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 |
| RA | 1,903 | G→A | E523K (GAA→AAA) | thrA → | fused aspartate kinase/homoserine dehydrogenase 1 |
| RA | 10,696 | C→T | A221T (GCC→ACC) | yaaW ← | putative enzyme‑specific chaperone YaaW |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375L (TTA→CTA) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| JC JC | 1,293,268 | IS5 (–) +4 bp | intergenic (‑346/‑256) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,301,998 | A→G | S273G (AGC→GGC) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| JC JC | 1,492,211 | IS150 (–) +3 bp | intergenic (+36/‑257) | sokB → / → trg | putative small regulatory RNA antitoxin SokB/methyl‑accepting chemotaxis protein Trg |
| RA | 1,507,867 | G→A | E363K (GAG→AAG) | rlhA → | 23S rRNA 5‑hydroxycytidine C2501 synthase |
| JC JC | 1,649,932 | IS2 (+) +5 bp | coding (139‑143/192 nt) | ydfD → | lysis protein |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,299,162 | G→A | Y139Y (TAC→TAT) | napH ← | ferredoxin‑type protein NapH |
| RA | 2,410,419 | G→A | L312L (CTG→TTG) | yfbS ← | putative transporter YfbS |
| RA | 2,484,827 | C→T | L152F (CTT→TTT) | evgS → | sensor histidine kinase EvgS |
| RA | 2,510,609 | C→T | P327L (CCG→CTG) | yfeO → | putative transport protein YfeO |
| RA | 2,732,992 | G→A | I394I (ATC→ATT) I394I (ATC→ATT) |
clpB ← clpB ← |
chaperone protein ClpB chaperone protein ClpB |
| RA | 2,804,133 | C→T | S211F (TCT→TTT) | nrdF → | ribonucleoside‑diphosphate reductase 2 subunit beta |
| RA | 2,814,459 | Δ1 bp | coding (275/516 nt) | luxS ← | S‑ribosylhomocysteine lyase |
| RA | 2,814,461 | C→T | L91L (CTG→CTA) | luxS ← | S‑ribosylhomocysteine lyase |
| RA | 2,817,197 | G→A | R103C (CGC→TGC) | yqaB ← | fructose‑1‑phosphate phosphatase YqaB |
| RA | 2,823,288 | C→T | G161D (GGC→GAC) | recA ← | DNA recombination/repair protein RecA |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,871,153 | T→G | N51T (AAC→ACC) | truD ← | tRNA pseudouridine(13) synthase |
| RA | 2,926,543 | 2 bp→TT | coding (236‑237/1365 nt) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 2,926,772 | C→A | G155G (GGC→GGA) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 4,182,791 | A→T | D516V (GAC→GTC) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,395,743 | T→C | G53G (GGT→GGC) | tsaE → | N(6)‑L‑threonylcarbamoyladenine synthase, TsaE subunit |
| RA | 4,570,550 | C→T | S342N (AGC→AAC) | yjiR ← | fused putative DNA‑binding transcriptional regulator/putative aminotransferase YjiR |
| RA | 4,571,280 | C→T | E99K (GAG→AAG) | yjiR ← | fused putative DNA‑binding transcriptional regulator/putative aminotransferase YjiR |
| RA | 4,585,673 | C→T | W363* (TGG→TGA) | hsdR ← | type I restriction enzyme EcoKI endonuclease subunit |
| RA | 4,587,365 | C→T | S139S (AGC→AGT) | mrr → | Type IV methyl‑directed restriction enzyme EcoKMrr |
| RA | 4,604,517 | C→T | L120L (CTG→TTG) | bglJ → | DNA‑binding transcriptional regulator BglJ |
| RA | 4,630,295 | C→T | Q76Q (CAG→CAA) | ettA ← | energy‑dependent translational throttle protein EttA |
| RA | 4,636,925 | G→C | R77P (CGC→CCC) | creC → | sensory histidine kinase CreC |
| RA | 4,638,058 | C→T | L455L (CTG→TTG) | creC → | sensory histidine kinase CreC |
| RA | 4,638,240 | G→A | L21L (TTG→TTA) | creD → | putative inner membrane protein CreD |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196302 | 1211439 | 15138 | 2 [1] | [1] 2 | [icd]–mcrA | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1396247–1397242 | 1403379 | 6138–7133 | 2 [1] | [1] 2 | [insH4]–[abgA] | [insH4],ynaJ,uspE,fnr,ogt,abgT,abgB,[abgA] |
| * | * | ÷ | NC_000913 | 1403496 | 1414441 | 10946 | 2 [1] | [0] 23 | [abgA]–[recT] | [abgA],abgR,mcaS,smrA,dgcM,ynaN,zntB,fnrS,ynaL,dbpA,ttcA,intR,xisR,rcbA,ralA,ralR,[recT] |
| * | * | ÷ | NC_000913 | 1650703 | 1662762 | 12060 | 29 [0] | [0] 2 | ynfP–[ynfF] | ynfP,rspB,rspA,ynfA,ynfB,speG,ynfC,ynfD,ynfE,[ynfF] |
| * | * | ÷ | NC_000913 | 1662934 | 1670813 | 7880 | 2 [0] | [0] 29 | [ynfF]–[ynfM] | [ynfF],ynfG,ynfH,dmsD,clcB,bidA,mlc,ynfL,[ynfM] |
| * | * | ÷ | NC_000913 | 1978495 | 1979270 | 776 | 15 [0] | [0] 8 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 2558699 | 2565484 | 6786 | 43 [0] | [1] 2 | intZ–[eutA] | intZ,yffL,yffM,yffN,yffO,yffP,yffQ,yffR,yffS,[eutA] |
| * | * | ÷ | NC_000913 | 2760245 | 2760393 | 149 | 2 [0] | [1] 2 | yfjI | DUF3987 domain‑containing protein YfjI |
| * | * | ÷ | NC_000913 | 3423896–3424230 | 3424414–3424239 | 10–519 | 2 [1] | [1] 2 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 3927268 | 3936974 | 9707 | 18 [0] | [1] 2 | [asnA]–[rbsB] | [asnA],viaA,ravA,kup,rbsD,rbsA,rbsC,[rbsB] |
| * | * | ÷ | NC_000913 | 3937153 | 3938724 | 1572 | 2 [1] | [0] 21 | [rbsB]–[rbsR] | [rbsB],[rbsZ],rbsK,[rbsR] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 10 (0.330) | 9/484 | 1.3 | 40.0% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1303803 = | 15 (0.500) | coding (905/921 nt) | oppB | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppB | |||||
| * | ? | NC_000913 | = 1303810 | 12 (0.400) | 16 (0.530) | 15/490 | 0.8 | 57.1% | coding (912/921 nt) | oppB | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppB |
| ? | NC_000913 | = 1979270 | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 23 (0.760) | 20/490 | 0.5 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1414442 = | 0 (0.000) | coding (352/810 nt) | recT | recombinase RecT | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 15 (0.490) | 15/490 | 0.8 | 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 | = 1650702 | 0 (0.000) | 29 (0.960) | 28/488 | 0.2 | 100% | intergenic (+717/+2026) | ydfD/ynfP | lysis protein/protein YnfP |
| ? | NC_000913 | 1670814 = | 0 (0.000) | coding (1116/1254 nt) | ynfM | putative transporter YnfM | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 8 (0.260) | 8/490 | 1.5 | 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 | = 2558698 | 0 (0.000) | 43 (1.470) | 39/474 | 0.0 | 100% | intergenic (‑19/‑160) | eutB/intZ | ethanolamine ammonia‑lyase subunit alpha/putative phage integrase IntZ |
| ? | NC_000913 | 2565489 = | 0 (0.000) | coding (1396/1404 nt) | eutA | ethanolamine ammonia‑lyase reactivase EutA | |||||
| * | ? | NC_000913 | 3652036 = | NA (NA) | 21 (0.690) | 20/488 | 0.5 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3938725 = | 0 (0.000) | coding (499/993 nt) | rbsR | DNA‑binding transcriptional dual regulator RbsR | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 18 (0.590) | 17/490 | 0.6 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3927267 | 0 (0.000) | coding (113/993 nt) | asnA | asparagine synthetase A | |||||