mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 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 |
| 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+ |
| RA | 1,197,822 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase,‑specific for NADP+ |
| RA | 1,197,824 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase,‑specific for NADP+ |
| MC JC | 1,301,041 | Δ1,336 bp | insC_8–insD_10 | insC_8, insD_10 | |
| 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 |
| JC | 2,288,259 | (TTATCGCCT)2→3 | coding (550/1761 nt) | yejM → | hydrolase, inner membrane |
| RA | 2,289,601 | C→A | noncoding (57/77 nt) | proL → | tRNA‑Pro |
| MC JC | 2,320,795 | Δ1,336 bp | insD_9–insC_5 | insD_9, insC_5 | |
| RA | 2,409,829 | C→A | intergenic (‑87/+544) | nuoA ← / ← lrhA | NADH:ubiquinone oxidoreductase, membrane subunitA/DNA‑binding transcriptional repressor |
| RA | 2,468,335 | (C)9→10 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membranetransporter/hypothetical protein |
| RA | 2,866,111 | A→G | intergenic (‑21/+159) | rpoS ← / ← nlpD | RNA polymerase, sigma S (sigma 38) factor/outer membrane lipoprotein |
| RA | 3,268,825 | A→G | T186A (ACA→GCA) | yhaC → | hypothetical protein |
| RA | 3,449,011 | A→C | I774S (ATC→AGC) | rpoC ← | RNA polymerase, beta prime subunit |
| RA | 3,666,710 | G→T | P314Q (CCG→CAG) | wzzE ← | Entobacterial Common Antigen (ECA)polysaccharide chain length modulation protein |
| 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 |
| RA | 4,291,189 | G→A | intergenic (‑228/‑165) | acs ← / → nrfA | bifunctional acetyl‑CoA synthetase/propionyl‑CoAsynthetase/nitrite reductase, formate‑dependent,cytochrome |
| 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 | 1197853 | 1213102 | 15250 | 56 [55] | [55] 56 | [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 | 1396609 | 1401726 | 5118 | 188 [0] | [0] 132 | [ynaI]–[ogt] | [ynaI],insH_8,ynaJ,uspE,fnr,[ogt] |
| * | * | ÷ | NC_007779_cfb | 3975089 | 3988279–3987179 | 12091–13191 | 112 [2] | [53] 57 | [gadX]–insH | [gadX],gadW,mdtF,mdtE,gadE,hdeD,hdeA,hdeB,yhiD,dctR,slp,insH |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779_cfb | 380484 = | NA (NA) | 131 (1.070) | 115/438 | 0.1 | 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) | 122 (1.000) | 94/434 | 0.4 | 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 | = 654213 | 0 (0.000) | 137 (1.140) | 112/428 | 0.1 | 100% | intergenic (+448/‑68) | dpiA/insH_12 | DNA‑binding response regulator in two‑componentregulatory system with citA/IS5 element protein |
| ? | NC_007779_cfb | 655413 = | 0 (0.000) | intergenic (+152/‑1566) | insH_12/pagP | IS5 element protein/palmitoyl transferase for Lipid A | |||||
| * | ? | NC_007779_cfb | = 1396608 | 0 (0.000) | 188 (1.530) | 150/438 | 0.0 | 100% | coding (1029/1032 nt) | ynaI | inner membrane protein |
| ? | NC_007779_cfb | 1397758 = | NA (NA) | intergenic (‑122/‑32) | ynaI/insH_8 | inner membrane protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_007779_cfb | 1401727 = | 0 (0.000) | 131 (1.070) | 100/438 | 0.3 | 100% | coding (224/516 nt) | ogt | O‑6‑alkylguanine‑DNA:cysteine‑proteinmethyltransf erase |
| ? | NC_007779_cfb | 1980209 = | NA (NA) | intergenic (‑289/+146) | flhD/insH_10 | DNA‑binding transcriptional dual regulator/IS5 element protein | |||||
| * | ? | NC_007779_cfb | = 3186081 | NA (NA) | 135 (1.100) | 107/436 | 0.2 | 99.3% | coding (26/2466 nt) | yqiG | outer membrane usher protein |
| ? | NC_007779_cfb | 3512753 = | 1 (0.010) | coding (529/1026 nt) | cytR | DNA‑binding transcriptional dual regulator | |||||
| * | ? | NC_007779_cfb | = 3261133 | 1 (0.010) | 141 (1.170) | 118/430 | 0.1 | 99.7% | intergenic (‑59/‑69) | tdcE/insH_16 | pyruvate formate‑lyase 4/2‑ketobutyrateformate‑lyase/IS5 element protein |
| ? | NC_007779_cfb | 3262333 = | 0 (0.000) | coding (1183/1296 nt) | tdcD | propionate kinase/acetate kinase C, anaerobic | |||||
| * | ? | NC_007779_cfb | = 3512759 | 0 (0.000) | 97 (0.790) | 89/436 | 0.6 | 100% | 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 | = 3744263 | NA (NA) | 153 (1.250) | 122/438 | 0.1 | 96.8% | intergenic (‑91/+30) | insC/yidZ | IS2 element protein/DNA‑binding transcriptional regulator |
| ? | NC_007779_cfb | 3903274 = | 5 (0.040) | coding (37/825 nt) | bax | hypothetical protein | |||||
| * | ? | NC_007779_cfb | = 3903279 | 8 (0.070) | 144 (1.180) | 115/436 | 0.1 | 94.8% | 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 | = 3975088 | 2 (0.020) | 109 (0.890) | 98/438 | 0.4 | 98.2% | coding (484/825 nt) | gadX | DNA‑binding transcriptional dual regulator |
| ? | NC_007779_cfb | 3987185 = | NA (NA) | intergenic (‑731/‑32) | slp/insH | outer membrane lipoprotein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_007779_cfb | = 4311556 | NA (NA) | 93 (0.760) | 83/436 | 0.8 | 97.9% | coding (922/1029 nt) | alsK | D‑allose kinase |
| ? | NC_007779_cfb | 4540915 = | 2 (0.020) | intergenic (+204/+379) | yjhR/nanS | frameshift suppressor/hypothetical protein | |||||