mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 29,546 | C→T | 18.2% | intergenic (+351/‑105) | dapB → / → carA | 4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha |
| RA | 76,805 | T→A | 100% | E165D (GAA→GAT) | sgrR ← | DNA‑binding transcriptional dual regulator SgrR |
| RA | 87,481 | C→A | 100% | T42K (ACA→AAA) | ilvH → | acetolactate synthase/acetohydroxybutanoate synthase, regulatory subunit |
| RA | 125,085 | Δ1 bp | 100% | coding (2069/2664 nt) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| JC JC | 568,268 | IS1 (–) +9 bp | 92.7% | intergenic (+21/‑39) | renD → / → emrE | DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE |
| RA | 710,595 | G→T | 34.0% | P18T (CCT→ACT) | fur ← | DNA‑binding transcriptional dual regulator Fur |
| RA | 1,196,220 | C→T | 100% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | 100% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | 100% | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | 100% | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,466,201 | T→C | 15.4% | pseudogene (810/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,607,039 | A→G | 16.7% | K14R (AAG→AGG) | lsrG → | (4S)‑4‑hydroxy‑5‑phosphonooxypentane‑2,3‑dione isomerase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,416,622 | C→G | 100% | Q626E (CAG→GAG) | pta → | phosphate acetyltransferase |
| RA | 2,637,438 | T→G | 16.3% | intergenic (‑82/+36) | der ← / ← bamB | 50S ribosomal subunit stability factor/outer membrane protein assembly factor BamB |
| RA | 2,661,866 | G→T | 42.3% | A89D (GCC→GAC) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,662,023 | T→C | 14.7% | I37V (ATT→GTT) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 3,041,398 | T→G | 100% | L29R (CTT→CGT) | ygfZ → | folate‑binding protein |
| RA | 3,140,352 | G→C | 9.9% | R150G (CGC→GGC) | hybE ← | hydrogenase 2‑specific chaperone |
| RA | 3,176,209 | C→A | 100% | D209Y (GAT→TAT) | cpdA ← | cAMP phosphodiesterase |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,781,051 | C→G | 12.3% | intergenic (+34/‑164) | lldD → / → trmL | L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,060 | C→T | 27.7% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,335,654 | T→A | 7.6% | intergenic (‑64/+40) | eptA ← / ← adiC | phosphoethanolamine transferase EptA/arginine:agmatine antiporter |
| RA | 4,335,655 | T→A | 7.7% | intergenic (‑65/+39) | eptA ← / ← adiC | phosphoethanolamine transferase EptA/arginine:agmatine antiporter |
| RA | 4,426,592 | T→A | 7.1% | intergenic (+35/+36) | rplI → / ← yjfZ | 50S ribosomal subunit protein L9/protein YjfZ |
| RA | 4,489,089 | A→T | 9.2% | A325A (GCT→GCA) | yjgR ← | DUF853 domain‑containing protein YjgR |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 366275 | 366450 | 176 | 7 [6] | [6] 7 | [lacZ]–[lacI] | [lacZ],[lacI] |
| * | * | ÷ | NC_000913 | 1196260 | 1211427 | 15168 | 7 [6] | [6] 7 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 3423755–3424520 | 3424520 | 1–766 | 8 [6] | [6] 7 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3621181–3622295 | 3653150–3652036 | 29742–31970 | 7 [6] | [6] 7 | [rhsB]–[insH‑11] | [rhsB],yhhH,yhhI,yhhJ,rbbA,yhiI,yhiJ,yhiL,yhiM,yhiN,pitA,uspB,uspA,dtpB,rsmJ,prlC,rlmJ,gor,dinQ,agrA,agrB,arsR,arsB,arsC,yhiS,[insH‑11] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1463445 | 83 (3.140) | 5 (0.200) | 4/250 | NT | 5.8% | intergenic (+7/‑94) | paaK/paaX | phenylacetate‑CoA ligase/DNA‑binding transcriptional repressor PaaX |
| ? | NC_000913 | = 1463482 | 85 (3.400) | intergenic (+44/‑57) | paaK/paaX | phenylacetate‑CoA ligase/DNA‑binding transcriptional repressor PaaX | |||||
| * | ? | NC_000913 | = 3895233 | 51 (1.930) | 3 (0.120) | 3/240 | NT | 5.8% | intergenic (+15/+39) | yieF/adeP | chromate reductase/adenine:H(+) symporter |
| ? | NC_000913 | = 3895244 | 51 (2.120) | intergenic (+26/+28) | yieF/adeP | chromate reductase/adenine:H(+) symporter | |||||
| * | ? | NC_000913 | = 3944978 | NA (NA) | 6 (0.240) | 5/252 | NT | 23.0% | noncoding (1275/2904 nt) | rrlC | 23S ribosomal RNA |
| ? | NC_000913 | = 4038811 | 21 (0.790) | noncoding (1293/2905 nt) | rrlA | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 4171803 | 40 (1.510) | 5 (0.190) | 5/260 | NT | 10.3% | intergenic (+47/‑254) | rrfB/murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase |
| ? | NC_000913 | = 4213162 | 48 (1.840) | intergenic (+3/‑72) | rrfE/yjaA | 5S ribosomal RNA/stress response protein | |||||
| * | ? | NC_000913 | 4227543 = | 57 (2.160) | 5 (0.200) | 5/250 | NT | 8.9% | intergenic (+32/‑188) | metH/yjbB | cobalamin‑dependent methionine synthase/putative inorganic phosphate export protein |
| ? | NC_000913 | 4227568 = | 48 (1.920) | intergenic (+57/‑163) | metH/yjbB | cobalamin‑dependent methionine synthase/putative inorganic phosphate export protein | |||||