E coli 36 all2

Revision as of 26 February 2013 21:03 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_C.m2.fasta 118 1 4632801 4639675 4 102 103 310 310 0 120 108 60508 1.3041 33636 0.726 0 17 1 1 52 4268 96511 25328 100 222423 105944 4269 105 105944 112 95959 7,(5,0,2)
A_E.m2.fasta 80 1 4622336 4639675 2 69 70 246 246 0 85 85 48361 1.0423 22945 0.4964 0 11 1 0 51 4269 119107 35440 122 226190 126232 4275 78 126232 89 113511 12,(9,0,3)
A_S.m2.fasta 128 1 4627108 4639675 8 112 115 350 350 0 130 124 55903 1.2049 29806 0.6442 0 19 1 1 56 4264 92932 25328 105 268389 96511 4250 108 96511 115 92933 7,(6,0,1)
A_V.m2.fasta 116 1 4661531 4639675 2 96 97 357 357 0 117 118 74219 1.5997 73288 1.5722 0 20 1 0 56 4264 105944 26693 100 222423 107040 4252 99 107040 107 95959 9,(7,0,2)
C_A.m2.fasta 118 1 4632801 4639675 2 101 102 297 297 0 117 108 60609 1.3063 38416 0.8292 0 17 1 0 54 4266 96511 25328 100 222423 105944 4269 105 105944 112 95959 7,(5,0,2)
C_E.m2.fasta 104 1 4587525 4639675 5 94 95 66 66 0 103 91 100426 2.1645 38321 0.8353 0 11 1 2 45 4275 101122 24930 123 209804 105835 4261 101 105835 108 101122 7,(3,2,2)
C_S.m2.fasta 327 1 4536804 4639675 9 293 294 124 124 0 290 288 128041 2.7597 4775 0.1053 0 36 1 4 59 4261 29937 8447 108 107343 30103 4223 286 29775 287 28466 2,(0,1,1)
C_V.m2.fasta 179 1 4589403 4639675 7 146 147 174 174 0 159 160 128909 2.7784 41861 0.9121 0 35 1 3 57 4263 63294 15280 100 184379 63512 4247 154 63512 163 60714 9,(6,0,3)
E_A.m2.fasta 80 1 4622436 4639675 2 70 71 244 244 0 85 85 48894 1.0538 24574 0.5316 0 10 1 0 52 4268 119107 35440 122 226190 126232 4275 78 126232 89 113511 12,(10,0,2)
E_C.m2.fasta 105 1 4587576 4639675 5 94 95 66 66 0 102 90 83511 1.7999 21336 0.4651 0 12 2 2 49 4271 101133 24930 123 209804 105835 4261 102 101133 108 101133 6,(2,2,2)
E_S.m2.fasta 135 1 4568724 4639675 2 121 122 93 93 0 119 110 84290 1.8167 4832 0.1058 0 14 1 0 66 4254 77079 18177 122 209786 77696 4226 131 77696 134 77079 5,(2,1,2)
E_V.m2.fasta 118 1 4612692 4639675 2 102 103 110 110 0 103 98 115498 2.4894 79703 1.7279 0 16 1 0 59 4261 86507 24325 122 209787 86974 4221 114 86974 120 83136 8,(5,1,2)
S_A.m2.fasta 128 1 4627108 4639675 11 113 117 346 346 0 131 126 55948 1.2059 30419 0.6574 0 20 1 1 55 4265 92932 25328 105 268389 96511 4250 108 96511 115 92933 7,(6,0,1)
S_C.m2.fasta 326 1 4536681 4639675 10 296 297 159 159 0 294 291 125769 2.7107 4857 0.1071 0 33 1 5 59 4261 29937 8447 108 107343 30103 4223 285 29775 286 28466 2,(0,1,1)
S_E.m2.fasta 135 1 4568686 4639675 2 121 122 88 88 0 119 110 84235 1.8155 4739 0.1037 0 14 1 0 65 4255 77079 18177 122 209786 77696 4226 131 77696 134 77079 5,(2,1,2)
S_V.m2.fasta 243 1 4549600 4639675 2 193 194 246 246 0 204 194 115159 2.482 3408 0.0749 0 50 1 0 72 4248 56801 12713 103 166923 57725 4202 197 56801 205 54360 9,(6,0,3)
V_A.m2.fasta 116 1 4661902 4639675 2 96 97 349 349 0 119 119 74234 1.6 73676 1.5804 0 20 1 0 57 4263 105944 26693 100 222423 107040 4252 99 107040 107 95959 9,(7,0,2)
V_C.m2.fasta 181 1 4591015 4639675 6 147 148 236 236 0 161 165 131013 2.8238 45805 0.9977 0 36 1 2 58 4262 63294 15280 100 184379 63512 4247 155 63512 163 60714 9,(6,0,3)
V_E.m2.fasta 117 1 4608607 4639675 2 101 102 120 120 0 108 97 112002 2.414 72122 1.5649 0 16 1 0 58 4262 86974 24325 122 209787 96641 4221 113 96641 119 86505 8,(5,1,2)
V_S.m2.fasta 245 1 4550043 4639675 2 190 191 133 133 0 198 185 115722 2.4942 3563 0.0783 0 55 1 0 72 4248 56801 12713 103 166923 57725 4202 198 56801 207 54360 9,(5,0,4)
A_C.gaa.fa.fas 140 1 4627307 4639675 2 111 112 345 311 34 124 121 57571 1.2408 29878 0.6457 0 29 1 0 57 4263 92933 25329 100 222425 96511 4256 110 96511 116 92933 6,(5,0,1)
A_E.gaa.fa.fas 136 1 4638015 4639675 2 105 106 361 327 34 117 113 54792 1.1809 28878 0.6226 0 31 1 0 57 4263 92933 25197 100 222425 96511 4258 111 96511 116 92933 6,(5,0,1)
A_S.gaa.fa.fas 135 1 4626731 4639675 2 109 110 370 336 34 122 119 57623 1.242 29389 0.6352 0 26 1 0 57 4263 92933 25329 100 222425 96511 4250 110 96511 116 92933 6,(5,0,1)
A_V.gaa.fa.fas 134 1 4626634 4639675 2 107 108 370 336 34 123 119 57749 1.2447 29366 0.6347 0 27 1 0 57 4263 92933 26096 100 222425 96511 4249 109 96511 116 92933 7,(5,0,2)
C_A.gaa.fa.fas 380 1 4587208 4639675 11 298 300 286 286 0 293 282 104200 2.2458 12316 0.2685 0 87 1 3 64 4256 28450 8495 100 107342 29767 4241 288 28450 280 28036 2,(0,1,1)
C_E.gaa.fa.fas 379 1 4555312 4639675 5 296 297 92 92 0 279 278 123665 2.6654 3517 0.0772 0 85 1 1 61 4259 29767 8368 100 107342 29905 4232 288 28450 289 28036 2,(0,1,1)
C_S.gaa.fa.fas 383 1 4550534 4639675 5 305 306 142 142 0 298 296 117524 2.533 4222 0.0928 0 80 1 1 62 4258 29775 8368 100 107343 29937 4228 288 28466 290 28036 2,(0,1,1)
C_V.gaa.fa.fas 382 1 4550334 4639675 5 299 300 122 122 0 284 284 116676 2.5147 3551 0.078 0 85 1 1 61 4259 29767 8368 100 107342 29905 4230 288 28577 290 28036 2,(0,1,1)
E_A.gaa.fa.fas 210 1 4602464 4639675 2 151 152 43 43 0 129 127 64510 1.3904 10756 0.2337 0 59 1 0 65 4255 54405 13156 100 186686 58030 4210 181 58030 179 52796 3,(2,0,1)
E_C.gaa.fa.fas 210 1 4570226 4639675 2 152 153 15 15 0 137 122 86539 1.8652 2349 0.0514 0 58 1 0 65 4255 54405 13654 100 186686 57790 4192 181 57790 186 52796 5,(2,2,1)
E_S.gaa.fa.fas 211 1 4571238 4639675 2 153 154 42 42 0 139 133 86271 1.8594 2978 0.0651 0 58 1 0 67 4253 54406 13654 100 186686 57790 4192 182 54406 186 52818 4,(2,1,1)
E_V.gaa.fa.fas 211 1 4570155 4639675 2 153 154 29 29 0 135 125 86669 1.868 2344 0.0513 0 58 1 0 66 4254 54420 13651 100 186686 57790 4191 182 54420 186 52796 4,(2,1,1)
S_A.gaa.fa.fas 552 1 4578180 4639675 2 463 464 63 63 0 449 406 102783 2.2153 10636 0.2323 0 89 1 0 102 4218 17902 5383 100 103369 17944 4146 449 17892 439 17892 1,(0,0,1)
S_C.gaa.fa.fas 558 1 4552640 4639675 2 463 464 48 48 0 449 416 133055 2.8678 7486 0.1644 0 95 1 0 100 4220 17902 5390 100 103374 17944 4143 449 17892 450 17892 1,(0,0,1)
S_E.gaa.fa.fas 553 1 4553014 4639675 2 465 466 35 35 0 451 401 120654 2.6005 6909 0.1517 0 88 1 0 100 4220 17902 5383 100 103369 17944 4132 449 17892 450 17892 1,(0,0,1)
S_V.gaa.fa.fas 554 1 4550719 4639675 2 467 468 56 56 0 458 410 123110 2.6534 7263 0.1596 0 87 1 0 99 4221 17902 5384 100 103372 17944 4140 450 17892 451 17892 1,(0,0,1)
V_A.gaa.fa.fas 284 1 4590316 4639675 2 192 193 188 188 0 197 195 91635 1.975 8907 0.194 0 92 1 0 76 4244 52438 12537 100 166094 52474 4210 217 52474 210 49022 8,(5,0,3)
V_C.gaa.fa.fas 289 1 4553691 4639675 2 202 203 139 139 0 205 201 132814 2.8626 3214 0.0706 0 87 1 0 74 4246 52474 12537 100 166107 54373 4199 217 52474 224 49037 8,(5,0,3)
V_E.gaa.fa.fas 284 1 4561370 4639675 2 199 200 147 147 0 198 195 108649 2.3417 3056 0.067 0 85 1 0 75 4245 52474 12537 100 166094 54420 4197 217 52474 221 49028 8,(5,0,3)
V_S.gaa.fa.fas 285 1 4552937 4639675 2 206 207 206 206 0 216 204 115137 2.4816 3295 0.0724 0 79 1 0 75 4245 52478 12537 100 166095 54360 4197 217 52478 222 49024 8,(5,0,3)

[^] 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.