mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
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 | 186,134 | +CCC | 10.2% | coding (2517/2673 nt) | glnD ← | uridylyltransferase |
| RA | 235,917 | C→T | 5.3% | R29H (CGC→CAC) | rnhA ← | ribonuclease HI, degrades RNA of DNA‑RNA hybrids |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 485,039 | A→G | 5.1% | L194S (TTG→TCG) | acrA ← | multidrug efflux system |
| RA | 524,811 | G→A | 5.3% | 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 | 59.0% | 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 | 927,611 | Δ1 bp | 6.5% | coding (1585/1722 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 |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| 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 | 1,963,203 | G→A | 8.2% | G616G (GGC→GGT) | flhA ← | putative flagellar export pore protein |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| JC JC | 2,389,401 | IS2 (+) +5 bp | 50.0% | coding (286‑290/849 nt) | yfbP → | TPR‑like repeats‑containing protein |
| RA | 2,846,101 | A→G | 5.1% | L124S (TTG→TCG) | hycE ← | hydrogenase 3, large subunit |
| RA | 2,876,376 | G→T | 20.0% | intergenic (‑47/‑205) | cysD ← / → iap | sulfate adenylyltransferase, subunit 2/aminopeptidase in alkaline phosphatase isozyme conversion |
| JC JC | 2,876,678 | IS5 (+) +4 bp | 63.2% | coding (98‑101/1038 nt) | iap → | aminopeptidase in alkaline phosphatase isozyme conversion |
| RA | 2,974,291 | Δ1 bp | 8.0% | coding (1724/2160 nt) | aas ← | fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,665,444 | A→G | 12.5% | S123P (TCT→CCT) | gadX ← | acid resistance regulon transcriptional activator; autoactivator |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,951,561 | 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 | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,031,045 | T→C | 9.1% | 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 | 4,125,618 | Δ1 bp | 5.5% | coding (1193/2199 nt) | priA ← | Primosome factor n' (replication factor Y) |
| RA | 4,125,619 | Δ1 bp | 5.5% | coding (1192/2199 nt) | priA ← | Primosome factor n' (replication factor Y) |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 10.9% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→G | 28.3% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 33.7% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 21.0% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 11.7% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 7.5% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 6.3% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| 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 | 755143 | 758392 | 3250 | 13 [11] | [10] 12 | sdhC–[sdhB] | sdhC,sdhD,sdhA,[sdhB] |
| * | * | ÷ | NC_000913 | 1978480 | 1979326 | 847 | 12 [9] | [10] 12 | insB1–insA | insB1,insA |
| * | * | ÷ | NC_000913 | 2106433 | 2107407 | 975 | 13 [10] | [11] 12 | [wbbH]–[glf] | [wbbH],[glf] |
| * | * | ÷ | NC_000913 | 3423912–3424232 | 3424382–3424239 | 8–471 | 12 [11] | [9] 13 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 3798873 | 3799653 | 781 | 13 [11] | [10] 14 | [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 (1.290) | 4 (0.080) | 4/494 | NT | 5.8% | coding (1146/1374 nt) | aroP | aromatic amino acid transporter |
| ? | NC_000913 | = 120807 | 61 (1.160) | coding (745/1374 nt) | aroP | aromatic amino acid transporter | |||||
| * | ? | NC_000913 | 231961 = | 46 (0.860) | 10 (0.190) | 4/498 | NT | 17.3% | coding (36/624 nt) | yafE | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase |
| ? | NC_000913 | 232463 = | 50 (0.940) | coding (538/624 nt) | yafE | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase | |||||
| * | ? | NC_000913 | = 243009 | 79 (1.470) | 5 (0.100) | 3/488 | NT | 6.8% | coding (295/2445 nt) | fadE | acyl coenzyme A dehydrogenase |
| ? | NC_000913 | = 243192 | 60 (1.150) | coding (112/2445 nt) | fadE | acyl coenzyme A dehydrogenase | |||||
| * | ? | NC_000913 | = 258675 | NA (NA) | 9 (0.170) | 8/502 | NT | 20.9% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | 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 | noncoding (204/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381851 = | NA (NA) | noncoding (592/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 762116 = | 61 (1.140) | 7 (0.140) | 4/474 | NT | 9.5% | coding (595/1218 nt) | sucB | dihydrolipoyltranssuccinase |
| ? | NC_000913 | 762340 = | 75 (1.480) | coding (819/1218 nt) | sucB | dihydrolipoyltranssuccinase | |||||
| * | ? | NC_000913 | 934793 = | 81 (1.510) | 4 (0.080) | 4/490 | NT | 5.4% | coding (1570/3990 nt) | ftsK | DNA translocase at septal ring sorting daughter chromsomes |
| ? | NC_000913 | 935128 = | 60 (1.150) | 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 (0.520) | 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 | = 1407323 | 51 (0.950) | 4 (0.080) | 4/482 | NT | 6.6% | coding (473/1233 nt) | ydaM | diguanylate cyclase, csgD regulator |
| ? | NC_000913 | = 1407695 | 64 (1.240) | coding (101/1233 nt) | ydaM | diguanylate cyclase, csgD regulator | |||||
| * | ? | NC_000913 | 1603870 = | 81 (1.510) | 4 (0.080) | 4/482 | NT | 5.8% | coding (852/1029 nt) | lsrC | autoinducer 2 import system permease protein |
| ? | NC_000913 | 1604608 = | 51 (0.990) | coding (562/993 nt) | lsrD | autoinducer 2 import system permease protein | |||||
| * | ? | NC_000913 | = 1709889 | 75 (1.400) | 4 (0.080) | 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 (1.060) | 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 | 2077808 = | 52 (0.970) | 8 (0.160) | 6/478 | NT | 14.9% | coding (240/375 nt) | cbtA | CP4‑44 prophage; toxin of the YeeV‑YeeU toxin‑antitoxin system |
| ? | NC_000913 | 2077982 = | 42 (0.820) | pseudogene (43/168 nt) | yeeW | CP4‑44 prophage; uncharacterized protein;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 2190007 | 46 (0.860) | 3 (0.060) | 3/496 | NT | 8.6% | coding (904/2481 nt) | yehB | putative outer membrane protein |
| ? | NC_000913 | = 2190342 | 18 (0.340) | coding (569/2481 nt) | yehB | putative outer membrane protein | |||||
| * | ? | NC_000913 | = 2220506 | 56 (1.040) | 3 (0.060) | 3/486 | NT | 5.4% | coding (1484/2298 nt) | bglX | beta‑D‑glucoside glucohydrolase, periplasmic |
| ? | NC_000913 | = 2220838 | 51 (0.980) | coding (1152/2298 nt) | bglX | beta‑D‑glucoside glucohydrolase, periplasmic | |||||
| * | ? | NC_000913 | = 2491688 | 21 (0.390) | 3 (0.060) | 3/490 | NT | 7.4% | coding (263/1695 nt) | oxc | oxalyl CoA decarboxylase, ThDP‑dependent |
| ? | NC_000913 | = 2492132 | 55 (1.050) | coding (1123/1251 nt) | frc | formyl‑CoA transferase, NAD(P)‑binding | |||||
| * | ? | NC_000913 | = 2707463 | 45 (0.840) | 4 (0.080) | 4/490 | NT | 8.2% | coding (339/480 nt) | rseC | SoxR iron‑sulfur cluster reduction factor component |
| ? | NC_000913 | = 2707650 | 46 (0.880) | coding (152/480 nt) | rseC | SoxR iron‑sulfur cluster reduction factor component | |||||
| * | ? | NC_000913 | 3620759 = | NA (NA) | 5 (0.100) | 5/486 | NT | 9.7% | coding (1568/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3621156 = | 48 (0.890) | coding (1965/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 3955668 = | 72 (1.340) | 5 (0.100) | 4/486 | NT | 8.2% | coding (338/1545 nt) | ilvA | l‑threonine dehydratase, biosynthetic; also known as threonine deaminase |
| ? | NC_000913 | 3955897 = | 42 (0.810) | coding (567/1545 nt) | ilvA | l‑threonine dehydratase, biosynthetic; also known as threonine deaminase | |||||
| * | ? | NC_000913 | 4056977 = | 70 (1.300) | 4 (0.080) | 4/492 | NT | 5.6% | coding (1058/1410 nt) | glnA | glutamine synthetase |
| ? | NC_000913 | 4057252 = | 67 (1.270) | coding (783/1410 nt) | glnA | glutamine synthetase | |||||
| * | ? | NC_000913 | = 4500858 | 49 (0.910) | 4 (0.080) | 4/492 | NT | 8.6% | intergenic (‑67/‑402) | yjgX/yjgZ | pseudogene fragment/uncharacterized protein |
| ? | NC_000913 | = 4500949 | 37 (0.700) | intergenic (‑158/‑311) | yjgX/yjgZ | pseudogene fragment/uncharacterized protein | |||||
| * | ? | NC_000913 | 4513936 = | 46 (0.860) | 3 (0.060) | 3/480 | NT | 5.3% | coding (373/903 nt) | fecB | ferric citrate ABC transporter periplasmic binding protein |
| ? | NC_000913 | 4514562 = | 63 (1.230) | coding (2116/2325 nt) | fecA | TonB‑dependent outer membrane ferric citrate transporter and signal transducer; ferric citrate extracelluar receptor; FecR‑interacting protein | |||||