mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 36,325 | G→A | 7.1% | A443V (GCT→GTT) | PP_0033 ← | undecaprenyl‑glycosyl transferase |
| RA | 122,224 | G→T | 17.6% | intergenic (+34/+27) | katE → / ← PP_0116 | hydroperoxidase/putative lipoprotein |
| RA | 158,258 | A→G | 6.8% | Q90R (CAG→CGG) | PP_0148 → | hypothetical protein |
| RA | 191,172 | A→T | 7.7% | I67N (ATC→AAC) | PP_0166 ← | HlyD family secretion protein |
| RA | 195,559 | C→A | 21.4% | T355T (ACC→ACA) | PP_0168 → | putative surface adhesion protein |
| RA | 195,628 | C→T | 6.8% | D378D (GAC→GAT) | PP_0168 → | putative surface adhesion protein |
| RA | 195,629 | A→G | 6.9% | T379A (ACC→GCC) | PP_0168 → | putative surface adhesion protein |
| RA | 195,634 | C→T | 42.7% | T380T (ACC→ACT) | PP_0168 → | putative surface adhesion protein |
| RA | 195,724 | A→G | 6.9% | V410V (GTA→GTG) | PP_0168 → | putative surface adhesion protein |
| RA | 196,306 | T→C | 18.2% | N604N (AAT→AAC) | PP_0168 → | putative surface adhesion protein |
| RA | 196,327 | A→C | 21.0% | T611T (ACA→ACC) | PP_0168 → | putative surface adhesion protein |
| RA | 196,351 | C→G | 23.4% | T619T (ACC→ACG) | PP_0168 → | putative surface adhesion protein |
| RA | 196,390 | T→C | 25.0% | D632D (GAT→GAC) | PP_0168 → | putative surface adhesion protein |
| RA | 196,795 | G→C | 9.1% | T767T (ACG→ACC) | PP_0168 → | putative surface adhesion protein |
| RA | 196,879 | G→A | 16.0% | V795V (GTG→GTA) | PP_0168 → | putative surface adhesion protein |
| RA | 197,032 | C→T | 6.8% | T846T (ACC→ACT) | PP_0168 → | putative surface adhesion protein |
| RA | 197,089 | T→C | 12.8% | N865N (AAT→AAC) | PP_0168 → | putative surface adhesion protein |
| RA | 197,179 | A→G | 7.2% | V895V (GTA→GTG) | PP_0168 → | putative surface adhesion protein |
| RA | 197,551 | C→G | 7.0% | T1019T (ACC→ACG) | PP_0168 → | putative surface adhesion protein |
| RA | 197,572 | G→A | 11.9% | K1026K (AAG→AAA) | PP_0168 → | putative surface adhesion protein |
| RA | 197,590 | T→C | 15.0% | D1032D (GAT→GAC) | PP_0168 → | putative surface adhesion protein |
| RA | 197,632 | T→C | 16.7% | T1046T (ACT→ACC) | PP_0168 → | putative surface adhesion protein |
| RA | 260,572 | C→T | 6.3% | G228G (GGC→GGT) | PP_0208 → | nitrate ABC transporter permease |
| RA | 278,742:1 | +A | 40.0% | intergenic (‑237/+77) | PP_0224 ← / ← sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein |
| RA | 307,865:1 | +C | 100% | intergenic (+880/‑989) | hslO → / → PP_0254 | molecular chaperone HslO/hypothetical protein |
| RA | 336,124:1 | +T | 100% | coding (209/237 nt) | PP_0278 → | hypothetical protein |
| RA | 337,825 | G→T | 16.0% | intergenic (‑75/+54) | PP_0279 ← / ← PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| RA | 353,067 | A→G | 100% | intergenic (+34/+84) | hisF → / ← cbcV | imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein |
| RA | 463,211 | G→A | 6.2% | G63G (GGC→GGT) | davA ← | 5‑aminopentanamidase |
| RA | 499,203 | A→G | 100% | intergenic (+47/‑249) | uhpA → / → PP_0411 | two‑component system response regulator UhpA/polyamine ABC transporter ATP‑binding protein |
| RA | 549,321 | C→T | 6.1% | intergenic (+23/‑5) | fusA → / → tufB | elongation factor G 1/elongation factor Tu‑B |
| RA | 600,757 | C→T | 6.0% | G36G (GGC→GGT) | ribD → | bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase |
| RA | 669,129 | C→T | 11.2% | H191Y (CAC→TAC) | pbpC → | peptidoglycan glycosyltransferase |
| RA | 684,005 | A→G | 7.0% | F748L (TTC→CTC) | cadA‑II ← | cadmium translocating P‑type ATPase |
| RA | 699,722 | A→G | 50.5% | intergenic (+115/‑129) | PP_t06 → / → PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| RA | 751,581 | A→G | 6.2% | L9P (CTA→CCA) | PP_5450 ← | hypothetical protein |
| RA | 774,345 | A→G | 6.0% | M318V (ATG→GTG) | PP_0665 → | glyceraldehyde‑3‑phosphate dehydrogenase |
| RA | 798,664 | T→G | 22.4% | intergenic (+19/+8) | fklB‑I → / ← PP_0685 | FKBP‑type peptidyl‑prolyl cis‑trans isomerase/hypothetical protein |
| RA | 803,429 | C→T | 6.2% | S201L (TCA→TTA) | proB → | glutamate 5‑kinase |
| RA | 938,836 | G→C | 6.3% | A2262A (GCC→GCG) | PP_0806 ← | surface adhesion protein |
| RA | 991,826 | Δ1 bp | 5.3% | coding (448/1464 nt) | der → | GTPase Der |
| RA | 995,741 | G→A | 5.1% | L619F (CTT→TTT) | PP_0860 ← | sulfite reductase flavoprotein subunit |
| RA | 998,257 | T→C | 5.5% | Q621R (CAG→CGG) | PP_0861 ← | outer membrane ferric siderophore receptor |
| RA | 1,070,246:1 | +GA | 100% | intergenic (+46/+96) | aroP‑I → / ← PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| RA | 1,072,332 | A→G | 6.0% | L354P (CTG→CCG) | gatB ← | aspartyl/glutamyl‑tRNA(Asn/Gln) amidotransferase subunit B |
| RA | 1,082,037 | A→G | 6.8% | Q564Q (CAA→CAG) | PP_0938 → | hypothetical protein |
| RA | 1,082,101 | Δ1 bp | 7.1% | coding (1756/3822 nt) | PP_0938 → | hypothetical protein |
| RA | 1,092,790 | C→A | 5.6% | G13C (GGT→TGT) | ptsH ← | phosphocarrier protein HPr |
| RA | 1,100,993 | T→A | 8.2% | I125N (ATC→AAC) | mlaE → | phospholipid ABC transporter permease |
| RA | 1,126,645:1 | +C | 100% | intergenic (‑99/+50) | tdcG‑II ← / ← gcvP‑I | L‑serine dehydratase/glycine dehydrogenase |
| RA | 1,210,421 | A→G | 5.5% | N344D (AAT→GAT) | ytnA → | amino acid permease YtnA |
| RA | 1,245,330 | G→C | 5.4% | A66A (GCC→GCG) | pyrC ← | dihydroorotase |
| RA | 1,274,936 | Δ1 bp | 6.2% | intergenic (‑133/+179) | PP_5462 ← / ← PP_5463 | hypothetical protein/hypothetical protein |
| JC | 1,311,719 | Δ84 bp | 27.6% | intergenic (‑187/+8) | PP_1144 ← / ← rapA | membrane protein/RNA polymerase‑associated protein RapA |
| RA | 1,314,390 | G→A | 7.4% | D89D (GAC→GAT) | rapA ← | RNA polymerase‑associated protein RapA |
| RA | 1,327,121 | C→T | 41.4% | intergenic (+97/‑196) | PP_16SE → / → PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| RA | 1,333,902 | G→A | 6.2% | A76A (GCG→GCA) | PP_1159 → | membrane protein |
| RA | 1,374,006 | T→C | 5.1% | intergenic (‑53/‑375) | PP_1199 ← / → kup | toxin‑antitoxin system HigB‑like toxin/potassium transport system protein Kup |
| RA | 1,419,548:1 | +C | 100% | intergenic (‑37/+99) | PP_1242 ← / ← PP_1244 | hypothetical protein/hypothetical protein |
| RA | 1,474,995 | T→G | 8.4% | intergenic (‑775/+26) | algD ← / ← PP_1289 | GDP‑mannose 6‑dehydrogenase/DUF328 domain‑containing protein |
| RA | 1,474,996 | C→A | 10.2% | intergenic (‑776/+25) | algD ← / ← PP_1289 | GDP‑mannose 6‑dehydrogenase/DUF328 domain‑containing protein |
| RA | 1,499,480 | 2 bp→AC | 100% | intergenic (+57/‑106) | trpS → / → zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| RA | 1,499,498 | 1 bp→CG | 100% | intergenic (+75/‑89) | trpS → / → zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| RA | 1,499,506:1 | +C | 100% | intergenic (+83/‑81) | trpS → / → zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| RA | 1,505,462 | C→A | 6.0% | L192M (CTG→ATG) | petB → | cytochrome b |
| RA | 1,517,656 | C→T | 7.0% | G282G (GGC→GGT) | murE → | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase |
| RA | 1,522,509 | G→C | 5.2% | L139L (CTG→CTC) | ftsW → | lipid II flippase |
| RA | 1,532,783 | T→C | 6.0% | I265T (ATC→ACC) | secA → | protein translocase subunit SecA |
| RA | 1,584,641 | C→T | 9.5% | G125S (GGC→AGC) | PP_1388 ← | EmrB/QacA family drug resistance transporter |
| RA | 1,603,018 | G→A | 8.1% | A289T (GCC→ACC) | PP_5469 → | SAM‑dependent methyltransferase |
| RA | 1,612,476 | G→A | 8.6% | T91T (ACG→ACA) | ung → | uracil‑DNA glycosylase |
| RA | 1,625,208 | A→C | 24.6% | intergenic (+31/+26) | PP_1425 → / ← nadB | hypothetical protein/L‑aspartate oxidase |
| RA | 1,641,813 | C→T | 6.4% | V120V (GTG→GTA) | PP_1442 ← | hypothetical protein |
| RA | 1,646,554 | G→A | 6.1% | A268V (GCC→GTC) | gcd ← | quinoprotein glucose dehydrogenase |
| RA | 1,654,382 | T→C | 7.7% | Q796R (CAG→CGG) | PP_1449 ← | hypothetical protein |
| RA | 1,703,605 | C→T | 6.0% | A96A (GCC→GCT) | PP_1497 → | TetR family transcriptional regulator |
| RA | 1,748,559 | C→T | 5.7% | A37T (GCC→ACC) | PP_1548 ← | hypothetical protein |
| RA | 1,842,575 | Δ2 bp | 100% | coding (2218‑2219/2754 nt) | gacS ← | sensor protein GacS |
| RA | 1,894,618 | C→T | 7.4% | F248F (TTC→TTT) | PP_1699 → | 2‑pyrone‑4,6‑dicarboxylic acid hydrolase |
| RA | 1,932,638:1 | +C | 100% | intergenic (‑105/+45) | rluA ← / ← minE | bifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA/cell division topological specificity factor |
| RA | 1,957,959 | G→A | 5.8% | Q369* (CAA→TAA) | fumC‑II ← | class 2 fumarate hydratase |
| RA | 1,973,451 | Δ1 bp | 6.1% | coding (2380/2772 nt) | gyrA → | DNA gyrase subunit A |
| RA | 1,973,452 | G→T | 6.1% | R794L (CGT→CTT) | gyrA → | DNA gyrase subunit A |
| RA | 2,017,246 | Δ1 bp | 100% | intergenic (‑854/‑1480) | PP_1795 ← / → PP_1797 | hypothetical protein/HlyD family secretion protein |
| RA | 2,060,542 | A→G | 9.3% | S29S (AGT→AGC) | PP_1836 ← | ZIP family metal transporter |
| RA | 2,117,823 | A→C | 6.0% | K500T (AAG→ACG) | PP_1884 → | hypothetical protein |
| RA | 2,154,159 | Δ1 bp | 7.7% | coding (613/615 nt) | PP_1909 ← | septum formation protein |
| RA | 2,274,307 | G→A | 6.6% | S20S (AGC→AGT) | PP_2004 ← | AraC family transcriptional regulator |
| RA | 2,282,770 | T→G | 20.7% | intergenic (‑162/+67) | PP_2010 ← / ← PP_2011 | cytochrome b561/hypothetical protein |
| RA | 2,285,371 | C→T | 7.8% | D208D (GAC→GAT) | PP_2013 → | hypothetical protein |
| RA | 2,285,394 | G→T | 8.0% | R216L (CGC→CTC) | PP_2013 → | hypothetical protein |
| RA | 2,299,989 | T→C | 8.2% | T45A (ACC→GCC) | sbcC ← | exonuclease subunit SbcC |
| RA | 2,337,885 | C→T | 6.5% | L59L (CTG→CTA) | ybhD ← | DNA‑binding transcriptional regulator |
| RA | 2,340,741 | G→T | 6.2% | intergenic (+75/‑40) | dctA‑II → / → yraO | C4‑dicarboxylate transport protein/transporter YraO |
| RA | 2,393,970 | G→T | 7.8% | intergenic (+96/+10) | PP_2097 → / ← dacB | sensory box protein/D‑alanyl‑D‑alanine carboxypeptidase |
| RA | 2,414,621 | T→C | 7.0% | intergenic (+163/‑182) | PP_2114 → / → PP_2115 | transposase/hypothetical protein |
| RA | 2,661,290 | C→T | 6.1% | A36V (GCC→GTC) | PP_2333 → | GntR family transcriptional regulator |
| RA | 2,747,879 | G→A | 6.9% | S209S (AGC→AGT) | PP_2403 ← | chemotaxis protein CheY |
| RA | 2,852,015 | A→G | 6.4% | I149V (ATT→GTT) | PP_5531 → | hypothetical protein |
| RA | 2,855,358 | C→T | 5.8% | V10I (GTC→ATC) | PP_5532 ← | hypothetical protein |
| RA | 2,864,833 | T→C | 6.1% | S184G (AGC→GGC) | gllP ← | porin‑like protein |
| RA | 2,933,074 | T→A | 6.7% | D343V (GAC→GTC) | PP_2566 ← | leucine‑rich repeat‑containing protein |
| RA | 2,951,342 | G→T | 12.6% | intergenic (‑121/+40) | oguA ← / ← PP_2585 | 8‑oxoguanine deaminase/alpha‑ketoglutaric semialdehyde dehydrogenase |
| RA | 2,951,349 | G→C | 17.3% | intergenic (‑128/+33) | oguA ← / ← PP_2585 | 8‑oxoguanine deaminase/alpha‑ketoglutaric semialdehyde dehydrogenase |
| JC | 2,957,081 | Δ84 bp | 47.2% | intergenic (+36/‑77) | PP_2588 → / → PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| RA | 2,958,523 | C→T | 100% | A428V (GCA→GTA) | PP_2589 → | aldehyde dehydrogenase family protein |
| JC | 2,958,780 | Δ61 bp | 22.1% | intergenic (+46/+36) | PP_2589 → / ← PP_2590 | aldehyde dehydrogenase family protein/ferric siderophore receptor |
| RA | 3,045,983 | G→T | 7.8% | G187V (GGC→GTC) | pstA → | phosphate ABC transporter permease |
| RA | 3,060,264 | G→A | 6.8% | R90H (CGC→CAC) | exaE → | transcriptional regulator ExaE |
| RA | 3,101,819 | C→T | 6.4% | C151C (TGC→TGT) | PP_2711 → | short‑chain dehydrogenase/reductase family oxidoreductase |
| RA | 3,133,531 | G→A | 6.2% | G243R (GGG→AGG) | PP_2750 → | branched‑chain amino acid ABC transporter permease |
| RA | 3,136,741 | T→C | 6.8% | intergenic (+59/‑58) | PP_2752 → / → PP_2753 | hypothetical protein/ABC transporter ATP‑binding protein |
| RA | 3,152,278 | G→C | 34.5% | A145P (GCA→CCA) | PP_2768 → | branched‑chain amino acid ABC transporter permease |
| RA | 3,209,304 | G→A | 7.0% | G176G (GGG→GGA) | PP_2813 → | BNR domain‑containing protein |
| RA | 3,228,097 | Δ1 bp | 10.5% | coding (936/1386 nt) | PP_2828 → | hypothetical protein |
| RA | 3,228,098 | Δ1 bp | 10.5% | coding (937/1386 nt) | PP_2828 → | hypothetical protein |
| RA | 3,320,242 | T→G | 6.3% | intergenic (‑97/‑24) | PP_2919 ← / → ybgL | LysR family transcriptional regulator/nitrogen‑containing compound degradation protein |
| RA | 3,336,459 | T→C | 5.5% | Q46R (CAG→CGG) | yghU ← | GSH‑dependent disulfide bond oxidoreductase |
| RA | 3,411,674 | G→A | 5.6% | R63H (CGC→CAC) | PP_5551 → | hypothetical protein |
| RA | 3,412,399 | A→G | 5.5% | D142D (GAT→GAC) | PP_3025 ← | LysE family transporter |
| RA | 3,421,049 | A→T | 6.9% | H26L (CAC→CTC) | PP_3036 → | hypothetical protein |
| RA | 3,478,682 | T→C | 5.6% | intergenic (‑79/+41) | PP_3089 ← / ← PP_3090 | hypothetical protein/OmpA domain‑containing protein |
| RA | 3,535,857 | C→T | 7.1% | I330I (ATC→ATT) | PP_3124 → | short chain fatty acid transporter |
| RA | 3,552,540 | C→T | 7.3% | A66V (GCA→GTA) | PP_3137 → | group 2 family glycosyl transferase |
| RA | 3,567,151 | T→A | 6.4% | W252R (TGG→AGG) | PP_3149 → | AraC family transcriptional regulator |
| RA | 3,578,282 | G→A | 6.6% | A233T (GCG→ACG) | PP_3158 → | hypothetical protein |
| RA | 3,611,147 | A→T | 10.3% | V846E (GTG→GAG) | mcoA ← | Mn(II) copper oxidase A |
| RA | 3,725,792 | G→A | 7.0% | A149T (GCC→ACC) | PP_3291 → | metallo‑beta‑lactamase family protein |
| RA | 3,759,812 | G→A | 7.0% | G149S (GGC→AGC) | folEB → | GTP cyclohydrolase I |
| RA | 3,785,022 | G→A | 6.2% | A73T (GCC→ACC) | PP_3348 → | GGDEF domain‑containing protein |
| RA | 3,845,703:1 | +G | 100% | intergenic (‑70/+28) | PP_3394 ← / ← PP_3395 | 3‑hydroxy‑3‑methylglutaryl‑CoA lyase/LysR family transcriptional regulator |
| RA | 3,894,752 | T→C | 6.2% | M103V (ATG→GTG) | yegH ← | putative transporter |
| RA | 3,951,159 | T→C | 100% | intergenic (‑123/+72) | PP_3486 ← / ← PP_3487 | cytochrome c/hypothetical protein |
| RA | 3,951,161 | A→T | 100% | intergenic (‑125/+70) | PP_3486 ← / ← PP_3487 | cytochrome c/hypothetical protein |
| RA | 4,091,956 | A→G | 5.2% | I189V (ATC→GTC) | garD → | galactarate dehydratase |
| RA | 4,110,684 | G→A | 6.3% | D836N (GAC→AAC) | PP_3616 → | membrane protein |
| RA | 4,116,786 | C→T | 8.7% | intergenic (‑201/‑70) | ycaO ← / → iorA‑II | ribosomal protein S12 methylthiotransferase accessory factor/isoquinoline 1‑oxidoreductase subunit alpha |
| RA | 4,158,466 | T→G | 38.6% | L159R (CTG→CGG) | PP_3661 → | membrane protein |
| RA | 4,158,471 | A→C | 38.3% | S161R (AGC→CGC) | PP_3661 → | membrane protein |
| RA | 4,174,550 | C→A | 6.1% | intergenic (‑772/‑770) | PP_3672 ← / → PP_3676 | hypothetical protein/hypothetical protein |
| RA | 4,252,194 | C→A | 7.2% | intergenic (‑162/+78) | PP_3726 ← / ← rocE | enoyl‑CoA hydratase/isomerase family protein/amino acid permease RocE |
| RA | 4,252,197 | A→G | 5.6% | intergenic (‑165/+75) | PP_3726 ← / ← rocE | enoyl‑CoA hydratase/isomerase family protein/amino acid permease RocE |
| RA | 4,252,202 | G→C | 5.8% | intergenic (‑170/+70) | PP_3726 ← / ← rocE | enoyl‑CoA hydratase/isomerase family protein/amino acid permease RocE |
| RA | 4,252,205 | G→C | 5.8% | intergenic (‑173/+67) | PP_3726 ← / ← rocE | enoyl‑CoA hydratase/isomerase family protein/amino acid permease RocE |
| RA | 4,252,210 | C→T | 6.1% | intergenic (‑178/+62) | PP_3726 ← / ← rocE | enoyl‑CoA hydratase/isomerase family protein/amino acid permease RocE |
| RA | 4,252,213 | T→G | 5.9% | intergenic (‑181/+59) | PP_3726 ← / ← rocE | enoyl‑CoA hydratase/isomerase family protein/amino acid permease RocE |
| MC JC | 4,274,119 | 32 bp→45 bp | 100% | intergenic (‑243/‑1) | glcC ← / → glcD | transcriptional regulator GlcC/glycolate oxidase FAD‑linked subunit |
| RA | 4,348,812 | A→G | 52.3% | intergenic (‑70/+404) | PP_3820 ← / ← galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| RA | 4,377,641 | T→A | 6.1% | K13M (AAG→ATG) | PP_3852 ← | BNR domain‑containing protein |
| RA | 4,428,432 | C→T | 7.0% | S147S (TCG→TCA) | sohB ← | peptidase |
| RA | 4,432,704 | C→T | 7.0% | A110T (GCC→ACC) | PP_3927 ← | type 12 methyltransferase |
| RA | 4,504,971 | C→T | 6.9% | S88L (TCG→TTG) | PP_3995 → | hypothetical protein |
| RA | 4,586,137 | 2 bp→TC | 100% | intergenic (+113/+101) | PP_4061 → / ← PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| RA | 4,586,140:1 | +G | 100% | intergenic (+116/+99) | PP_4061 → / ← PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| RA | 4,586,163:1 | +C | 100% | intergenic (+139/+76) | PP_4061 → / ← PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| RA | 4,636,025 | C→T | 7.0% | L97L (TTG→TTA) | PP_4100 ← | Cro/CI family transcriptional regulator |
| RA | 4,674,436 | C→A | 6.3% | R367R (CGC→CGA) | PP_4137 → | outer membrane siderophore receptor |
| RA | 4,680,824 | T→C | 8.8% | D19G (GAC→GGC) | PP_4143 ← | hypothetical protein |
| RA | 4,697,676 | T→A | 6.1% | T156T (ACA→ACT) | kdpE ← | two‑component system DNA‑binding response regulator KdpE |
| RA | 4,740,912 | Δ1 bp | 100% | intergenic (+42/+711) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,740,923 | T→G | 100% | intergenic (+53/+700) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,740,926 | 2 bp→CT | 100% | intergenic (+56/+696) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,740,948 | T→A | 20.3% | intergenic (+78/+675) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,336 | A→C | 100% | intergenic (+466/+287) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,338 | C→G | 100% | intergenic (+468/+285) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,341 | C→T | 100% | intergenic (+471/+282) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,343 | 2 bp→TG | 100% | intergenic (+473/+279) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,346 | A→G | 100% | intergenic (+476/+277) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,350 | 3 bp→TGC | 100% | intergenic (+480/+271) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,362 | C→T | 100% | intergenic (+492/+261) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,364 | A→C | 100% | intergenic (+494/+259) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,367 | 2 bp→GC | 100% | intergenic (+497/+255) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,370 | A→C | 100% | intergenic (+500/+253) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,379 | A→G | 100% | intergenic (+509/+244) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,381 | A→C | 100% | intergenic (+511/+242) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,383 | G→C | 100% | intergenic (+513/+240) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,385 | C→T | 100% | intergenic (+515/+238) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,390:1 | +T | 100% | intergenic (+520/+233) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,396 | C→G | 100% | intergenic (+526/+227) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,399 | C→T | 100% | intergenic (+529/+224) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,401 | C→G | 100% | intergenic (+531/+222) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,403 | A→C | 100% | intergenic (+533/+220) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,405 | C→T | 100% | intergenic (+535/+218) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,767,982 | A→T | 100% | intergenic (+89/‑93) | fpvA → / → tpaK | TonB‑dependent outer membrane ferripyoverdine receptor FpvA/probable terephthalate transporter, MFS superfamily protein |
| RA | 4,767,984 | T→G | 100% | intergenic (+91/‑91) | fpvA → / → tpaK | TonB‑dependent outer membrane ferripyoverdine receptor FpvA/probable terephthalate transporter, MFS superfamily protein |
| RA | 4,768,005 | T→A | 100% | intergenic (+112/‑70) | fpvA → / → tpaK | TonB‑dependent outer membrane ferripyoverdine receptor FpvA/probable terephthalate transporter, MFS superfamily protein |
| RA | 4,768,667 | G→A | 6.0% | R198H (CGC→CAC) | tpaK → | probable terephthalate transporter, MFS superfamily protein |
| RA | 4,806,266 | G→C | 7.6% | L169V (CTC→GTC) | PP_4233 ← | oxidoreductase small subunit |
| RA | 4,865,420 | Δ1 bp | 5.4% | coding (2156/3489 nt) | smc ← | chromosome partition protein Smc |
| RA | 4,865,421 | Δ1 bp | 5.5% | coding (2155/3489 nt) | smc ← | chromosome partition protein Smc |
| MC JC | 4,875,480 | Δ756 bp | 100% | coding (1‑756/756 nt) | PP_4283 ← | GntR family transcriptional regulator |
| RA | 4,887,735 | Δ1 bp | 7.5% | coding (523/612 nt) | PP_4295 → | TetR family transcriptional regulator |
| RA | 4,946,920 | C→T | 30.2% | intergenic (+577/+221) | PP_5673 → / ← flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein |
| RA | 4,946,923 | G→A | 33.3% | intergenic (+580/+218) | PP_5673 → / ← flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein |
| RA | 4,946,925 | T→C | 33.3% | intergenic (+582/+216) | PP_5673 → / ← flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein |
| RA | 4,946,935 | A→G | 30.1% | intergenic (+592/+206) | PP_5673 → / ← flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein |
| RA | 4,946,950 | G→A | 30.9% | intergenic (+607/+191) | PP_5673 → / ← flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein |
| RA | 4,946,968 | A→G | 32.4% | intergenic (+625/+173) | PP_5673 → / ← flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein |
| RA | 4,952,229 | T→C | 9.5% | N109D (AAC→GAC) | fliL ← | flagellar protein FliL |
| JC | 4,982,288 | +GGC | 100% | intergenic (‑24/+44) | PP_4387 ← / ← flgE | hypothetical protein/flagellar hook protein FlgE |
| RA | 5,109,824 | G→A | 7.1% | intergenic (‑10/‑143) | ydiJ ← / → PP_4494 | putative oxidoreductase/LysR family transcriptional regulator |
| RA | 5,120,308 | G→A | 6.3% | G127S (GGC→AGC) | PP_4505 → | sensor histidine kinase |
| RA | 5,123,536 | A→C | 23.2% | L306R (CTG→CGG) | PP_4508 ← | AraC family transcriptional regulator |
| RA | 5,196,590 | T→G | 20.3% | intergenic (+29/+24) | PP_4574 → / ← PP_4575 | hypothetical protein/urea amidolyase‑like protein |
| RA | 5,197,824 | A→C | 6.4% | F132V (TTC→GTC) | ybgJ ← | allophanate hydrolase subunit 1 |
| RA | 5,205,935 | C→A | 6.6% | L13I (CTC→ATC) | yajD → | endonuclease |
| RA | 5,222,479 | A→G | 6.8% | intergenic (‑43/‑99) | moaB‑II ← / → PP_4601 | molybdenum cofactor biosynthesis protein B/LysR family transcriptional regulator |
| RA | 5,235,605 | T→A | 6.6% | L86Q (CTG→CAG) | PP_4612 → | fec operon regulator FecR |
| JC | 5,290,103 | Δ142 bp | 12.7% | [mdaB] | [mdaB] | |
| RA | 5,339,756 | C→G | 9.4% | intergenic (+60/‑224) | PP_4696 → / → PP_mr53 | nitrogen regulation protein NR(I)/CrcZ ncRNA |
| RA | 5,377,973 | T→C | 6.1% | N432S (AAC→AGC) | dnaK ← | chaperone protein DnaK |
| RA | 5,379,654 | A→G | 5.2% | D91D (GAT→GAC) | grpE ← | heat shock protein GrpE |
| RA | 5,396,064 | A→G | 100% | V231A (GTA→GCA) | tphBII ← | 4‑hydroxythreonine‑4‑phosphate dehydrogenase |
| RA | 5,462,375 | T→G | 18.9% | intergenic (+18/‑22) | PP_4795 → / → holA | lipoprotein/DNA polymerase III subunit delta |
| RA | 5,512,711 | A→C | 37.6% | Q32P (CAG→CCG) | urtB → | urea ABC transporter permease |
| RA | 5,512,720 | T→G | 29.7% | L35R (CTG→CGG) | urtB → | urea ABC transporter permease |
| RA | 5,512,723 | T→G | 43.5% | L36R (CTC→CGC) | urtB → | urea ABC transporter permease |
| JC | 5,558,423 | +GCC | 100% | intergenic (‑84/+87) | PP_4887 ← / ← PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| RA | 5,677,565:1 | +G | 100% | intergenic (+112/+28) | rhlE‑II → / ← yceI | ATP‑dependent RNA helicase/polyisoprene‑binding acidic stress response factor |
| RA | 5,677,568 | G→C | 100% | intergenic (+115/+25) | rhlE‑II → / ← yceI | ATP‑dependent RNA helicase/polyisoprene‑binding acidic stress response factor |
| JC | 5,684,230 | +CGGG | 87.8% | intergenic (‑133/+71) | PP_4986 ← / ← PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| RA | 5,684,514 | C→T | 6.9% | A87A (GCG→GCA) | PP_4987 ← | putative Chemotaxis protein |
| RA | 5,703,946 | C→T | 7.8% | P537S (CCG→TCG) | phaA → | poly(3‑hydroxyalkanoate) polymerase |
| RA | 5,754,540 | A→G | 17.9% | intergenic (‑163/‑308) | thiI ← / → glnA | tRNA sulfurtransferase/glutamine synthetase |
| RA | 5,754,544 | G→T | 12.8% | intergenic (‑167/‑304) | thiI ← / → glnA | tRNA sulfurtransferase/glutamine synthetase |
| RA | 5,754,545 | G→T | 12.9% | intergenic (‑168/‑303) | thiI ← / → glnA | tRNA sulfurtransferase/glutamine synthetase |
| RA | 5,754,550 | A→C | 10.6% | intergenic (‑173/‑298) | thiI ← / → glnA | tRNA sulfurtransferase/glutamine synthetase |
| RA | 5,754,551 | A→C | 13.1% | intergenic (‑174/‑297) | thiI ← / → glnA | tRNA sulfurtransferase/glutamine synthetase |
| RA | 5,754,561 | A→C | 25.2% | intergenic (‑184/‑287) | thiI ← / → glnA | tRNA sulfurtransferase/glutamine synthetase |
| RA | 5,769,028 | A→G | 5.7% | I1553I (ATT→ATC) | PP_5060 ← | hypothetical protein |
| RA | 5,822,142 | C→T | 6.4% | T199M (ACG→ATG) | proI → | pyrroline‑5‑carboxylate reductase |
| RA | 5,829,091 | C→T | 8.3% | D7N (GAC→AAC) | thiG ← | thiazole synthase |
| RA | 5,888,983 | C→T | 7.8% | G283D (GGC→GAC) | PP_5161 ← | lysophospholipase |
| RA | 5,902,160 | C→T | 6.5% | G515R (GGG→AGG) | PP_5173 ← | RND family transporter |
| RA | 5,903,171 | T→C | 5.4% | K178E (AAG→GAG) | PP_5173 ← | RND family transporter |
| RA | 5,991,726 | Δ1 bp | 13.3% | intergenic (+205/‑341) | kefB‑III → / → PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| RA | 6,016,700 | T→C | 100% | intergenic (+90/+20) | xpt → / ← PP_5266 | xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein |
| RA | 6,032,527 | A→G | 5.0% | Y19C (TAC→TGC) | PP_5279 → | hypothetical protein |
| RA | 6,141,022 | A→T | 6.7% | D221V (GAT→GTT) | czcC → | CzcC family metal RND transporter outer membrane protein |
| RA | 6,160,557 | G→A | 6.6% | V36M (GTG→ATG) | PP_5401 → | hypothetical protein |
| RA | 6,178,303 | T→C | 5.4% | K370R (AAG→AGG) | atpD ← | ATP synthase subunit beta |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_002947_CJ‑RC | 171361–172965 | 176317–172967 | 3–4957 | 26 [25] | [25] 26 | PP_16SA–[PP_5SA] | PP_16SA,PP_23SA,[PP_5SA] |
| * | * | ÷ | NC_002947_CJ‑RC | 176652–178395 | 181709–178397 | 3–5058 | 26 [25] | [23] 26 | PP_16SB–[PP_r01] | PP_16SB,PP_23SB,[PP_r01] |
| * | * | ÷ | NC_002947_CJ‑RC | 5399905 | 5407332 | 7428 | 41 [2] | [4] 38 | [hsdS]–[PP_4748] | [hsdS],PP_5711,PP_4743,PP_4745,PP_4746,[PP_4748] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 278744 | 9 (0.160) | 7 (0.140) | 6/250 | NT | 40.9% | intergenic (‑239/+75) | PP_0224/sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein |
| ? | NC_002947_CJ‑RC | = 278792 | 12 (0.230) | intergenic (‑287/+27) | PP_0224/sctC | DszC family monooxygenase/sulfur compound ABC transporter ATP‑binding protein | |||||
| * | ? | NC_002947_CJ‑RC | = 353066 | 6 (0.110) | 3 (0.060) | 3/260 | NT | 19.5% | intergenic (+33/+85) | hisF/cbcV | imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein |
| ? | NC_002947_CJ‑RC | = 6011988 | 19 (0.350) | intergenic (+70/+12) | norM/PP_5263 | multidrug resistance protein NorM/GGDEF domain‑containing protein | |||||
| * | ? | NC_002947_CJ‑RC | 533510 = | NA (NA) | 3 (0.060) | 3/246 | NT | 6.9% | coding (775/1194 nt) | tufA | elongation factor Tu‑A |
| ? | NC_002947_CJ‑RC | = 533506 | 45 (0.800) | coding (771/1194 nt) | tufA | elongation factor Tu‑A | |||||
| * | ? | NC_002947_CJ‑RC | 1149928 = | 41 (0.730) | 4 (0.080) | 3/248 | NT | 11.1% | intergenic (‑175/+82) | PP_1008/gapA | RNA polymerase subunit sigma‑24/glyceraldehyde‑3‑phosphate dehydrogenase |
| ? | NC_002947_CJ‑RC | 1149989 = | 27 (0.530) | intergenic (‑236/+21) | PP_1008/gapA | RNA polymerase subunit sigma‑24/glyceraldehyde‑3‑phosphate dehydrogenase | |||||
| * | ? | NC_002947_CJ‑RC | = 1254517 | 52 (0.920) | 4 (0.070) | 4/258 | NT | 7.2% | coding (984/2040 nt) | metG | methionine‑‑tRNA ligase |
| ? | NC_002947_CJ‑RC | = 1254566 | 54 (1.010) | coding (935/2040 nt) | metG | methionine‑‑tRNA ligase | |||||
| * | ? | NC_002947_CJ‑RC | 1309845 = | 54 (0.960) | 3 (0.050) | 3/266 | NT | 5.5% | coding (1688/2265 nt) | PP_1144 | membrane protein |
| ? | NC_002947_CJ‑RC | 1309946 = | 51 (0.930) | coding (1587/2265 nt) | PP_1144 | membrane protein | |||||
| * | ? | NC_002947_CJ‑RC | 2314199 = | 52 (0.920) | 4 (0.070) | 4/258 | NT | 7.5% | intergenic (‑112/+38) | benE‑I/PP_2036 | benzoate transport protein/4‑hydroxy‑tetrahydrodipicolinate synthase |
| ? | NC_002947_CJ‑RC | 2314228 = | 49 (0.920) | intergenic (‑141/+9) | benE‑I/PP_2036 | benzoate transport protein/4‑hydroxy‑tetrahydrodipicolinate synthase | |||||
| * | ? | NC_002947_CJ‑RC | = 3343823 | 51 (0.910) | 3 (0.050) | 3/264 | NT | 5.9% | coding (226/330 nt) | PP_5541 | hypothetical protein |
| ? | NC_002947_CJ‑RC | = 3343856 | 46 (0.840) | coding (259/330 nt) | PP_5541 | hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 3522716 | 34 (0.600) | 3 (0.060) | 3/242 | NT | 8.7% | intergenic (+503/‑194) | PP_5584/PP_3113 | hypothetical protein/transposase |
| ? | NC_002947_CJ‑RC | = 3522773 | 33 (0.660) | intergenic (+560/‑137) | PP_5584/PP_3113 | hypothetical protein/transposase | |||||
| * | ? | NC_002947_CJ‑RC | 3712397 = | 56 (0.990) | 3 (0.060) | 3/260 | NT | 5.6% | coding (599/990 nt) | paaA | ring 1,2‑phenylacetyl‑CoA epoxidase subunit alpha |
| ? | NC_002947_CJ‑RC | 3712438 = | 48 (0.890) | coding (558/990 nt) | paaA | ring 1,2‑phenylacetyl‑CoA epoxidase subunit alpha | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 0 (0.000) | 12 (0.290) | 9/202 | NT | 42.1% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 33 (0.790) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 0 (0.000) | 13 (0.260) +CGGCGCTTCGCGG |
6/246 | NT | 49.0% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 4946919 = | 30 (0.530) | intergenic (+576/+222) | PP_5673/flhB | D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5002237 | 55 (0.980) | 3 (0.060) | 3/258 | NT | 5.1% | intergenic (+4/‑1682) | PP_4407/PP_4409 | gamma‑aminobutyrate transporter/site‑specific recombinase |
| ? | NC_002947_CJ‑RC | = 5002254 | 59 (1.110) | intergenic (+21/‑1665) | PP_4407/PP_4409 | gamma‑aminobutyrate transporter/site‑specific recombinase | |||||
| * | ? | NC_002947_CJ‑RC | 5114262 = | 33 (0.590) | 3 (0.060) | 3/228 | NT | 11.9% | intergenic (‑148/+118) | rluB/PP_4497 | 23S rRNA pseudouridylate synthase B/hypothetical protein |
| ? | NC_002947_CJ‑RC | 5114367 = | 17 (0.360) | intergenic (‑253/+13) | rluB/PP_4497 | 23S rRNA pseudouridylate synthase B/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5398627 | 54 (0.960) | 31 (0.550) | 29/270 | NT | 51.8% | coding (38/1218 nt) | hsdM | type I restriction modification system methylase |
| ? | NC_002947_CJ‑RC | 5407333 = | 4 (0.070) | coding (702/801 nt) | PP_4748 | amino acid ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5399904 | 2 (0.040) | 35 (0.620) | 31/272 | NT | 72.2% | coding (101/1731 nt) | hsdS | type I restriction modification system specificity protein |
| ? | NC_002947_CJ‑RC | 5412150 = | 25 (0.440) | coding (1541/2037 nt) | stcD | N‑methylproline demethylase | |||||
| * | ? | NC_002947_CJ‑RC | = 5655773 | 5 (0.090) | 3 (0.060) | 3/230 | NT | 29.7% | intergenic (‑59/+102) | PP_4961/PP_4962 | lipoprotein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 5655787 | 10 (0.210) | intergenic (‑73/+88) | PP_4961/PP_4962 | lipoprotein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5672241 | 56 (0.990) | 3 (0.060) | 3/244 | NT | 5.8% | intergenic (+27/‑98) | ahcY/metF | adenosylhomocysteinase/5,10‑methylenetetrahydrofolate reductase |
| ? | NC_002947_CJ‑RC | = 5672262 | 47 (0.930) | intergenic (+48/‑77) | ahcY/metF | adenosylhomocysteinase/5,10‑methylenetetrahydrofolate reductase | |||||
| * | ? | NC_002947_CJ‑RC | = 6022085 | 5 (0.090) | 4 (0.090) | 4/226 | NT | 34.6% | intergenic (‑71/+74) | dadX/dadA‑II | alanine racemase/D‑amino acid:quinone oxidoreductase |
| ? | NC_002947_CJ‑RC | = 6022115 | 11 (0.240) | intergenic (‑101/+44) | dadX/dadA‑II | alanine racemase/D‑amino acid:quinone oxidoreductase | |||||
| * | ? | NC_002947_CJ‑RC | 6103836 = | 62 (1.100) | 3 (0.050) | 3/272 | NT | 5.0% | coding (173/2187 nt) | uvrD | DNA‑dependent ATPase I/helicase II |
| ? | NC_002947_CJ‑RC | 6103899 = | 52 (0.920) | coding (236/2187 nt) | uvrD | DNA‑dependent ATPase I/helicase II | |||||