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 | annotation | gene | description |
| RA | 278,744 | +A | intergenic (‑239/+75) | PP_0224 ← / ← sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein |
| RA | 307,866 | +C | intergenic (+881/‑988) | hslO → / → PP_0254 | molecular chaperone HslO/hypothetical protein |
| RA | 336,125 | +T | coding (210/237 nt) | PP_0278 → | hypothetical protein |
| RA | 353,067 | A→G | intergenic (+34/+84) | hisF → / ← cbcV | imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein |
| RA | 499,203 | A→G | intergenic (+47/‑249) | uhpA → / → PP_0411 | two‑component system response regulator UhpA/polyamine ABC transporter ATP‑binding protein |
| RA | 549,164 | C→T | L672F (CTC→TTC) | fusA → | elongation factor G 1 |
| RA | 1,070,248 | +GA | intergenic (+48/+94) | aroP‑I → / ← PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| RA | 1,126,647 | +C | intergenic (‑101/+48) | tdcG‑II ← / ← gcvP‑I | L‑serine dehydratase/glycine dehydrogenase |
| RA | 1,419,549 | +C | intergenic (‑38/+98) | PP_1242 ← / ← PP_1244 | hypothetical protein/hypothetical protein |
| RA | 1,434,472 | C→T | V498I (GTC→ATC) | PP_1256 ← | alpha‑ketoglutarate semialdehyde dehydrogenase |
| RA | 1,499,480 | 2 bp→AC | intergenic (+57/‑106) | trpS → / → zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| RA | 1,499,498 | 1 bp→CG | intergenic (+75/‑89) | trpS → / → zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| RA | 1,499,508 | +C | intergenic (+85/‑79) | trpS → / → zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| RA | 1,932,640 | +C | intergenic (‑107/+43) | rluA ← / ← minE | bifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA/cell division topological specificity factor |
| RA | 2,017,254 | (G)9→8 | intergenic (‑862/‑1472) | PP_1795 ← / → PP_1797 | hypothetical protein/HlyD family secretion protein |
| RA | 2,958,523 | C→T | A428V (GCA→GTA) | PP_2589 → | aldehyde dehydrogenase family protein |
| RA | 3,845,705 | +G | intergenic (‑72/+26) | PP_3394 ← / ← PP_3395 | 3‑hydroxy‑3‑methylglutaryl‑CoA lyase/LysR family transcriptional regulator |
| RA | 3,951,159 | T→C | intergenic (‑123/+72) | PP_3486 ← / ← PP_3487 | cytochrome c/hypothetical protein |
| RA | 3,951,161 | A→T | intergenic (‑125/+70) | PP_3486 ← / ← PP_3487 | cytochrome c/hypothetical protein |
| MC JC | 4,274,119 | 32 bp→45 bp | intergenic (‑243/‑1) | glcC ← / → glcD | transcriptional regulator GlcC/glycolate oxidase FAD‑linked subunit |
| RA | 4,586,137 | 2 bp→TC | intergenic (+113/+101) | PP_4061 → / ← PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| RA | 4,586,142 | +G | intergenic (+118/+97) | PP_4061 → / ← PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| RA | 4,586,164 | +C | intergenic (+140/+75) | PP_4061 → / ← PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| RA | 4,740,918 | (T)7→6 | intergenic (+48/+705) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,740,923 | T→G | intergenic (+53/+700) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,740,926 | 2 bp→CT | intergenic (+56/+696) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,336 | A→C | intergenic (+466/+287) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,338 | C→G | intergenic (+468/+285) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,341 | C→T | intergenic (+471/+282) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,343 | 2 bp→TG | intergenic (+473/+279) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,346 | A→G | intergenic (+476/+277) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,350 | 3 bp→TGC | intergenic (+480/+271) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,362 | C→T | intergenic (+492/+261) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,364 | A→C | intergenic (+494/+259) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,367 | 2 bp→GC | intergenic (+497/+255) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,370 | A→C | intergenic (+500/+253) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,379 | A→G | intergenic (+509/+244) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,381 | A→C | intergenic (+511/+242) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,383 | G→C | intergenic (+513/+240) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,385 | C→T | intergenic (+515/+238) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,390 | +T | intergenic (+520/+233) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,396 | C→G | intergenic (+526/+227) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,399 | C→T | intergenic (+529/+224) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,401 | C→G | intergenic (+531/+222) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,403 | A→C | intergenic (+533/+220) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,405 | C→T | intergenic (+535/+218) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,767,982 | A→T | intergenic (+89/‑93) | fpvA → / → tpaK | TonB‑dependent outer membrane ferripyoverdine receptor FpvA/probable terephthalate transporter, MFS superfamily protein |
| RA | 4,767,984 | T→G | intergenic (+91/‑91) | fpvA → / → tpaK | TonB‑dependent outer membrane ferripyoverdine receptor FpvA/probable terephthalate transporter, MFS superfamily protein |
| RA | 4,768,005 | T→A | intergenic (+112/‑70) | fpvA → / → tpaK | TonB‑dependent outer membrane ferripyoverdine receptor FpvA/probable terephthalate transporter, MFS superfamily protein |
| MC JC | 4,871,635 | Δ33,851 bp | [xdhB]–[PP_4311] | 32 genes [xdhB], xdhC, guaD, aqpZ, PP_4283, PP_4284, pucM, puuE, pucL, allA, PP_4289, uacT, PP_4291, PP_4293, yedI, PP_4295, PP_4296, gcl, hyi, glxR, ttuD, pyk, PP_4302, PP_4303, PP_4304, sbp‑I, PP_4306, PP_4307, PP_4308, PP_4309, PP_4310, [PP_4311] |
|
| JC | 4,982,288 | +GGC | intergenic (‑24/+44) | PP_4387 ← / ← flgE | hypothetical protein/flagellar hook protein FlgE |
| RA | 5,396,064 | A→G | V231A (GTA→GCA) | tphBII ← | 4‑hydroxythreonine‑4‑phosphate dehydrogenase |
| MC JC | 5,399,352 | Δ35,234 bp | [hsdM]–[PP_4771] | 31 genes [hsdM], hsdS, PP_5711, PP_4743, PP_4745, PP_4746, PP_4748, PP_4749, PP_4750, PP_4751, PP_4752, stcD, PP_4754, PP_4755, gabP‑V, gudD, PP_4758, PP_4759, PP_4760, PP_4761, tesB, PP_4763, PP_5712, PP_4764, PP_4765, rhlE‑I, yedA, PP_4768, PP_4769, PP_4770, [PP_4771] |
|
| RA | 5,558,423 | +GCC | intergenic (‑84/+87) | PP_4887 ← / ← PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| RA | 5,677,566 | +G | intergenic (+113/+27) | rhlE‑II → / ← yceI | ATP‑dependent RNA helicase/polyisoprene‑binding acidic stress response factor |
| RA | 5,677,568 | G→C | intergenic (+115/+25) | rhlE‑II → / ← yceI | ATP‑dependent RNA helicase/polyisoprene‑binding acidic stress response factor |
| RA | 5,684,230 | +CGGG | intergenic (‑133/+71) | PP_4986 ← / ← PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| RA | 6,016,700 | T→C | intergenic (+90/+20) | xpt → / ← PP_5266 | xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_002947_CJ‑RC | 171356–176302 | 176302 | 1–4947 | 32 [29] | [31] 32 | PP_16SA–[PP_5SA] | PP_16SA,PP_23SA,[PP_5SA] |
| * | * | ÷ | NC_002947_CJ‑RC | 176650–181715 | 181715 | 1–5066 | 32 [30] | [31] 34 | PP_16SB–[PP_r01] | PP_16SB,PP_23SB,[PP_r01] |
| * | * | ÷ | NC_002947_CJ‑RC | 5509254 | 5509503 | 250 | 32 [31] | [31] 32 | [PP_4839] | [PP_4839] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 1355334 | 24 (0.340) | 38 (0.570) | 34/274 | 1.5 | 63.1% | coding (43/2880 nt) | nrdA | ribonucleoside‑diphosphate reductase subunit alpha |
| ? | NC_002947_CJ‑RC | 1355350 = | 22 (0.330) | coding (27/2880 nt) | nrdA | ribonucleoside‑diphosphate reductase subunit alpha | |||||
| * | ? | NC_002947_CJ‑RC | 1844134 = | 0 (0.000) | 91 (1.320) | 79/282 | 0.0 | 72.5% | coding (660/2754 nt) | gacS | sensor protein GacS |
| ? | NC_002947_CJ‑RC | = 2179376 | 69 (1.000) | intergenic (+175/+93) | PP_1931/PP_5486 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1844137 | 0 (0.000) | 73 (1.050) | 65/284 | 0.1 | 64.6% | coding (657/2754 nt) | gacS | sensor protein GacS |
| ? | NC_002947_CJ‑RC | 2177702 = | 80 (1.150) | intergenic (+103/‑63) | PP_5485/PP_1931 | GNAT family acetyltransferase/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 30 (0.420) | 27 (0.390) | 25/282 | 3.0 | 46.2% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 34 (0.490) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||