mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 28,116 | T→A | 6.2% | L275Q (CTG→CAG) | rihC → | ribonucleoside hydrolase 3 |
| JC | 186,137:1 | +CCC | 10.1% | coding (2514/2673 nt) | glnD ← | uridylyltransferase |
| RA | 235,917 | C→T | 5.2% | R29H (CGC→CAC) | rnhA ← | ribonuclease HI, degrades RNA of DNA‑RNA hybrids |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 375,176 | A→G | 8.3% | intergenic (+295/‑283) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,326 | A→G | 7.4% | intergenic (+445/‑133) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 377,392 | A→G | 8.6% | intergenic (+81/+143) | yaiL → / ← frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| RA | 377,431:1 | +A | 8.5% | intergenic (+120/+104) | yaiL → / ← frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| RA | 377,432 | C→G | 8.6% | intergenic (+121/+103) | yaiL → / ← frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| RA | 485,039 | A→G | 5.1% | L194S (TTG→TCG) | acrA ← | multidrug efflux system |
| RA | 524,811 | G→A | 5.1% | A517A (GCG→GCA) | rhsD → | Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor |
| RA | 753,730 | C→T | 8.7% | A247T (GCG→ACG) | gltA ← | citrate synthase |
| RA | 759,776 | C→A | 59.6% | D357E (GAC→GAA) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 761,422 | C→T | 9.3% | A906V (GCC→GTC) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 864,741 | Δ1 bp | 5.3% | coding (389/750 nt) | moeB ← | molybdopterin synthase sulfurylase |
| RA | 927,612 | Δ1 bp | 6.5% | coding (1584/1722 nt) | cydC ← | glutathione/cysteine ABC transporter export permease/ATPase |
| RA | 966,796 | C→T | 5.9% | T59I (ACA→ATA) | msbA → | lipid ABC transporter permease/ATPase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,777,953 | C→T | 3.6% | A253V (GCC→GTC) | ydiO → | putative acyl‑CoA dehydrogenase |
| RA | 1,963,203 | G→A | 8.2% | G616G (GGC→GGT) | flhA ← | putative flagellar export pore protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,846,099 | A→G | 5.0% | L124S (TTG→TCG) | hycE ← | hydrogenase 3, large subunit |
| RA | 2,876,374 | G→T | 20.0% | intergenic (‑47/‑205) | cysD ← / → iap | sulfate adenylyltransferase, subunit 2/aminopeptidase in alkaline phosphatase isozyme conversion |
| RA | 2,974,289 | Δ1 bp | 7.8% | coding (1724/2160 nt) | aas ← | fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase |
| RA | 3,665,443 | A→G | 12.5% | S123P (TCT→CCT) | gadX ← | acid resistance regulon transcriptional activator, autoactivator |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,951,560 | C→T | 40.1% | pseudogene (20/663 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive, acetolactate synthase II, large subunit, cryptic, interrupted |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,031,044 | T→C | 8.9% | intergenic (‑74/‑116) | fadB ← / → pepQ | fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase/proline dipeptidase |
| RA | 4,125,617 | Δ1 bp | 5.5% | coding (1193/2199 nt) | priA ← | Primosome factor n' (replication factor Y) |
| RA | 4,125,618 | Δ1 bp | 5.5% | coding (1192/2199 nt) | priA ← | Primosome factor n' (replication factor Y) |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,217,318 | G→A | 4.9% | A71T (GCA→ACA) | aceA → | isocitrate lyase |
| RA | 4,296,154 | T→C | 18.6% | intergenic (+361/+283) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 51.6% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 58.7% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,298,945 | G→A | 7.3% | H141H (CAC→CAT) | fdhF ← | formate dehydrogenase‑H, selenopolypeptide subunit |
| RA | 4,407,487 | A→G | 4.4% | D278G (GAC→GGC) | rnr → | exoribonuclease R, RNase R |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 384794 | 385094 | 301 | 12 [11] | [11] 12 | yaiS/tauA | putative PIG‑L family deacetylase/taurine ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 755144 | 758379 | 3236 | 12 [10] | [11] 13 | sdhC–[sdhB] | sdhC, sdhD, sdhA, [sdhB] |
| * | * | ÷ | NC_000913 | 2106433 | 2107384 | 952 | 13 [10] | [11] 12 | [wbbH]–[glf] | [wbbH], [glf] |
| * | * | ÷ | NC_000913 | 3423910–3424230 | 3424380–3424237 | 8–471 | 12 [11] | [9] 13 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 3798872 | 3799583 | 712 | 13 [11] | [10] 12 | [waaU]–[waaZ] | [waaU], [waaZ] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 120406 | 69 (1.280) | 4 (0.080) | 4/494 | NT | 5.8% | coding (1146/1374 nt) | aroP | aromatic amino acid transporter |
| ? | NC_000913 | = 120807 | 62 (1.170) | coding (745/1374 nt) | aroP | aromatic amino acid transporter | |||||
| * | ? | NC_000913 | 231961 = | 46 (0.850) | 10 (0.190) | 4/498 | NT | 17.3% | coding (36/624 nt) | yafE | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase |
| ? | NC_000913 | 232463 = | 50 (0.930) | coding (538/624 nt) | yafE | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase | |||||
| * | ? | NC_000913 | = 243009 | 79 (1.460) | 5 (0.100) | 3/488 | NT | 6.8% | coding (295/2445 nt) | fadE | acyl coenzyme A dehydrogenase |
| ? | NC_000913 | = 243192 | 60 (1.140) | coding (112/2445 nt) | fadE | acyl coenzyme A dehydrogenase | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 43 (0.800) | 33/502 | NT | 100% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 258675 | NA (NA) | 9 (0.170) | 8/502 | NT | 20.9% | intergenic (+776/‑1) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | 1303476 = | 34 (0.630) | coding (578/921 nt) | oppB | oligopeptide ABC transporter permease | |||||
| * | ? | NC_000913 | 381463 = | NA (NA) | 3 (0.060) | 3/480 | NT | NA | coding (113/366 nt) | insC1 | IS2 repressor TnpA |
| ? | NC_000913 | 381851 = | NA (NA) | coding (178/906 nt) | insD1 | IS2 transposase TnpB | |||||
| * | ? | NC_000913 | 762116 = | 61 (1.130) | 7 (0.140) | 4/474 | NT | 9.5% | coding (595/1218 nt) | sucB | dihydrolipoyltranssuccinase |
| ? | NC_000913 | 762340 = | 75 (1.470) | coding (819/1218 nt) | sucB | dihydrolipoyltranssuccinase | |||||
| * | ? | NC_000913 | 934793 = | 81 (1.500) | 4 (0.080) | 4/490 | NT | 5.4% | coding (1570/3990 nt) | ftsK | DNA translocase at septal ring sorting daughter chromsomes |
| ? | NC_000913 | 935128 = | 62 (1.180) | coding (1905/3990 nt) | ftsK | DNA translocase at septal ring sorting daughter chromsomes | |||||
| * | ? | NC_000913 | 1207790 = | 16 (0.300) | 20 (0.400) | 19/470 | NT | 54.8% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 18 (0.360) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 16 (0.300) | 26 (0.510) | 20/470 | NT | 61.2% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 18 (0.360) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 40 (0.740) | 33/502 | NT | 100% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1407323 | 51 (0.940) | 4 (0.080) | 4/482 | NT | 6.6% | coding (473/1233 nt) | ydaM | diguanylate cyclase, csgD regulator |
| ? | NC_000913 | = 1407695 | 65 (1.250) | coding (101/1233 nt) | ydaM | diguanylate cyclase, csgD regulator | |||||
| * | ? | NC_000913 | 1603870 = | 84 (1.560) | 4 (0.080) | 4/482 | NT | 5.7% | coding (852/1029 nt) | lsrC | autoinducer 2 import system permease protein |
| ? | NC_000913 | 1604608 = | 51 (0.980) | coding (562/993 nt) | lsrD | autoinducer 2 import system permease protein | |||||
| * | ? | NC_000913 | = 1709889 | 76 (1.410) | 4 (0.070) | 4/496 | NT | 5.8% | coding (748/1059 nt) | rsxD | SoxR iron‑sulfur cluster reduction factor component, putative membrane protein of electron transport complex |
| ? | NC_000913 | = 1710391 | 56 (1.050) | coding (188/621 nt) | rsxG | SoxR iron‑sulfur cluster reduction factor component, putative membrane protein of electron transport complex | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 9 (0.170) | 8/486 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 17 (0.310) | 15/502 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 30 (0.560) | 23/502 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | = 2070271 | NA (NA) | 11 (0.200) | 11/502 | NT | 40.7% | intergenic (‑91/‑6) | insC1/yoeA | IS2 repressor TnpA/CP4‑44 prophage, putative disrupted hemin or colicin receptor,Phage or Prophage Related, interrupted by IS2 and C‑terminal deletion |
| ? | NC_000913 | = 2389403 | 16 (0.300) | coding (290/849 nt) | yfbP | TPR‑like repeats‑containing protein | |||||
| * | ? | NC_000913 | 2077808 = | 54 (1.000) | 8 (0.160) | 6/478 | NT | 14.5% | coding (240/375 nt) | cbtA | CP4‑44 prophage, toxin of the YeeV‑YeeU toxin‑antitoxin system |
| ? | NC_000913 | 2077982 = | 43 (0.840) | pseudogene (43/168 nt) | yeeW | CP4‑44 prophage, uncharacterized protein,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 2190005 | 46 (0.850) | 3 (0.060) | 3/496 | NT | 8.6% | coding (904/2481 nt) | yehB | putative outer membrane protein |
| ? | NC_000913 | = 2190340 | 18 (0.340) | coding (569/2481 nt) | yehB | putative outer membrane protein | |||||
| * | ? | NC_000913 | = 2220504 | 57 (1.060) | 3 (0.060) | 3/486 | NT | 5.3% | coding (1484/2298 nt) | bglX | beta‑D‑glucoside glucohydrolase, periplasmic |
| ? | NC_000913 | = 2220836 | 52 (0.990) | coding (1152/2298 nt) | bglX | beta‑D‑glucoside glucohydrolase, periplasmic | |||||
| * | ? | NC_000913 | 2288917 = | NA (NA) | 19 (0.350) | 17/502 | NT | 57.6% | intergenic (‑5/+146) | yejO/insH1 | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator |
| ? | NC_000913 | 2876676 = | 14 (0.260) | coding (98/1038 nt) | iap | aminopeptidase in alkaline phosphatase isozyme conversion | |||||
| * | ? | NC_000913 | = 2290111 | NA (NA) | 30 (0.560) | 25/502 | NT | 68.2% | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
| ? | NC_000913 | = 2876679 | 14 (0.260) | coding (101/1038 nt) | iap | aminopeptidase in alkaline phosphatase isozyme conversion | |||||
| * | ? | NC_000913 | 2389398 = | 16 (0.300) | 21 (0.390) | 17/500 | NT | 56.9% | coding (285/849 nt) | yfbP | TPR‑like repeats‑containing protein |
| ? | NC_000913 | 2996360 = | NA (NA) | intergenic (‑2/+10) | ygeO/insD1 | pseudogene, orgA family, part of T3SS PAI ETT2 remnant/IS2 transposase TnpB | |||||
| * | ? | NC_000913 | = 2491686 | 21 (0.390) | 3 (0.060) | 3/490 | NT | 7.4% | coding (263/1695 nt) | oxc | oxalyl CoA decarboxylase, ThDP‑dependent |
| ? | NC_000913 | = 2492130 | 55 (1.040) | coding (1123/1251 nt) | frc | formyl‑CoA transferase, NAD(P)‑binding | |||||
| * | ? | NC_000913 | = 2707461 | 49 (0.910) | 4 (0.080) | 4/490 | NT | 7.9% | coding (339/480 nt) | rseC | SoxR iron‑sulfur cluster reduction factor component |
| ? | NC_000913 | = 2707648 | 46 (0.870) | coding (152/480 nt) | rseC | SoxR iron‑sulfur cluster reduction factor component | |||||
| * | ? | NC_000913 | = 2924977 | 68 (1.260) | 3 (0.060) | 3/486 | NT | 4.3% | coding (302/546 nt) | syd | SecY‑interacting protein |
| ? | NC_000913 | = 2925356 | 67 (1.280) | coding (11/849 nt) | queF | 7‑cyano‑7‑deazaguanine reductase (NADPH‑dependent) | |||||
| * | ? | NC_000913 | 3620758 = | NA (NA) | 5 (0.100) | 5/486 | NT | 9.5% | coding (1568/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3621155 = | 49 (0.910) | coding (1965/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 3955667 = | 72 (1.330) | 5 (0.100) | 4/486 | NT | 8.2% | coding (338/1545 nt) | ilvA | l‑threonine dehydratase, biosynthetic, also known as threonine deaminase |
| ? | NC_000913 | 3955896 = | 42 (0.800) | coding (567/1545 nt) | ilvA | l‑threonine dehydratase, biosynthetic, also known as threonine deaminase | |||||
| * | ? | NC_000913 | 4056976 = | 70 (1.300) | 4 (0.080) | 4/492 | NT | 5.6% | coding (1058/1410 nt) | glnA | glutamine synthetase |
| ? | NC_000913 | 4057251 = | 67 (1.270) | coding (783/1410 nt) | glnA | glutamine synthetase | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 7 (0.150) | 5/424 | NT | NA | intergenic (+38/+606) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | = 4296395 | NA (NA) | noncoding (562/602 nt) | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | |||||
| * | ? | NC_000913 | 4374936 = | 85 (1.570) | 3 (0.060) | 3/488 | NT | 3.3% | coding (723/1029 nt) | epmB | EF‑P‑Lys34 lysylation protein, weak lysine 2,3‑aminomutase |
| ? | NC_000913 | 4375111 = | 92 (1.750) | coding (548/1029 nt) | epmB | EF‑P‑Lys34 lysylation protein, weak lysine 2,3‑aminomutase | |||||
| * | ? | NC_000913 | = 4500859 | 51 (0.940) | 4 (0.080) | 4/492 | NT | 8.2% | intergenic (‑67/‑402) | yjgX/yjgZ | pseudogene fragment/uncharacterized protein |
| ? | NC_000913 | = 4500950 | 39 (0.740) | intergenic (‑158/‑311) | yjgX/yjgZ | pseudogene fragment/uncharacterized protein | |||||
| * | ? | NC_000913 | 4513937 = | 47 (0.870) | 3 (0.060) | 3/480 | NT | 5.3% | coding (373/903 nt) | fecB | ferric citrate ABC transporter periplasmic binding protein |
| ? | NC_000913 | 4514563 = | 63 (1.220) | coding (2116/2325 nt) | fecA | TonB‑dependent outer membrane ferric citrate transporter and signal transducer, ferric citrate extracelluar receptor, FecR‑interacting protein | |||||