mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| MC JC | 258,999 | Δ14,956 bp | IS5‑mediated | [crl]–[ykfC] | 21 genes [crl], phoE, proB, proA, thrW, ykfI, yafW, ykfH, ykfG, yafX, ykfF, ykfB, yafY, yafZ, ykfA, perR, insN, insI1, insN, eyeA, [ykfC] |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| JC JC | 308,899 | IS2 (+) +5 bp | coding (430‑434/2526 nt) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 635,355 | G→A | R8* (CGA→TGA) N405N (AAC→AAT) |
ybdM ← ybdN ← |
ParB‑like nuclease domain‑containing protein YbdM putative PAPS reductase/DUF3440 domain‑containing protein YbdN |
| RA | 696,582 | C→T | noncoding (35/75 nt) | glnV ← | tRNA‑Gln |
| RA | 811,531 | G→A | G384D (GGT→GAT) V4I (GTT→ATT) |
bioF → bioC → |
8‑amino‑7‑oxononanoate synthase malonyl‑acyl carrier protein methyltransferase |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,705,108 | G→A | G54R (GGG→AGG) | cnu → | H‑NS‑ and StpA‑binding protein |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,176,322 | IS1 (–) +9 bp | intergenic (‑1/+20) | gatZ ← / ← gatY | putative tagatose‑1,6‑bisphosphate aldolase 2 chaperone/tagatose‑1,6‑bisphosphate aldolase 2 |
| RA | 2,816,088 | G→A | Q118* (CAG→TAG) | gshA ← | glutamate‑‑cysteine ligase |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| MC JC | 2,942,765 | Δ8 bp | noncoding (70‑77/206 nt) | gcvB → | small regulatory RNA GcvB |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| MC JC | 3,933,149 | Δ5,543 bp | [kup]–[rbsR] | [kup], rbsD, rbsA, rbsC, rbsB, rbsZ, rbsK, [rbsR] | |
| JC JC | 3,948,258 | IS3 (–) +5 bp :: +TC | coding (173‑177/339 nt) | maoP → | macrodomain Ori protein |
| RA | 4,132,697 | G→A | E28K (GAG→AAG) | metF → | 5,10‑methylenetetrahydrofolate reductase |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,566,642 | G→A | S202L (TCG→TTG) | yjiN ← | DUF445 domain‑containing protein YjiN |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1978495 | 1979270–1978503 | 9–776 | 34 [0] | [0] 37 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423859–3424231 | 3424426–3424238 | 8–568 | 6 [5] | [5] 6 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4035377–4035732 | 4036859–4035736 | 5–1483 | 6 [5] | [5] 6 | [rrsA] | [rrsA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 257655 | 21 (0.440) | 29 (0.610) | 28/488 | 0.7 | 58.0% | coding (1129/1245 nt) | frsA | fermentation‑respiration switch protein |
| ? | NC_000913 | 273955 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 13 (0.270) | 13/488 | 1.9 | 52.0% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 401515 | 12 (0.250) | coding (130/261 nt) | iraP | anti‑adaptor protein IraP | |||||
| * | ? | NC_000913 | = 258675 | NA (NA) | 9 (0.190) | 9/486 | 2.5 | 45.0% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 401508 = | 11 (0.230) | coding (123/261 nt) | iraP | anti‑adaptor protein IraP | |||||
| * | ? | NC_000913 | 273955 = | NA (NA) | 17 (0.360) | 16/488 | 1.6 | 33.3% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1052284 = | 34 (0.710) | intergenic (+44/+5) | gnsA/yccM | putative phosphatidylethanolamine synthesis regulator GnsA/putative electron transport protein YccM | |||||
| * | ? | NC_000913 | 381260 = | NA (NA) | 10 (0.210) | 10/488 | 2.4 | 24.4% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 1109385 = | 31 (0.650) | coding (51/1536 nt) | opgG | osmoregulated periplasmic glucans biosynthesis protein G | |||||
| * | ? | NC_000913 | = 566774 | 44 (0.920) | 38 (0.800) | 23/484 | 1.0 | 49.5% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 34 (0.720) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 689045 | NA (NA) | 37 (0.780) | 35/488 | 0.4 | 50.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 758570 = | 36 (0.750) | intergenic (+165/‑136) | sdhB/sucA | succinate:quinone oxidoreductase, iron‑sulfur cluster binding protein/subunit of E1(0) component of 2‑oxoglutarate dehydrogenase | |||||
| * | ? | NC_000913 | = 1052287 | 34 (0.710) | 11 (0.230) | 11/488 | 2.2 | 24.4% | intergenic (+47/+2) | gnsA/yccM | putative phosphatidylethanolamine synthesis regulator GnsA/putative electron transport protein YccM |
| ? | NC_000913 | = 1300693 | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1109389 | 31 (0.650) | 17 (0.360) | 17/488 | 1.5 | 35.4% | coding (55/1536 nt) | opgG | osmoregulated periplasmic glucans biosynthesis protein G |
| ? | NC_000913 | 1467910 = | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1165257 | 38 (0.800) | 19 (0.400) | 18/486 | 1.4 | 35.9% | coding (115/543 nt) | ycfP | PF05728 family protein YcfP |
| ? | NC_000913 | 1229152 = | 30 (0.630) | coding (338/462 nt) | ycgN | putative metal‑chelating domain‑containing protein YcgN | |||||
| * | ? | NC_000913 | 1207790 = | 34 (0.710) | 13 (0.290) | 11/456 | 2.1 | 37.8% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 11 (0.250) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 32 (0.670) | 25 (0.560) | 24/456 | 0.8 | 55.0% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 11 (0.250) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | 1237207 = | 24 (0.500) | 44 (0.920) | 41/488 | 0.3 | 64.7% | coding (35/1533 nt) | ycgB | PF04293 family protein YcgB |
| ? | NC_000913 | = 1469240 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1237211 | 24 (0.500) | 48 (1.010) | 46/488 | 0.2 | 66.7% | coding (31/1533 nt) | ycgB | PF04293 family protein YcgB |
| ? | NC_000913 | 1467910 = | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 33 (0.730) | 29/464 | 0.6 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | = 1300693 | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1299499 = | NA (NA) | 29 (0.640) | 27/464 | 0.7 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1300694 = | 0 (0.000) | intergenic (+147/‑488) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1389137 | 43 (0.900) | 12 (0.250) | 12/488 | 2.1 | 21.8% | coding (208/966 nt) | ycjG | L‑Ala‑D/L‑Glu epimerase |
| ? | NC_000913 | 1396044 = | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 34 (0.710) | 31/488 | 0.6 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1427599 = | NA (NA) | 14 (0.290) | 13/488 | 1.9 | 46.7% | noncoding (1196/1196 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3262450 | 16 (0.340) | intergenic (‑32/+2) | tdcE/tdcD | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase 4/propionate kinase | |||||
| * | ? | NC_000913 | = 1428794 | NA (NA) | 24 (0.510) | 23/486 | 1.0 | 60.1% | noncoding (1/1196 nt) | IS5 | repeat region |
| ? | NC_000913 | 3262447 = | 16 (0.340) | intergenic (‑29/+5) | tdcE/tdcD | 2‑ketobutyrate formate‑lyase/pyruvate formate‑lyase 4/propionate kinase | |||||
| * | ? | NC_000913 | = 1469240 | NA (NA) | 8 (0.170) | 7/486 | 2.9 | 27.6% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 1657375 = | 21 (0.440) | coding (83/711 nt) | ynfC | PF06788 family lipoprotein YnfC | |||||
| * | ? | NC_000913 | 1492211 = | 15 (0.320) | 12 (0.250) | 12/484 | 2.0 | 44.4% | intergenic (+36/‑259) | sokB/trg | putative small regulatory RNA antitoxin SokB/methyl‑accepting chemotaxis protein Trg |
| ? | NC_000913 | 3720633 = | NA (NA) | noncoding (1/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | = 1492213 | 15 (0.310) | 15 (0.310) | 15/488 | 1.7 | 50.0% | intergenic (+38/‑257) | sokB/trg | putative small regulatory RNA antitoxin SokB/methyl‑accepting chemotaxis protein Trg |
| ? | NC_000913 | = 3722075 | NA (NA) | noncoding (1443/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | = 1651548 | NA (NA) | 11 (0.230) | 11/486 | 2.2 | 23.9% | noncoding (706/706 nt) | IS2 | repeat region |
| ? | NC_000913 | = 1671880 | 35 (0.740) | intergenic (+20/‑80) | ydgU/ydgD | uncharacterized protein YdgU/putative serine protease YdgD | |||||
| * | ? | NC_000913 | 1907165 = | 28 (0.590) | 19 (0.400) | 18/488 | 1.4 | 40.4% | intergenic (‑105/+61) | rlmA/cspC | 23S rRNA m(1)G745 methyltransferase/transcription antiterminator and regulator of mRNA stability CspC |
| ? | NC_000913 | 3720633 = | NA (NA) | noncoding (1/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | = 1907167 | 27 (0.570) | 11 (0.230) | 10/484 | 2.3 | 29.0% | intergenic (‑107/+59) | rlmA/cspC | 23S rRNA m(1)G745 methyltransferase/transcription antiterminator and regulator of mRNA stability CspC |
| ? | NC_000913 | = 3722075 | NA (NA) | noncoding (1443/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 36 (0.750) | 34/488 | 0.5 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||
| * | ? | NC_000913 | 2068941 = | NA (NA) | 23 (0.480) | 22/488 | 1.0 | 56.1% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 2320130 | 18 (0.380) | coding (88/1827 nt) | atoS | sensor histidine kinase AtoS | |||||
| * | ? | NC_000913 | = 2102943 | NA (NA) | 16 (0.340) | 16/488 | 1.6 | 53.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2111448 = | 14 (0.290) | coding (529/900 nt) | rfbD | dTDP‑4‑dehydrorhamnose reductase | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 10 (0.210) | 10/488 | 2.4 | 23.8% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3152958 = | 32 (0.670) | coding (723/1188 nt) | metC | cystathionine beta‑lyase/L‑cysteine desulfhydrase/alanine racemase | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 19 (0.400) | 19/488 | 1.3 | 57.6% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3890674 | 14 (0.290) | coding (439/1248 nt) | tnaB | tryptophan:H(+) symporter TnaB | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 9 (0.190) | 9/488 | 2.5 | 30.0% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4360758 = | 21 (0.440) | coding (1177/1539 nt) | cadC | DNA‑binding transcriptional activator CadC | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 7 (0.150) | 7/486 | 2.9 | 28.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3079323 | 18 (0.380) | coding (8/444 nt) | cmtB | mannitol‑specific PTS enzyme IIA component CmtB | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 7 (0.150) | 7/488 | 2.9 | 26.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3267918 | 19 (0.400) | coding (65/540 nt) | yhaB | protein YhaB | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 13 (0.270) | 12/488 | 2.1 | 27.1% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3844024 = | 35 (0.730) | coding (61/1767 nt) | adeD | adenine deaminase | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 25 (0.520) | 23/488 | 1.0 | 65.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3890671 = | 13 (0.270) | coding (436/1248 nt) | tnaB | tryptophan:H(+) symporter TnaB | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 12 (0.250) | 12/488 | 2.1 | 36.4% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 4360761 | 21 (0.440) | coding (1174/1539 nt) | cadC | DNA‑binding transcriptional activator CadC | |||||
| * | ? | NC_000913 | 2320126 = | 18 (0.380) | 19 (0.400) | 16/488 | 1.6 | 51.3% | coding (84/1827 nt) | atoS | sensor histidine kinase AtoS |
| ? | NC_000913 | = 2997691 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 2558698 | 46 (0.960) | 13 (0.280) | 13/472 | 1.8 | 26.7% | intergenic (‑19/‑160) | eutB/intZ | ethanolamine ammonia‑lyase subunit alpha/putative phage integrase IntZ |
| ? | NC_000913 | 2565489 = | 27 (0.590) | coding (1396/1404 nt) | eutA | ethanolamine ammonia‑lyase reactivase EutA | |||||
| * | ? | NC_000913 | = 3102862 | 19 (0.400) | 25 (0.520) | 24/488 | 0.9 | 56.8% | intergenic (‑10/‑151) | trmB/mutY | tRNA m(7)G46 methyltransferase/adenine DNA glycosylase |
| ? | NC_000913 | 3130146 = | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 3267915 = | 17 (0.360) | 7 (0.150) | 7/488 | 2.9 | 29.2% | coding (62/540 nt) | yhaB | protein YhaB |
| ? | NC_000913 | 3365556 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 3366750 | NA (NA) | 23 (0.480) | 22/488 | 1.0 | 33.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3368931 | 45 (0.940) | coding (1105/1128 nt) | yhcG | DUF1016 domain‑containing protein YhcG | |||||