E coli 100 all2

Revision as of 26 February 2013 21:07 by admin (Comments | Contribs)
Name NumContigs NumRefReplicons NumAssemblyBases NumReferenceBases NumLCBs DCJ_Distance NumDCJBlocks NumSNPs NumMisCalled NumUnCalled NumGapsRef NumGapsAssembly TotalBasesMissed PercBasesMissed ExtraBases PercExtraBases MissingChromosomes ExtraContigs NumSharedBoundaries NumInterLcbBoundaries BrokenCDS IntactCDS ContigN50^ ContigN90 MinContigLength MaxContigLength N50^ Blast Units(>200) N50^ cor.Units cor.N50 Error,(Indel>=5,Inv,Rel)
A_E.m2.fasta 115 1 4621932 4639675 2 97 98 78 78 0 121 109 58491 1.2607 22851 0.4944 0 18 1 0 64 4256 81936 25717 198 222525 83025 4234 114 81936 120 70581 8,(5,0,3)
A_S.m2.fasta 137 1 4651710 4639675 2 111 112 269 269 0 142 126 68144 1.4687 62523 1.3441 0 26 1 0 80 4240 71818 24405 113 222417 76987 4232 122 76987 129 62530 9,(6,0,3)
A_V.m2.fasta 109 1 4561228 4639675 10 98 100 152 152 0 125 116 169693 3.6574 45947 1.0073 0 14 1 4 74 4246 80921 25721 163 222411 83032 4155 107 83032 121 69083 13,(5,3,5)
E_A.m2.fasta 114 1 4603015 4639675 2 96 97 75 75 0 120 108 76532 1.6495 21975 0.4774 0 18 1 0 62 4258 81936 25717 198 222525 83025 4221 113 81936 119 70581 8,(5,0,3)
E_S.m2.fasta 225 1 4603180 4639675 2 189 190 169 169 0 170 167 104866 2.2602 27739 0.6026 0 35 1 0 92 4228 43550 10813 151 116269 44099 4164 221 43550 222 41922 3,(1,1,1)
E_V.m2.fasta 190 1 4594054 4639675 14 174 177 148 148 0 161 163 108118 2.3303 30522 0.6644 0 22 1 4 87 4233 47048 12130 149 161826 47643 4169 189 47643 201 44201 12,(4,6,2)
S_A.m2.fasta 135 1 4700242 4639675 2 107 108 250 250 0 134 122 69877 1.5061 62227 1.3239 0 28 1 0 78 4242 71817 24405 115 222416 76987 4232 122 76987 127 64914 8,(5,0,3)
S_E.m2.fasta 221 1 4602753 4639675 2 189 190 284 284 0 173 167 103100 2.2221 27959 0.6074 0 32 1 0 91 4229 44099 10813 151 116269 44296 4163 217 44099 219 42370 3,(1,1,1)
S_V.m2.fasta 211 1 4519527 4639675 9 178 180 164 164 0 179 182 191337 4.1239 31657 0.7004 0 35 1 3 82 4238 47039 11721 150 161836 47631 4119 202 45908 215 44098 14,(5,5,4)
V_A.m2.fasta 107 1 4497254 4639675 16 97 99 181 181 0 129 114 232438 5.0098 44805 0.9963 0 15 1 8 75 4245 80921 26897 163 222411 83033 4095 106 83033 119 69083 13,(5,3,5)
V_E.m2.fasta 190 1 4596978 4639675 18 178 181 168 168 0 167 170 104187 2.2456 29759 0.6474 0 21 1 5 84 4236 47643 12130 149 161826 47831 4171 189 47643 201 45414 12,(4,6,2)
V_S.m2.fasta 214 1 4565564 4639675 13 183 185 224 224 0 182 187 100680 2.17 11231 0.246 0 36 1 5 83 4237 47746 11721 150 161837 48004 4169 201 47746 214 47039 14,(5,5,4)
A_E.gaa.fa.fas 192 1 4647990 4639675 2 116 117 163 87 76 146 118 47994 1.0344 25214 0.5425 0 76 1 0 73 4247 66424 20705 100 222524 68560 4244 135 68560 134 68561 3,(0,0,3)
A_S.gaa.fa.fas 190 1 4644821 4639675 2 114 115 200 124 76 147 120 49705 1.0713 24083 0.5185 0 76 1 0 76 4244 68584 22153 102 222412 69083 4246 132 69083 131 69083 3,(0,0,3)
A_V.gaa.fa.fas 187 1 4646249 4639675 2 113 114 176 101 75 149 116 49027 1.0567 23904 0.5145 0 74 1 0 74 4246 71815 22180 102 222412 76986 4248 131 76986 131 71810 5,(2,0,3)
E_A.gaa.fa.fas 421 1 4611298 4639675 2 329 330 35 35 0 279 269 70734 1.5245 11034 0.2393 0 92 1 0 143 4177 24191 6689 100 104739 24375 4058 377 24375 359 24375 2,(1,0,1)
E_S.gaa.fa.fas 424 1 4593644 4639675 2 333 334 63 63 0 282 278 79938 1.7229 7850 0.1709 0 91 1 0 144 4176 24389 6676 100 104748 24632 4056 377 24389 372 24389 3,(1,1,1)
E_V.gaa.fa.fas 423 1 4596515 4639675 2 330 331 69 69 0 287 274 79891 1.7219 10044 0.2185 0 93 1 0 144 4176 24382 6675 100 104739 24632 4054 378 24382 366 24378 3,(1,1,1)
S_A.gaa.fa.fas 559 1 4632385 4639675 2 273 274 118 118 0 246 259 89349 1.9258 11441 0.247 0 286 1 0 109 4211 31788 7901 100 106314 31849 4122 355 31849 331 31845 3,(1,0,2)
S_E.gaa.fa.fas 561 1 4610906 4639675 2 272 273 166 166 0 245 252 99902 2.1532 8092 0.1755 0 289 1 0 109 4211 31913 7901 100 105667 32166 4111 357 32166 352 32167 3,(1,0,2)
S_V.gaa.fa.fas 562 1 4602062 4639675 2 275 276 212 212 0 252 261 108734 2.3436 7976 0.1733 0 287 1 0 111 4209 31788 7901 100 105719 31837 4109 357 31837 355 31837 3,(1,0,2)
V_A.gaa.fa.fas 196 1 4638405 4639675 14 128 130 237 158 79 148 143 55741 1.2014 20672 0.4457 0 75 1 4 69 4251 71909 18783 149 215971 77822 4229 161 77822 154 68585 15,(5,5,5)
V_E.gaa.fa.fas 265 1 4594601 4639675 15 190 192 139 106 33 179 178 85057 1.8333 10168 0.2213 0 81 1 6 85 4235 47048 11188 100 161826 47643 4174 228 47048 235 44201 14,(5,5,4)
V_S.gaa.fa.fas 267 1 4579080 4639675 18 202 204 184 149 35 189 201 92125 1.9856 5833 0.1274 0 74 1 6 83 4237 47039 11192 149 161836 47631 4176 229 47039 242 44098 16,(4,7,5)

[^] Please note that the ContigN50 calculated by Mauve Assembly Metrics is incorrect (off-by-one error). We have followed the definition of N50 (A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list. ref) to calculate N50s. GAGE's N50 was calculated using the total reference genome length rather than the sum total of contig lengths. The GAGE's cor.N50 values were computed after correcting contigs by breaking them at each error.