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 | 130,072 | C→T | 8.9% | A397T (GCC→ACC) | yacH ← | DUF3300 family protein |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 383,153 | C→T | 10.3% | L261L (CTG→CTA) | yaiP ← | putative family 2 glycosyltransferase |
| RA | 526,792 | A→C | 20.8% | S1178R (AGC→CGC) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,796 | C→G | 19.9% | A1179G (GCG→GGG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 526,800 | A→G | 22.7% | E1180E (GAA→GAG) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 621,005 | G→C | 9.4% | R62G (CGC→GGC) | fepG ← | iron‑enterobactin ABC transporter permease |
| RA | 1,269,897 | T→G | 14.3% | noncoding (40/66 nt) | rdlB → | sRNA antisense regulator affects LdrB translation; proposed addiction module in LDR‑B repeat, with toxic peptide LdrB |
| RA | 1,311,346 | G→A | 8.8% | P86P (CCG→CCA) | tonB → | membrane spanning protein in TonB‑ExbB‑ExbD transport complex |
| RA | 1,529,203 | C→A | 100% | pseudogene (1302/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,218 | C→T | 100% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,583,846 | C→A | 12.6% | S38S (TCG→TCT) | safA ← | two‑component system connector membrane protein, EvgSA to PhoQP |
| RA | 1,882,636 | C→T | 8.7% | A242V (GCG→GTG) | dmlA → | D‑malate oxidase, NAD‑dependent; putative tartrate dehydrogenase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,028,158 | G→C | 12.0% | intergenic (‑141/+30) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,028,159 | T→A | 11.3% | intergenic (‑142/+29) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,028,160 | G→C | 11.5% | intergenic (‑143/+28) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,158,283 | C→T | 8.6% | S1007S (AGC→AGT) | mdtB → | multidrug efflux system, subunit B |
| 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 |
| RA | 2,263,081 | G→A | 8.6% | L139L (CTG→TTG) | fruB ← | fused fructose‑specific PTS enzymes: IIA component/HPr component |
| RA | 2,304,649 | C→T | 21.5% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,436,694 | G→A | 6.6% | intergenic (‑45/+21) | usg ← / ← pdxB | putative semialdehyde dehydrogenase/erythronate‑4‑phosphate dehydrogenase |
| RA | 2,872,915 | C→G | 11.8% | intergenic (‑95/+99) | ftsB ← / ← ygbE | cell division protein/DUF3561 family inner membrane protein |
| RA | 3,439,588 | G→C | 6.4% | intergenic (‑79/+28) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| RA | 3,439,589 | G→C | 6.1% | intergenic (‑80/+27) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| RA | 3,491,704 | G→T | 7.2% | intergenic (‑84/+21) | yhfG ← / ← ppiA | putative antitoxin for Fic/peptidyl‑prolyl cis‑trans isomerase A (rotamase A) |
| RA | 3,539,413 | C→T | 8.3% | L677L (CTG→TTG) | yhgF → | putative transcriptional accessory 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 | 3,724,829 | T→C | 6.7% | T164A (ACC→GCC) | glyQ ← | glycine tRNA synthetase, alpha subunit |
| RA | 3,772,736 | G→A | 7.5% | P152P (CCG→CCA) | mtlA → | mannitol‑specific PTS enzyme: IIA, IIB and IIC components |
| RA | 3,815,809 | Δ1 bp | 19.4% | intergenic (‑41/+25) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| JC | 3,815,859 | Δ82 bp | 28.9% | [rph]–[rph] | [rph], [rph] | |
| RA | 4,088,091 | G→C | 10.0% | intergenic (+34/+16) | yiiG → / ← frvR | DUF3829 family lipoprotein/putative frv operon regulator; contains a PTS EIIA domain |
| RA | 4,182,791 | A→G | 54.3% | D516G (GAC→GGC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,235,433 | Δ1 bp | 100% | intergenic (‑2200/‑501) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,296,088 | C→T | 31.3% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,408:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,506,107 | C→T | 9.6% | Q265* (CAG→TAG) | yjhC → | GFO/IDH/MOCA family putative oxidoreductase. NAD(P)‑dependent |
| RA | 4,561,832 | G→A | 9.1% | T291I (ACT→ATT) | yjiJ ← | DUF1228 family putative inner membrane MFS superfamily transporter |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_hsa_pgi | 662343 = | 44 (0.820) | 3 (0.060) | 3/254 | NT | 6.5% | intergenic (‑65/+36) | lipB/ybeD | octanoyltransferase; octanoyl‑[ACP]:protein N‑octanoyltransferase/UPF0250 family protein |
| ? | NC_000913_3_hsa_pgi | 662368 = | 45 (0.900) | intergenic (‑90/+11) | lipB/ybeD | octanoyltransferase; octanoyl‑[ACP]:protein N‑octanoyltransferase/UPF0250 family protein | |||||
| * | ? | NC_000913_3_hsa_pgi | 993282 = | 38 (0.710) | 3 (0.060) | 3/262 | NT | 7.6% | coding (763/768 nt) | ssuB | aliphatic sulfonate ABC transporter ATPase |
| ? | NC_000913_3_hsa_pgi | 993296 = | 36 (0.700) | coding (749/768 nt) | ssuB | aliphatic sulfonate ABC transporter ATPase | |||||
| * | ? | NC_000913_3_hsa_pgi | 1207790 = | 15 (0.280) | 9 (0.190) | 9/238 | NT | 35.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_pgi | 1209619 = | 20 (0.430) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_pgi | = 1207805 | 14 (0.260) | 16 (0.340) | 14/238 | NT | 49.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_pgi | = 1209602 | 20 (0.430) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_pgi | = 1299498 | 0 (0.000) | 42 (0.810) | 37/262 | NT | 98.8% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_hsa_pgi | 1300698 = | 1 (0.020) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_hsa_pgi | = 1343176 | 20 (0.370) | 3 (0.060) | 3/258 | NT | 11.7% | coding (153/219 nt) | osmB | osmotically and stress inducible lipoprotein |
| ? | NC_000913_3_hsa_pgi | = 1343184 | 26 (0.510) | coding (145/219 nt) | osmB | osmotically and stress inducible lipoprotein | |||||
| * | ? | NC_000913_3_hsa_pgi | = 1435164 | 54 (1.010) | 3 (0.060) | 3/256 | NT | 5.4% | intergenic (‑156/+21) | ttcC/uspF | pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related/stress‑induced protein, ATP‑binding protein |
| ? | NC_000913_3_hsa_pgi | = 1435170 | 53 (1.050) | intergenic (‑162/+15) | ttcC/uspF | pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related/stress‑induced protein, ATP‑binding protein | |||||
| * | ? | NC_000913_3_hsa_pgi | = 3093426 | 59 (1.110) | 4 (0.080) | 4/258 | NT | 6.5% | coding (490/564 nt) | yqgE | uncharacterized protein |
| ? | NC_000913_3_hsa_pgi | = 3093441 | 58 (1.140) | coding (505/564 nt) | yqgE | uncharacterized protein | |||||
| * | ? | NC_000913_3_hsa_pgi | 3583428 = | NA (NA) | 25 (0.470) | 25/270 | NT | 43.1% | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA |
| ? | NC_000913_3_hsa_pgi | 3665150 = | 33 (0.620) | coding (661/825 nt) | gadX | acid resistance regulon transcriptional activator; autoactivator | |||||
| * | ? | NC_000913_3_hsa_pgi | = 3584195 | NA (NA) | 20 (0.370) | 18/270 | NT | 37.7% | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E |
| ? | NC_000913_3_hsa_pgi | = 3665158 | 33 (0.620) | coding (653/825 nt) | gadX | acid resistance regulon transcriptional activator; autoactivator | |||||
| * | ? | NC_000913_3_hsa_pgi | 3908414 = | NA (NA) | 5 (0.100) | 5/242 | NT | 9.1% | noncoding (28/64 nt) | REP283 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP283 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913_3_hsa_pgi | = 4614382 | 50 (1.050) | noncoding (98/388 nt) | REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP352 (repetitive extragenic palindromic) element; contains 8 REP sequences | |||||
| * | ? | NC_000913_3_hsa_pgi | 4218555 = | 63 (1.180) | 6 (0.130) +AAAACGCCTTATCCA |
5/240 | NT | 9.7% | noncoding (120/132 nt) | REP311 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP311 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | NC_000913_3_hsa_pgi | = 4254030 | NA (NA) | noncoding (102/130 nt) | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_hsa_pgi | 4218556 = | 64 (1.200) | 6 (0.110) +T |
6/268 | NT | 8.6% | noncoding (121/132 nt) | REP311 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP311 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | NC_000913_3_hsa_pgi | = 4254045 | NA (NA) | noncoding (117/130 nt) | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_hsa_pgi | 4218558 = | 65 (1.220) | 10 (0.190) +A |
9/268 | NT | 13.4% | noncoding (123/132 nt) | REP311 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP311 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | NC_000913_3_hsa_pgi | = 4254047 | NA (NA) | noncoding (119/130 nt) | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_hsa_pgi | 4218566 = | 70 (1.310) | 9 (0.170) +T |
9/268 | NT | 11.5% | noncoding (131/132 nt) | REP311 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP311 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | NC_000913_3_hsa_pgi | = 4254055 | NA (NA) | noncoding (127/130 nt) | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_hsa_pgi | 4218567 = | 70 (1.310) | 8 (0.150) +T |
7/268 | NT | 10.3% | noncoding (132/132 nt) | REP311 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP311 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | NC_000913_3_hsa_pgi | = 4254056 | NA (NA) | noncoding (128/130 nt) | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_hsa_pgi | 4218568 = | 61 (1.270) | 762 (16.920) | 197/228 | NT | 93.0% | intergenic (+155/‑28) | aceA/aceK | isocitrate lyase/isocitrate dehydrogenase kinase/phosphatase |
| ? | NC_000913_3_hsa_pgi | = 4254058 | NA (NA) | noncoding (130/130 nt) | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP317 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_hsa_pgi | 4240185 = | NA (NA) | 7 (0.140) | 6/256 | NT | NA | noncoding (1/37 nt) | REP314 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP314 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913_3_hsa_pgi | 4240218 = | NA (NA) | noncoding (34/37 nt) | REP314 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP314 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913_3_hsa_pgi | = 4245215 | NA (NA) | 3 (0.060) | 3/258 | NT | NA | noncoding (96/126 nt) | REP315 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP315 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | NC_000913_3_hsa_pgi | = 4245245 | NA (NA) | noncoding (126/126 nt) | REP315 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP315 (repetitive extragenic palindromic) element; contains 3 REP sequences | |||||
| * | ? | NC_000913_3_hsa_pgi | 4542710 = | 43 (0.810) | 5 (0.100) | 5/252 | NT | 10.9% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913_3_hsa_pgi | 4543024 = | 42 (0.840) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||