mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 370,176 | G→T | D226Y (GAT→TAT) | mhpB → | 2,3‑dihydroxyphenylpropionate 1,2‑dioxygenase |
| RA | 547,694 | A→G | intergenic (+123/‑1156) | fdrA → / → ylbF | acyl‑CoA synthetase with NAD(P)‑bindingRossmann‑fold domain/hypothetical protein |
| RA | 547,835 | +G | intergenic (+264/‑1015) | fdrA → / → ylbF | acyl‑CoA synthetase with NAD(P)‑bindingRossmann‑fold domain/hypothetical protein |
| RA | 556,858 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional 5,10‑methylene‑tetrahydrofolatedehydrogenase/5,10‑methylene ‑tetrahydrofolatecyclohydrolase |
| MC JC | 654,214 | Δ1,199 bp | insH_12 | insH_12 | |
| RA | 967,490 | G→T | G150C (GGT→TGT) | msbA → | lipid ABC transporter ATP‑bindingprotein/membrane protein |
| RA | 987,574 | G→T | intergenic (‑170/+433) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 1,093,686 | T→C | V130A (GTA→GCA) | ycdT → | diguanylate cyclase |
| RA | 1,197,797 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase,‑specific for NADP+ |
| RA | 1,197,809 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase,‑specific for NADP+ |
| MC JC | 1,301,041 | Δ1,336 bp | insC_8–insD_10 | insC_8, insD_10 | |
| RA | 1,422,016 | C→A | intergenic (‑61/‑63) | racR ← / → ydaS | DNA‑binding transcriptional regulator/DNA‑binding transcriptional regulator |
| RA | 1,519,222 | G→T | V40V (GTG→GTT) | ydcX → | inner membrane protein |
| RA | 1,669,601 | Δ1 bp | coding (678/1221 nt) | dgsA ← | DNA‑binding transcriptional repressor |
| RA | 1,979,957 | G→T | intergenic (‑37/+398) | flhD ← / ← insH_10 | DNA‑binding transcriptional dual regulator/IS5 element protein |
| RA | 2,005,401 | C→T | E115K (GAA→AAA) | fliC ← | flagellar filament structural protein |
| MC JC | 2,176,983 | Δ1,199 bp | insH_11 | insH_11 | |
| RA | 2,245,455 | A→G | S283P (TCG→CCG) | yeiB ← | inner membrane protein |
| RA | 2,273,529 | C→A | Q73K (CAG→AAG) | spr → | peptidase, outer membrane lipoprotein |
| MC JC | 2,320,795 | Δ1,336 bp | insD_9–insC_5 | insD_9, insC_5 | |
| JC | 2,764,119 | (TATGGCAC)6→7 | intergenic (‑310/+50) | yfjL ← / ← yfjM | hypothetical protein/hypothetical protein |
| RA | 2,866,111 | A→G | intergenic (‑21/+159) | rpoS ← / ← nlpD | RNA polymerase, sigma S (sigma 38) factor/outer membrane lipoprotein |
| RA | 3,212,521 | G→A | M273I (ATG→ATA) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| MC JC | 3,261,134 | Δ1,199 bp | insH_16–[tdcD] | insH_16, [tdcD] | |
| RA | 3,268,825 | A→G | T186A (ACA→GCA) | yhaC → | hypothetical protein |
| RA | 3,327,050 | G→A | P157L (CCA→CTA) | rlmE ← | 23S rRNA methyltransferase |
| RA | 3,693,457 | +A | noncoding (1417/1542 nt) | rrsC ← | 16S ribosomal RNA |
| MC JC | 3,742,936 | Δ1,336 bp | insD_8–insC | insD_8, insC | |
| MC JC | 3,746,911 | Δ1,199 bp | insH_13 | insH_13 | |
| MC JC | 3,750,591 | Δ1,199 bp | insH_14 | insH_14 | |
| MC JC | 3,958,123 | Δ34 bp | coding (1156‑1189/1287 nt) | dctA → | C4‑dicarboxylic acid, orotate and citratetransporter |
| MC JC | 4,310,363 | Δ1,199 bp | insH_15–[alsK] | insH_15, [alsK] | |
| RA | 4,371,274 | (A)5→3 | intergenic (‑9/+296) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_007779_cfb | 1197815 | 1213100 | 15286 | 64 [62] | [63] 67 | [icd]–mcrA | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,cohE,croE,ymfL,ymfM,ymfN,ymfR,ymfO,ymfP,ymfQ,stfP,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_007779_cfb | 3972854 | 3988264–3987179 | 14326–15411 | 137 [0] | [61] 64 | [gadA]–insH | [gadA],gadX,gadW,mdtF,mdtE,gadE,hdeD,hdeA,hdeB,yhiD,dctR,slp,insH |
| * | * | ÷ | NC_007779_cfb | 4357359 | 4366926 | 9568 | 168 [2] | [2] 179 | [yjdK]–cadC | [yjdK],yjdO,lysU,yjdL,cadA,cadB,cadC |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779_cfb | 380484 = | NA (NA) | 125 (0.920) | 108/430 | 0.3 | NA | intergenic (‑418/‑46) | yaiO/insC_2 | hypothetical protein/IS2 insertion element repressor InsA |
| ? | NC_007779_cfb | = 381407 | NA (NA) | coding (510/906 nt) | insD | IS2 insertion element transposase InsAB' | |||||
| * | ? | NC_007779_cfb | 381401 = | NA (NA) | 133 (0.990) | 115/426 | 0.2 | NA | coding (504/906 nt) | insD | IS2 insertion element transposase InsAB' |
| ? | NC_007779_cfb | = 381812 | NA (NA) | coding (303/387 nt) | yaiF | hypothetical protein | |||||
| * | ? | NC_007779_cfb | = 3186081 | NA (NA) | 136 (1.010) | 113/428 | 0.2 | 100% | coding (26/2466 nt) | yqiG | outer membrane usher protein |
| ? | NC_007779_cfb | 3512753 = | 0 (0.000) | coding (529/1026 nt) | cytR | DNA‑binding transcriptional dual regulator | |||||
| * | ? | NC_007779_cfb | = 3512759 | 6 (0.040) | 94 (0.690) | 86/428 | 1.0 | 94.0% | coding (535/1026 nt) | cytR | DNA‑binding transcriptional dual regulator |
| ? | NC_007779_cfb | = 3744262 | NA (NA) | intergenic (‑90/+31) | insC/yidZ | IS2 element protein/DNA‑binding transcriptional regulator | |||||
| * | ? | NC_007779_cfb | 3670529 = | 2 (0.010) | 177 (1.300) | 120/430 | 0.1 | 98.9% | intergenic (‑79/+62) | rhoL/trxA | rho operon leader peptide/thioredoxin 1 |
| ? | NC_007779_cfb | 3746911 = | NA (NA) | intergenic (‑509/‑68) | mdtL/insH_13 | multidrug efflux system protein/IS5 element protein | |||||
| * | ? | NC_007779_cfb | = 3670532 | 0 (0.000) | 151 (1.110) | 106/430 | 0.4 | 100% | intergenic (‑82/+59) | rhoL/trxA | rho operon leader peptide/thioredoxin 1 |
| ? | NC_007779_cfb | = 3748105 | NA (NA) | intergenic (+146/+966) | insH_13/tnaA | IS5 element protein/tryptophanase/L‑cysteine desulfhydrase,PLP‑dependent | |||||
| * | ? | NC_007779_cfb | = 3744263 | NA (NA) | 169 (1.240) | 136/430 | 0.0 | 100% | intergenic (‑91/+30) | insC/yidZ | IS2 element protein/DNA‑binding transcriptional regulator |
| ? | NC_007779_cfb | 3903274 = | 0 (0.000) | coding (37/825 nt) | bax | hypothetical protein | |||||
| * | ? | NC_007779_cfb | 3746911 = | NA (NA) | 137 (1.010) | 113/430 | 0.2 | 100% | intergenic (‑509/‑68) | mdtL/insH_13 | multidrug efflux system protein/IS5 element protein |
| ? | NC_007779_cfb | = 3972853 | 0 (0.000) | coding (19/1401 nt) | gadA | glutamate decarboxylase A, PLP‑dependent | |||||
| * | ? | NC_007779_cfb | = 3903279 | 11 (0.080) | 149 (1.100) | 122/428 | 0.1 | 93.2% | coding (42/825 nt) | bax | hypothetical protein |
| ? | NC_007779_cfb | = 4504190 | NA (NA) | intergenic (+10/‑89) | insD_3/yjgW | IS2 insertion element transposase InsAB'/hypothetical protein | |||||
| * | ? | NC_007779_cfb | 4056220 = | NA (NA) | 176 (1.300) | 150/430 | 0.0 | 98.9% | intergenic (‑209/+15) | yrhD/insB | Gene added/IS1 transposase InsAB' |
| ? | NC_007779_cfb | 4366927 = | 2 (0.010) | intergenic (‑315/+302) | cadC/pheU | DNA‑binding transcriptional activator/tRNA‑Phe | |||||
| * | ? | NC_007779_cfb | = 4056987 | NA (NA) | 166 (1.220) | 136/430 | 0.0 | 98.8% | coding (388/414 nt) | yrhA | hypothetical protein |
| ? | NC_007779_cfb | = 4357358 | 2 (0.010) | coding (97/297 nt) | yjdK | hypothetical protein | |||||
| * | ? | NC_007779_cfb | = 4311556 | NA (NA) | 123 (0.910) | 101/428 | 0.5 | 99.2% | coding (922/1029 nt) | alsK | D‑allose kinase |
| ? | NC_007779_cfb | 4540915 = | 1 (0.010) | intergenic (+204/+379) | yjhR/nanS | frameshift suppressor/hypothetical protein | |||||