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 | 148,502 | G→A | I98I (ATC→ATT) | panC ← | pantothenate synthetase |
| RA | 209,247 | G→A | L209L (CTG→CTA) | accA → | acetyl‑CoA carboxyltransferase subunit alpha |
| RA | 228,767 | C→A | noncoding (12/120 nt) | rrfH → | 5S ribosomal RNA |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 320,156 | T→C | intergenic (‑155/‑71) | rclA ← / → rclR | cupric reductase RclA/DNA‑binding transcriptional activator RclR |
| RA | 405,638 | T→C | K3E (AAG→GAG) | proC ← | pyrroline‑5‑carboxylate reductase |
| RA | 431,460 | T→A | Y185F (TAC→TTC) | tsx ← | nucleoside‑specific channel‑forming protein Tsx |
| RA | 431,647 | C→A | E123* (GAG→TAG) | tsx ← | nucleoside‑specific channel‑forming protein Tsx |
| RA | 467,730 | G→A | D107N (GAC→AAC) | cof → | HMP‑PP phosphatase |
| RA | 495,201 | A→T | K28* (AAA→TAA) | htpG → | chaperone protein HtpG |
| RA | 495,211 | T→C | F31S (TTC→TCC) | htpG → | chaperone protein HtpG |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| RA | 581,072 | G→A | G80E (GGG→GAG) | nohD → | putative DNA‑packaging protein NohD |
| RA | 727,250 | C→T | G495R (GGG→AGG) | kdpA ← | K(+) transporting P‑type ATPase subunit KdpA |
| RA | 736,715 | C→T | intergenic (+16/‑1377) | ybfQ → / → ybfD | inactive transposase YbfQ/H repeat‑associated putative transposase YbfD |
| RA | 749,898 | G→A | R758C (CGC→TGC) | ybgQ ← | putative fimbrial usher protein YbgQ |
| RA | 753,860 | G→T | F203L (TTC→TTA) | gltA ← | citrate synthase |
| MC JC | 787,320 | Δ126,470 bp | [gpmA]–[hcp] | 124 genes [gpmA], galM, galK, galT, galE, modF, modE, acrZ, modA, modB, modC, ybhA, pgl, ybhD, ybhH, ybhI, ybhJ, ybhC, ybhB, bioA, bioB, bioF, bioC, bioD, uvrB, ybhK, moaA, moaB, moaC, moaD, moaE, ybhL, ybhM, ybhN, clsB, ybhP, ybhQ, ybhR, ybhS, ybhF, ybhG, cecR, rhlE, ybiA, dinG, ybiB, hcxB, zbiJ, ybiE, ybiJ, ybiI, ybiX, fiu, mcbA, rlmF, ybiO, glnQ, glnP, glnH, dps, rhtA, yliM, ompX, opgE, rybA, mntS, mntR, ybiR, ldtB, ybiT, ybiU, ybiV, ybiW, ybiY, fsaA, moeB, moeA, iaaA, gsiA, gsiB, gsiC, gsiD, pdeI, dgcI, rimO, bssR, yliI, gstB, dacC, deoR, ybjG, mdfA, ybjH, ybjI, ybjJ, rcdA, rybB, ybjL, ybjM, grxA, ybjC, nfsA, rimK, ybjN, potF, potG, potH, potI, ybjO, rlmC, artJ, artM, artQ, artI, artP, ybjP, ybjQ, amiD, ybjS, ybjT, ltaE, poxB, hcr, [hcp] |
|
| RA | 987,152 | G→T | intergenic (‑170/+433) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| RA | 1,050,039 | A→C | T69T (ACA→ACC) S5R (AGC→CGC) |
insA4 → insB4 → |
IS1 family protein InsA IS1 family protein InsB |
| JC JC | 1,093,279 | IS5 (+) +4 bp | coding (404‑407/1359 nt) | dgcT → | putative diguanylate cyclase DgcT |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| RA | 1,112,653 | C→G | Y597* (TAC→TAG) | opgH → | osmoregulated periplasmic glucans biosynthesis protein H |
| RA | 1,136,605 | G→A | G111E (GGA→GAA) | flgI → | flagellar P‑ring protein |
| 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 |
| RA | 1,196,283 | A→G | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,292 | C→T | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| JC JC | 1,303,314 | IS186 (–) +6 bp :: Δ1 bp | coding (416‑421/921 nt) | oppB → | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppB |
| RA | 1,322,868 | G→A | Q27* (CAG→TAG) | trpE ← | anthranilate synthase subunit TrpE |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,345,203 | Δ1 bp | coding (1540/1986 nt) | pdeR ← | cyclic di‑GMP phosphodiesterase PdeR |
| MC JC | 1,381,646 | Δ14,398 bp | IS5‑mediated | ompG–ynaI | ompG, ycjW, ycjX, ycjF, tyrR, tpx, ycjG, mpaA, ymjC, ymjD, ycjY, pgrR, mppA, ynaI |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,667,887 | Δ1 bp | coding (678/1221 nt) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,684,504 | G→T | Q82H (CAG→CAT) | tus → | DNA replication terminus site‑binding protein |
| RA | 1,866,085 | C→T | G130S (GGC→AGC) | mipA ← | MltA‑interacting protein |
| RA | 1,895,329 | G→A | Q175Q (CAG→CAA) | pabB → | aminodeoxychorismate synthase subunit 1 |
| RA | 1,969,375 | C→A | intergenic (‑11/+8) | cheR ← / ← tap | chemotaxis protein methyltransferase/methyl‑accepting chemotaxis protein Tap |
| JC JC | 1,981,809 | IS2 (–) +5 bp | coding (575‑579/801 nt) | otsB ← | trehalose‑6‑phosphate phosphatase |
| RA | 2,003,264 | C→T | E115K (GAA→AAA) | fliC ← | flagellar filament structural protein |
| RA | 2,026,349 | G→A | R557W (CGG→TGG) | dgcQ ← | diguanylate cyclase DgcQ |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| RA | 2,108,470 | C→T | S372N (AGT→AAT) | rfbX ← | polyisoprenol‑linked O16‑antigen repeat unit flippase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,202,345 | T→A | D689E (GAT→GAA) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,388,299 | T→C | Q43R (CAA→CGA) | yfbN ← | uncharacterized protein YfbN |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| RA | 2,420,652 | 2 bp→TG | coding (32‑33/648 nt) | yfcG → | disulfide bond oxidoreductase YfcG |
| RA | 2,430,737 | G→A | I9I (ATC→ATT) | cvpA ← | colicin V production protein |
| RA | 2,537,509 | G→A | A56A (GCG→GCA) | yfeK → | DUF5329 domain‑containing protein YfeK |
| RA | 2,577,284 | G→A | S365L (TCA→TTA) | maeB ← | malate dehydrogenase (oxaloacetate‑decarboxylating) (NADP(+)) |
| RA | 2,680,564 | G→A | P728S (CCG→TCG) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,704,184 | C→T | intergenic (‑121/+151) | rnc ← / ← lepB | RNase III/signal peptidase I |
| RA | 2,739,388 | C→A | E228* (GAG→TAG) | tyrA ← | fused chorismate mutase/prephenate dehydrogenase |
| RA | 2,789,030 | C→T | Q16* (CAG→TAG) | glaH → | glutarate dioxygenase GlaH |
| RA | 2,864,262 | C→T | S9S (TCC→TCT) | ygbM → | putative 2‑oxo‑tetronate isomerase YgbM |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,870,068 | G→A | T69T (ACC→ACT) | umpG ← | broad specificity 5'(3')‑nucleotidase and polyphosphatase |
| RA | 2,900,293 | 2 bp→CT | intergenic (‑20/‑298) | ygcW ← / → yqcE | putative deoxygluconate dehydrogenase/putative transport protein YqcE |
| RA | 2,966,382 | C→T | G685R (GGG→AGG) | ptsP ← | phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 3,156,738 | A→T | E39V (GAA→GTA) | dkgA → | methylglyoxal reductase DkgA |
| RA | 3,160,398 | G→A | P250L (CCA→CTA) | ygiQ ← | radical SAM superfamily protein YgiQ |
| RA | 3,166,817 | G→A | P301L (CCG→CTG) | ygiS ← | putative deoxycholate binding periplasmic protein |
| MC JC | 3,241,797 | Δ386 bp | [uxaA] | [uxaA] | |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,486,724 | A→T | K202I (AAA→ATA) | 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 |
| JC JC | 3,578,523 | IS2 (–) +5 bp | coding (200‑204/996 nt) | gntR ← | DNA‑binding transcriptional repressor GntR |
| RA | 3,632,121 | C→T | W157* (TGG→TAG) | yhiJ ← | DUF4049 domain‑containing protein YhiJ |
| MC JC | 3,635,703 | Δ16,333 bp | IS5‑mediated | [yhiM]–[yhiS] | 19 genes [yhiM], yhiN, pitA, uspB, uspA, yriA, yriB, dtpB, rsmJ, prlC, rlmJ, gor, dinQ, agrA, agrB, arsR, arsB, arsC, [yhiS] |
| RA | 3,664,986 | C→T | *275* (TAG→TAA) | gadX ← | DNA‑binding transcriptional dual regulator GadX |
| RA | 3,676,176 | A→G | intergenic (+68/+114) | yhjE → / ← yhjG | putative transporter YhjE/AsmA family protein YhjG |
| MC JC | 3,682,261 | Δ34 bp | coding (1154‑1187/1287 nt) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| RA | 3,689,865 | T→C | K133E (AAA→GAA) | bcsZ ← | endo‑1,4‑D‑glucanase |
| JC JC | 3,737,137 | IS2 (+) +5 bp | coding (37‑41/825 nt) | bax ← | putative glycoside hydrolase Bax |
| RA | 3,900,993 | C→T | D410N (GAT→AAT) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,970,864 | G→A | P244P (CCG→CCA) | wecB → | UDP‑N‑acetylglucosamine 2‑epimerase |
| RA | 4,001,322 | T→A | intergenic (+48/‑104) | ysgD → / → corA | protein YsgD/Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| JC JC | 4,002,526 | IS5 (–) +4 bp | coding (271‑274/381 nt) | yigF ← | DUF2628 domain‑containing protein YigF |
| RA | 4,026,734 | Δ1 bp | coding (208/702 nt) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,037,750 | G→A | noncoding (232/2905 nt) | rrlA → | 23S ribosomal RNA |
| RA | 4,078,687 | G→T | intergenic (+249/‑604) | fabY → / → yiiE | putative fatty acid biosynthesis enzyme FabY/putative DNA‑binding transcriptional regulator YiiE |
| JC JC | 4,123,923 | IS2 (–) +5 bp | coding (530‑534/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,131,369 | C→A | A512D (GCC→GAC) | metL → | fused aspartate kinase/homoserine dehydrogenase 2 |
| RA | 4,152,733 | G→A | I122I (ATC→ATT) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,360,480 | G→A | T485T (ACC→ACT) | cadC ← | DNA‑binding transcriptional activator CadC |
| RA | 4,372,088 | A→G | E355G (GAA→GGA) | groL → | chaperonin GroEL |
| JC JC | 4,480,604 | IS5 (+) +4 bp | coding (875‑878/1197 nt) | yjgN → | inner membrane protein YjgN |
| JC JC | 4,514,261 | IS3 (–) +3 bp :: +TCA | coding (46‑48/903 nt) | fecB ← | ferric citrate ABC transporter periplasmic binding protein |
| RA | 4,561,138 | T→C | F70S (TTT→TCT) | kptA → | RNA 2'‑phosphotransferase |
| JC JC | 4,640,418 | IS30 (–) +2 bp | coding (17‑18/141 nt) | yjjY → | uncharacterized protein YjjY |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 223942–224771 | 225411–224799 | 29–1470 | 45 [42] | [43] 48 | [rrsH]–[ileV] | [rrsH],[ileV] |
| * | * | ÷ | NC_000913 | 732292–732532 | 733050–732817 | 286–759 | 46 [43] | [44] 45 | rhsC | rhs element protein RhsC |
| * | * | ÷ | NC_000913 | 1196302 | 1211460 | 15159 | 45 [44] | [43] 49 | [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 | 147 [0] | [0] 183 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423756–3424233 | 3424457–3424238 | 6–702 | 45 [43] | [44] 45 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 4035371–4036899 | 4036899 | 1–1529 | 45 [44] | [43] 45 | [rrsA] | [rrsA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381260 = | NA (NA) | 81 (0.650) | 54/598 | 1.0 | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382183 | NA (NA) | noncoding (924/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 382179 = | NA (NA) | 51 (0.410) | 40/594 | 2.0 | NA | noncoding (920/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 676784 = | 151 (1.220) | 104 (0.840) | 66/596 | 0.5 | 40.8% | coding (74/708 nt) | ybeR | DUF1266 domain‑containing protein YbeR |
| ? | NC_000913 | = 689045 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 191 (1.560) | 102/590 | 0.0 | 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) | 147 (1.190) | 95/598 | 0.0 | 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) | 183 (1.480) | 102/598 | 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 | |||||