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 | freq | annotation | gene | description |
| RA | 177,549 | G→A | 7.0% | R26C (CGT→TGT) | yadS ← | UPF0126 family inner membrane protein |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 262,732:1 | +G | 5.4% | coding (1230/1254 nt) | proA → | gamma‑glutamylphosphate reductase |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 100% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 762,841 | G→T | 6.4% | intergenic (+102/‑173) | sucB → / → sucC | dihydrolipoyltranssuccinase/succinyl‑CoA synthetase, beta subunit |
| RA | 876,148 | C→T | 13.8% | R272C (CGC→TGC) | yliF → | putative membrane‑anchored diguanylate cyclase |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| 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 | 1,466,438 | T→G | 10.7% | pseudogene (1047/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,498,623 | Δ1 bp | 6.6% | intergenic (+112/‑28) | opgD → / → ydcH | OPG biosynthetic periplasmic protein/DUF465 family protein |
| RA | 1,501,720 | T→A | 8.4% | Y53* (TAT→TAA) | tehB → | tellurite, selenium methyltransferase, SAM‑dependent; tellurite, selenium resistance protein |
| RA | 1,612,932 | T→A | 6.1% | E107V (GAG→GTG) | glsB ← | glutaminase 2 |
| JC | 1,619,080 | Δ35 bp | 25.9% | intergenic (‑172/‑6) | marC ← / → marR | UPF0056 family inner membrane protein/transcriptional repressor of multiple antibiotic resistance |
| RA | 1,936,648 | C→T | 62.2% | intergenic (‑334/‑4) | zwf ← / → yebK | glucose‑6‑phosphate 1‑dehydrogenase/putative DNA‑binding transcriptional regulator |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| 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 | 2,151,859 | A→G | 9.5% | F205S (TTT→TCT) | yegK ← | ser/thr phosphatase‑related protein |
| 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 | 2,413,513 | Δ10 bp | 20.1% | coding (44‑53/1203 nt) | ackA → | acetate kinase A and propionate kinase 2 |
| JC | 2,526,111 | Δ3 bp | 5.1% | coding (744‑746/927 nt) | yfeR ← | transcriptional regulator of yefH |
| RA | 3,213,426 | T→G | 40.3% | I127S (ATC→AGC) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,361,441 | C→T | 13.8% | A89V (GCA→GTA) | gltF → | periplasmic protein |
| 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 | 3,729,754 | A→G | 6.4% | F338L (TTC→CTC) | xylA ← | D‑xylose isomerase |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,011,944 | A→T | 5.8% | D290V (GAT→GTT) D291E (GAT→GAA) |
yigM → metR ← |
putative inner membrane EamA‑like transporter methionine biosynthesis regulon transcriptional regulator |
| JC JC | 4,049,859 | IS2 (–) +5 bp | 82.7% | intergenic (+107/‑36) | polA → / → spf | 5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease/Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent |
| JC | 4,049,991 | Δ12 bp | 40.7% | noncoding (93‑104/109 nt) | spf → | Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent |
| RA | 4,157,050 | A→G | 5.4% | E67E (GAA→GAG) | argH → | argininosuccinate lyase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,190 | A→G | 17.7% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 18.2% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 25.0% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 12.9% | intergenic (+492/+150) | 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 |
| RA | 4,308,355 | G→T | 22.1% | L42M (CTG→ATG) | alsE ← | allulose‑6‑phosphate 3‑epimerase |
| RA | 4,326,048 | G→A | 8.3% | intergenic (‑307/+351) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,088 | T→G | 15.4% | intergenic (‑347/+311) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,629,274 | T→G | 5.8% | I417L (ATC→CTC) | ettA ← | energy‑dependent translational throttle A |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2990844 | 2991370 | 527 | 20 [15] | [15] 16 | [ygeF]–[ygeG] | [ygeF],ygeF,[ygeG] |
| * | * | ÷ | NC_000913 | 3423894–3424233 | 3424402–3424239 | 7–509 | 17 [15] | [15] 17 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 4233700 | 4235471 | 1772 | 16 [15] | [15] 17 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 17 (0.290) | 29 (0.520) | 28/474 | NT | 64.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 16 (0.290) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 16 (0.270) | 45 (0.810) | 39/474 | NT | 74.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 16 (0.290) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 9 (0.150) | 9/506 | NT | 18.0% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2101469 | 41 (0.690) | pseudogene (276/349 nt) | wbbL | pseudogene, lipopolysaccharide biosynthesis protein | |||||
| * | ? | NC_000913 | = 1840621 | 72 (1.210) | 4 (0.070) | 4/500 | NT | 6.2% | coding (1155/1308 nt) | ynjE | molybdopterin synthase sulfurtransferase |
| ? | NC_000913 | = 1841095 | 50 (0.850) | coding (309/621 nt) | ynjF | CDP‑alcohol phosphatidyltransferase family inner membrane protein | |||||
| * | ? | NC_000913 | 1928538 = | 52 (0.870) | 4 (0.070) | 3/492 | NT | 6.9% | coding (302/2061 nt) | ptrB | protease II |
| ? | NC_000913 | 1928806 = | 58 (1.000) | coding (34/2061 nt) | ptrB | protease II | |||||
| * | ? | NC_000913 | = 3135413 | 65 (1.090) | 4 (0.070) | 3/488 | NT | 5.4% | coding (959/1500 nt) | pitB | phosphate transporter |
| ? | NC_000913 | = 3135486 | 77 (1.340) | coding (886/1500 nt) | pitB | phosphate transporter | |||||