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 | 9,907 | A→C | 14.0% | intergenic (+14/+21) | mog → / ← satP | molybdopterin adenylyltransferase/acetate/succinate:H(+) symporter |
| RA | 125,387 | C→T | 100% | Q791* (CAG→TAG) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 639,685 | Δ1 bp | 14.7% | intergenic (+177/‑68) | ahpC → / → ahpF | alkyl hydroperoxide reductase, AhpC component/alkyl hydroperoxide reductase, AhpF component |
| RA | 696,470 | C→T | 100% | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 759,250 | G→T | 100% | R182L (CGC→CTC) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 786,458 | Δ1 bp | 100% | coding (826/1053 nt) | aroG → | 3‑deoxy‑7‑phosphoheptulonate synthase, Phe‑sensitive |
| RA | 1,068,231 | A→G | 11.7% | S51G (AGT→GGT) | ymdF → | conserved protein YmdF |
| RA | 1,098,045 | G→C | 9.8% | G54R (GGG→CGG) | ghrA → | glyoxylate/hydroxypyruvate reductase A |
| RA | 1,098,054 | C→T | 10.9% | L57F (CTT→TTT) | ghrA → | glyoxylate/hydroxypyruvate reductase A |
| RA | 1,111,164 | G→T | 32.1% | R101L (CGT→CTT) | opgH → | osmoregulated periplasmic glucans (OPGs) biosynthesis protein H |
| 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 | 1,406,853 | C→A | 11.3% | A315S (GCC→TCC) | dgcM ← | diguanylate cyclase DgcM |
| RA | 1,764,427 | G→A | 12.4% | intergenic (‑41/+286) | sufA ← / ← rydB | iron‑sulfur cluster insertion protein SufA/small regulatory RNA RydB |
| 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 | 2,321,822 | T→C | 12.3% | F594L (TTC→CTC) | atoS → | sensory histidine kinase AtoS |
| RA | 2,399,516 | C→A | 16.9% | R217L (CGT→CTT) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| JC | 2,399,711 | Δ123 bp | 11.6% | coding (333‑455/2727 nt) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| RA | 2,661,969 | C→G | 100% | V55L (GTT→CTT) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 3,041,632 | T→A | 100% | V107E (GTG→GAG) | ygfZ → | folate‑binding protein |
| RA | 3,134,229 | T→C | 8.2% | Y33Y (TAT→TAC) | yghT → | putative ATP‑binding protein YghT |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,637,645:1 | +T | 100% | coding (4/1500 nt) | pitA → | metal phosphate:H(+) symporter PitA |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,051,262 | A→C | 8.4% | noncoding (227/245 nt) | csrC → | small regulatory RNA CsrC |
| RA | 4,159,147 | C→G | 16.9% | R220G (CGC→GGC) | oxyR → | DNA‑binding transcriptional dual regulator OxyR |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,060 | C→T | 30.1% | 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 | 4,391,920 | G→C | 15.6% | G106A (GGT→GCT) | orn → | oligoribonuclease |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 366265 | 366398 | 134 | 12 [11] | [11] 12 | [lacZ] | [lacZ] |
| * | * | ÷ | NC_000913 | 3423763–3424234 | 3424536–3424238 | 5–774 | 12 [11] | [11] 13 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 315520 | NA (NA) | 3 (0.080) | 3/250 | NT | NA | noncoding (292/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315537 | NA (NA) | noncoding (309/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 392272 | NA (NA) | 5 (0.140) | 5/258 | NT | NA | noncoding (695/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 392297 | NA (NA) | noncoding (670/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 1798 (48.410) | 253/262 | NT | 98.3% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 32 (0.860) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | = 572471 | 32 (0.860) | 8 (0.290) +34 bp |
6/196 | NT | 30.2% | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein |
| ? | NC_000913 | = 2170235 | 18 (0.480) | noncoding (65/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 1080908 = | 40 (1.070) | 4 (0.120) | 3/240 | NT | 9.7% | intergenic (+95/‑448) | putP/efeU | proline:Na(+) symporter/inactive ferrous iron permease EfeU, N‑terminal fragment |
| ? | NC_000913 | 2229207 = | 38 (1.120) | intergenic (+142/+231) | yohP/dusC | putative membrane protein YohP/tRNA‑dihydrouridine(16) synthase | |||||
| * | ? | NC_000913 | 1207790 = | 5 (0.130) | 24 (0.730) | 20/232 | NT | 75.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 11 (0.330) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 4 (0.110) | 16 (0.490) | 15/232 | NT | 68.8% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 11 (0.330) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1437201 = | 28 (0.750) | 3 (0.080) | 3/250 | NT | 10.3% | noncoding (81/109 nt) | micC | small regulatory RNA MicC |
| ? | NC_000913 | 1437225 = | 26 (0.730) | noncoding (105/109 nt) | micC | small regulatory RNA MicC | |||||
| * | ? | NC_000913 | = 4254000 | NA (NA) | 4 (0.110) | 4/250 | NT | NA | noncoding (32/34 nt) | other | REP317c |
| ? | NC_000913 | = 4254030 | NA (NA) | noncoding (2/34 nt) | other | REP317c | |||||
| * | ? | NC_000913 | 4628744 = | NA (NA) | 3 (0.080) | 3/250 | NT | NA | noncoding (1/37 nt) | other | REP354b |
| ? | NC_000913 | 4628775 = | NA (NA) | noncoding (32/37 nt) | other | REP354b | |||||