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] | |
| JC JC | 258,928 | IS2 (+) +5 bp | pseudogene (253‑257/331 nt) | crl → | RNA polymerase holoenzyme assembly factor Crl |
| RA | 440,202 | T→A | *300Y (TAA→TAT) | ispA ← | geranyl diphosphate/farnesyl diphosphate synthase |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| RA | 706,759 | G→A | E223K (GAA→AAA) | glnS → | glutamine‑‑tRNA ligase |
| RA | 708,774 | G→A | A147A (GCG→GCA) | chiP → | chitooligosaccharide outer membrane channel |
| JC JC | 785,074 | IS2 (+) +5 bp | coding (240‑244/381 nt) | ybgS ← | PF13985 family protein YbgS |
| JC JC | 949,487 | IS5 (+) +4 bp | coding (79‑82/909 nt) | ycaN ← | putative DNA‑binding transcriptional regulator YcaN |
| RA | 1,076,997 | C→T | R629H (CGC→CAC) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,093,264 | C→T | A130V (GCA→GTA) | dgcT → | putative diguanylate cyclase DgcT |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| RA | 1,171,950 | C→T | R672H (CGT→CAT) | mfd ← | transcription‑repair coupling factor |
| 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 |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| JC JC | 1,305,759 | IS2 (–) +5 bp | coding (1006‑1010/1014 nt) | oppD → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppD |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| MC JC | 1,397,239 | Δ10,478 bp | IS5‑mediated | ynaJ–[dgcM] | ynaJ, uspE, fnr, ogt, abgT, abgB, abgA, abgR, mcaS, smrA, [dgcM] |
| RA | 1,428,387 | G→T | Q114K (CAG→AAG) | insH5 ← | IS5 family transposase and trans‑activator |
| JC JC | 1,596,299 | IS2 (+) +5 bp | intergenic (‑3857/+2314) | hipB ← / ← lsrK | antitoxin/DNA‑binding transcriptional repressor HipB/autoinducer‑2 kinase |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| JC JC | 1,655,849 | IS2 (–) +5 bp | coding (42‑46/342 nt) | ynfB → | DUF1283 domain‑containing protein YnfB |
| RA | 1,738,006 | A→G | K55E (AAG→GAG) | purR → | DNA‑binding transcriptional repressor PurR |
| JC JC | 1,859,380 | IS5 (+) +4 bp | coding (847‑850/1380 nt) | ydjK ← | putative transporter YdjK |
| RA | 1,876,930 | G→A | V8I (GTT→ATT) | yeaO → | DUF488 domain‑containing protein YeaO |
| RA | 1,876,942 | G→C | A12P (GCT→CCT) | yeaO → | DUF488 domain‑containing protein YeaO |
| RA | 1,881,105 | G→A | L235L (CTC→CTT) | dmlR ← | DNA‑binding transcriptional regulator DmlR |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| RA | 2,043,522 | C→A | noncoding (36/90 nt) | serU ← | tRNA‑Ser |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,317,455 | IS2 (–) +5 bp | coding (2418‑2422/2850 nt) | rcsC ← | histidine kinase RcsC |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| JC JC | 2,771,973 | IS2 (+) +5 bp | coding (178‑182/315 nt) | yfjU ← | putative arsenate reductase‑like protein YfjU |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| JC JC | 2,993,579 | IS5 (+) +4 bp | intergenic (+109/‑56) | ygeH → / → ygeI | putative transcriptional regulator YgeH/protein YgeI |
| RA | 3,036,972 | C→T | E379K (GAG→AAG) | recJ ← | ssDNA‑specific exonuclease RecJ |
| RA | 3,090,656 | A→G | K104E (AAA→GAA) | endA → | DNA‑specific endonuclease I |
| JC JC | 3,368,586 | IS2 (+) +5 bp | coding (760‑764/1128 nt) | yhcG → | DUF1016 domain‑containing protein YhcG |
| 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 | 3,803,378 | C→T | E254K (GAA→AAA) | waaB ← | UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑1, 6‑D‑galactosyltransferase |
| RA | 3,803,540 | C→T | D200N (GAT→AAT) | waaB ← | UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑1, 6‑D‑galactosyltransferase |
| RA | 3,948,012 | G→T | intergenic (‑45/‑74) | hdfR ← / → maoP | DNA‑binding transcriptional dual regulator HdfR/macrodomain Ori protein |
| RA | 4,029,259 | G→A | A571A (GCC→GCT) | fadB ← | multifunctional enoyl‑CoA hydratase, 3‑hydroxyacyl‑CoA epimerase, Delta(3)‑cis‑ Delta(2)‑trans‑enoyl‑CoA isomerase, L‑3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,080,436 | G→A | L265F (CTC→TTC) | fdhE ← | formate dehydrogenase formation protein |
| RA | 4,200,353 | C→T | L25L (CTG→TTG) | hupA → | DNA‑binding protein HU‑alpha |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,567,746 | A→T | V258V (GTT→GTA) | mdtM ← | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196277 | 1211480 | 15204 | 39 [36] | [37] 38 | [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 | 776 | 119 [0] | [0] 139 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423816–3424231 | 3424486–3424238 | 8–671 | 38 [37] | [35] 39 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 118 (1.100) | 78/598 | 0.1 | 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) | 139 (1.300) | 88/598 | 0.0 | 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 | 2375828 = | 19 (0.180) | 68 (0.640) | 51/590 | 0.9 | 78.2% | coding (135/963 nt) | menC | o‑succinylbenzoate synthase |
| ? | NC_000913 | = 2515617 | NA (NA) | noncoding (1345/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | = 2375831 | 21 (0.200) | 62 (0.590) | 47/590 | 1.1 | 74.7% | coding (132/963 nt) | menC | o‑succinylbenzoate synthase |
| ? | NC_000913 | 2514273 = | NA (NA) | noncoding (1/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 3720633 = | NA (NA) | 100 (0.930) | 65/598 | 0.4 | NA | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | 3762460 = | NA (NA) | coding (278/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3722075 | NA (NA) | 101 (0.940) | 56/598 | 0.7 | 100% | noncoding (1443/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | = 3762462 | 0 (0.000) | coding (280/4134 nt) | rhsA | rhs element protein RhsA | |||||