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 |
| RA | 158,615 | C→A | S171I (AGC→ATC) | pcnB ← | poly(A) polymerase I |
| 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 | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,277 | C→T | N385N (AAC→AAT) | 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 |
| 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 |
| MC JC | 1,397,239 | Δ17,203 bp | IS5‑mediated | ynaJ–[recT] | 23 genes ynaJ, uspE, fnr, ogt, abgT, abgB, abgA, abgR, mcaS, smrA, dgcM, ynaN, zntB, fnrS, ynaL, dbpA, ttcA, intR, xisR, rcbA, ralA, ralR, [recT] |
| 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 |
| MC JC | 1,650,703 | Δ20,111 bp | ynfP–[ynfM] | 18 genes ynfP, rspB, rspA, ynfA, ynfB, speG, ynfC, ynfD, ynfE, ynfF, ynfG, ynfH, dmsD, clcB, bidA, mlc, ynfL, [ynfM] |
|
| 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 | 2,523,109 | G→A | L293L (CTG→TTG) | xapB ← | xanthosine:H(+) symporter XapB |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,725,858 | G→A | intergenic (‑112/‑67) | kgtP ← / → yfiS | alpha‑ketoglutarate:H(+) symporter/protein YfiS |
| 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 | 3,533,518 | C→T | S234F (TCC→TTC) | pck → | phosphoenolpyruvate carboxykinase (ATP) |
| JC | 3,553,460 | (ATCTGG)1→2 | coding (376/2706 nt) | malT → | DNA‑binding transcriptional activator MalT |
| 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 | 1196361 | 1211431 | 15071 | 3 [2] | [2] 3 | [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 | 1978495 | 1979270–1978503 | 9–776 | 36 [0] | [0] 23 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423893–3424406 | 3424406 | 1–514 | 5 [2] | [2] 3 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 3927268 | 3938724 | 11457 | 75 [0] | [0] 79 | [asnA]–[rbsR] | [asnA],viaA,ravA,kup,rbsD,rbsA,rbsC,rbsB,rbsZ,rbsK,[rbsR] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 566774 | 53 (0.920) | 16 (0.280) | 8/488 | 2.2 | 28.4% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 28 (0.490) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 21 (0.370) | 20/484 | 1.1 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 36 (0.630) | 33/492 | 0.5 | 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 | 1979271 = | 0 (0.000) | 23 (0.400) | 22/492 | 1.0 | 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 | 3652036 = | NA (NA) | 79 (1.380) | 70/490 | 0.1 | 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) | 75 (1.300) | 68/492 | 0.1 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3927267 | 0 (0.000) | coding (113/993 nt) | asnA | asparagine synthetase A | |||||