511 16s_rRNA 98 10 18 None None
rRNA 3873937 3876824 23s_rRNA 107 14 21 None None
CAETHG_4028 4315106 4316413 VanW family protein 98 24 66 Complete Partial
CAETHG_4029 4316730 4319132 Collagen triple helix repeat-containing protein 94 13 38 Complete Partial
CAETHG_4035 4325792 4326292 VanW family protein 78 21 54 Complete Partial
  1. aThe genomic regions which were not assembled in 454/Draft assembly are listed above; bthe ‘x’ coverage defines the raw-read coverage averaged over given coordinates; c‘Complete/partial’ contig coverage defines whether the region was completely/partially assembled while ‘None’ defines that this region is missing in the respective assembly. Missing regions in either 454/Draft assembly are shown in bold.