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 | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| JC JC | 572,138 | IS2 (+) +5 bp | coding (685‑689/798 nt) | ybcM → | putative DNA‑binding transcriptional regulator |
| RA | 680,015 | C→T | L170F (CTC→TTC) | ybeU → | DUF1266 domain‑containing protein YbeU |
| RA | 706,052 | C→A | intergenic (+162/‑41) | nagE → / → glnS | N‑acetylglucosamine‑specific PTS enzyme IIABC component/glutamine‑‑tRNA ligase |
| 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 | 820,823 | IS5 (–) +4 bp | coding (31‑34/714 nt) | ybhM → | Bax1‑I family protein YbhM |
| RA | 956,539 | C→T | E32K (GAA→AAA) | ycaO ← | ribosomal protein S12 methylthiotransferase accessory factor YcaO |
| RA | 956,691 | C→T | intergenic (‑59/‑71) | ycaO ← / → ycaP | ribosomal protein S12 methylthiotransferase accessory factor YcaO/DUF421 domain‑containing protein YcaP |
| 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 | 1,196,220 | 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 | 1,279,000 | C→A | F348L (TTC→TTA) | narK → | nitrate:nitrite antiporter NarK |
| 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 | 1,567,492 | A→G | intergenic (‑273/+12) | yddY ← / ← digH | protein YddY/divisome localized glycosyl hydrolase |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,689,119 | G→A | E182K (GAA→AAA) | manA → | mannose‑6‑phosphate isomerase |
| RA | 1,772,818 | C→T | L103F (CTC→TTC) | ydiN → | putative transporter YdiN |
| RA | 1,844,295 | C→T | G193R (GGA→AGA) | ynjI ← | DUF1266 domain‑containing protein YnjI |
| JC JC | 1,859,380 | IS5 (+) +4 bp | coding (847‑850/1380 nt) | ydjK ← | putative transporter YdjK |
| JC JC | 1,909,378 | IS2 (–) +5 bp | coding (718‑722/792 nt) | kdgR ← | DNA‑binding transcriptional repressor KdgR |
| RA | 2,015,789 | G→A | E304K (GAA→AAA) | fliG → | flagellar motor switch protein FliG |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| JC JC | 2,034,215 | +A :: IS3 (+) +5 bp | intergenic (+476/‑1616) | rseX → / → hchA | small regulatory RNA RseX/protein/nucleic acid deglycase 1 |
| 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] | |
| RA | 2,745,600 | A→G | Y107H (TAC→CAC) | rimM ← | ribosome maturation factor RimM |
| RA | 2,774,947 | G→A | G544S (GGT→AGT) | yfjW → | uncharacterized protein YfjW |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,109,181 | A→G | intergenic (‑26/+136) | speC ← / ← yqgH | constitutive ornithine decarboxylase/protein YqgH |
| JC JC | 3,189,075 | IS5 (+) +4 bp | pseudogene (1644‑1647/2434 nt) | yqiG → | putative outer membrane usher protein YqiG |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,490,498 | C→G | G111A (GGT→GCT) | pabA ← | aminodeoxychorismate synthase subunit 2 |
| RA | 3,526,483 | G→A | V5V (GTG→GTA) | igaA → | inner membrane protein IgaA |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,948,012 | G→T | intergenic (‑45/‑74) | hdfR ← / → maoP | DNA‑binding transcriptional dual regulator HdfR/macrodomain Ori protein |
| RA | 3,954,923 | C→T | G482G (GGC→GGT) | ilvD → | dihydroxy‑acid dehydratase |
| RA | 4,123,447 | G→T | T337K (ACA→AAA) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,486,856 | C→A | F213L (TTC→TTA) | lptF → | lipopolysaccharide transport system protein LptF |
| RA | 4,548,969 | C→G | N54K (AAC→AAG) | fimH → | type 1 fimbriae D‑mannose specific adhesin |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 253488 | 258675–257908 | 4421–5188 | 122 [0] | [0] 112 | pepD–insA9 | pepD,gpt,frsA,crl,insB9,insA9 |
| * | * | ÷ | NC_000913 | 1196266 | 1211459 | 15194 | 45 [42] | [42] 45 | [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 | 142 [0] | [0] 158 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 2755515 | 2755726 | 212 | 46 [42] | [42] 44 | [ssrA] | [ssrA] |
| * | * | ÷ | NC_000913 | 3423760–3424490 | 3424490 | 1–731 | 44 [42] | [42] 44 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 253487 | 0 (0.000) | 117 (0.980) | 90/596 | 0.1 | 100% | intergenic (+326/+772) | yafP/pepD | putative N‑acetyltransferase YafP/peptidase D |
| ? | NC_000913 | 391709 = | NA (NA) | noncoding (1258/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 258676 = | 0 (0.000) | 107 (0.940) +CGAATATACGGGCCTAG |
76/564 | 0.2 | 100% | pseudogene (1/331 nt) | crl | RNA polymerase holoenzyme assembly factor Crl |
| ? | NC_000913 | = 392966 | NA (NA) | noncoding (1/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 391883 = | NA (NA) | 89 (0.740) | 68/598 | 0.4 | NA | noncoding (1084/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 392966 | NA (NA) | noncoding (1/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 567858 = | 17 (0.140) | 125 (1.040) | 84/596 | 0.1 | 88.0% | noncoding (1082/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 568034 | NA (NA) | noncoding (1258/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 141 (1.170) | 85/598 | 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) | 158 (1.310) | 96/598 | 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 | 3720633 = | NA (NA) | 116 (0.960) | 64/598 | 0.6 | 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) | 104 (0.860) | 61/598 | 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 | |||||
| * | ? | NC_000913 | 4542682 = | 123 (1.020) | 90 (0.770) | 61/580 | 0.6 | 46.0% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 92 (0.790) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 130 (1.080) | 77 (0.660) | 55/580 | 0.9 | 41.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 92 (0.790) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||