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 | 68,532 | T→C | 5.7% | G247G (GGA→GGG) | PP_0058 ← | 1‑acyl‑sn‑glycerol‑3‑phosphate acyltransferase |
| RA | 117,271 | A→T | 28.5% | intergenic (+51/+43) | PP_0111 → / ← metQ | electron transport protein SCO1/SenC/methionine ABC transporter substrate‑binding protein |
| RA | 152,348 | C→T | 6.4% | G420D (GGC→GAC) | PP_0144 ← | insulinase family metalloprotease |
| RA | 181,805 | T→C | 5.5% | intergenic (+19/‑87) | PP_r01 → / → PP_5SB | 5S ribosomal RNA/5S ribosomal RNA |
| RA | 181,811 | C→T | 5.2% | intergenic (+25/‑81) | PP_r01 → / → PP_5SB | 5S ribosomal RNA/5S ribosomal RNA |
| RA | 181,812 | A→G | 5.2% | intergenic (+26/‑80) | PP_r01 → / → PP_5SB | 5S ribosomal RNA/5S ribosomal RNA |
| RA | 181,818 | G→A | 5.3% | intergenic (+32/‑74) | PP_r01 → / → PP_5SB | 5S ribosomal RNA/5S ribosomal RNA |
| RA | 182,035 | A→T | 8.7% | intergenic (+24/+41) | PP_5SB → / ← PP_0160 | 5S ribosomal RNA/ferrioxamine receptor |
| RA | 182,036 | T→C | 9.5% | intergenic (+25/+40) | PP_5SB → / ← PP_0160 | 5S ribosomal RNA/ferrioxamine receptor |
| RA | 195,559 | C→A | 25.2% | T355T (ACC→ACA) | PP_0168 → | putative surface adhesion protein |
| RA | 195,628 | C→T | 9.6% | D378D (GAC→GAT) | PP_0168 → | putative surface adhesion protein |
| RA | 195,629 | A→G | 9.7% | T379A (ACC→GCC) | PP_0168 → | putative surface adhesion protein |
| RA | 195,634 | C→T | 40.8% | T380T (ACC→ACT) | PP_0168 → | putative surface adhesion protein |
| RA | 196,306 | T→C | 25.0% | N604N (AAT→AAC) | PP_0168 → | putative surface adhesion protein |
| RA | 196,327 | A→C | 26.7% | T611T (ACA→ACC) | PP_0168 → | putative surface adhesion protein |
| RA | 196,351 | C→G | 29.2% | T619T (ACC→ACG) | PP_0168 → | putative surface adhesion protein |
| RA | 196,390 | T→C | 31.7% | D632D (GAT→GAC) | PP_0168 → | putative surface adhesion protein |
| RA | 197,089 | T→C | 13.5% | N865N (AAT→AAC) | PP_0168 → | putative surface adhesion protein |
| RA | 197,551 | C→G | 11.7% | T1019T (ACC→ACG) | PP_0168 → | putative surface adhesion protein |
| RA | 197,572 | G→A | 20.0% | K1026K (AAG→AAA) | PP_0168 → | putative surface adhesion protein |
| RA | 197,590 | T→C | 21.8% | D1032D (GAT→GAC) | PP_0168 → | putative surface adhesion protein |
| RA | 197,632 | T→C | 15.6% | T1046T (ACT→ACC) | PP_0168 → | putative surface adhesion protein |
| RA | 197,695 | G→C | 15.6% | T1067T (ACG→ACC) | PP_0168 → | putative surface adhesion protein |
| RA | 278,742:1 | +A | 100% | 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 | 346,486 | G→A | 6.0% | R454C (CGC→TGC) | PP_0287 ← | hypothetical protein |
| 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 | 441,313 | A→C | 22.4% | E65A (GAG→GCG) | bioF → | 8‑amino‑7‑oxononanoate synthase |
| 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 | 549,164 | C→T | 100% | L672F (CTC→TTC) | fusA → | elongation factor G 1 |
| RA | 556,678 | G→A | 6.3% | D94N (GAC→AAC) | rplE → | 50S ribosomal protein L5 |
| RA | 568,446 | G→A | 5.5% | S350S (AGC→AGT) | uvrA ← | uvrABC excinuclease protein A |
| RA | 578,118 | C→T | 5.9% | I29I (ATC→ATT) | fdoH → | formate dehydrogenase‑O subunit beta |
| RA | 653,752 | C→T | 5.8% | G331R (GGA→AGA) | ctpL ← | methyl‑accepting chemotaxis protein CtpL |
| RA | 669,264 | T→A | 7.1% | W236R (TGG→AGG) | pbpC → | peptidoglycan glycosyltransferase |
| RA | 699,722 | A→G | 51.9% | intergenic (+115/‑129) | PP_t06 → / → PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| RA | 759,811 | A→G | 5.8% | intergenic (+123/‑51) | PP_mr12 → / → PP_5453 | C4 ncRNA/hypothetical protein |
| RA | 777,159 | T→C | 6.3% | L70P (CTG→CCG) | PP_0669 → | ferric siderophore receptor |
| RA | 811,064 | G→C | 5.4% | V82V (GTG→GTC) | PP_5455 → | hypothetical protein |
| RA | 837,327 | A→G | 7.1% | L10P (CTG→CCG) | ychF ← | ribosome‑associated potassium‑dependent ATP/GTPase |
| RA | 1,032,274 | T→A | 8.2% | F123Y (TTC→TAC) | PP_0889 → | hypothetical protein |
| RA | 1,126,645:1 | +C | 100% | intergenic (‑99/+50) | tdcG‑II ← / ← gcvP‑I | L‑serine dehydratase/glycine dehydrogenase |
| RA | 1,155,012 | G→A | 8.0% | S57N (AGC→AAC) | PP_1013 → | sensor histidine kinase |
| RA | 1,327,121 | C→T | 55.9% | intergenic (+97/‑196) | PP_16SE → / → PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| RA | 1,419,548:1 | +C | 100% | intergenic (‑37/+99) | PP_1242 ← / ← PP_1244 | hypothetical protein/hypothetical protein |
| RA | 1,429,310 | C→T | 7.3% | P471S (CCG→TCG) | mqo‑II → | malate:quinone oxidoreductase |
| RA | 1,456,328 | C→A | 5.7% | A219S (GCC→TCC) | PP_1274 ← | short‑chain dehydrogenase/reductase family oxidoreductase |
| RA | 1,474,995 | T→G | 9.5% | intergenic (‑775/+26) | 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 | 1,536,064 | A→G | 7.0% | Y358C (TAT→TGT) | argJ → | glutamate N‑acetyltransferase/amino acid acetyltransferase |
| RA | 1,649,745 | Δ1 bp | 7.1% | coding (1315/2043 nt) | PP_1446 ← | TonB‑dependent receptor |
| RA | 1,671,666 | G→A | 6.0% | A408V (GCC→GTC) | PP_1467 ← | NhaP‑type Na+(K+)/H+ antiporter |
| RA | 1,691,786 | T→G | 9.7% | intergenic (+53/‑118) | PP_1487 → / → PP_1488 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| RA | 1,691,796 | C→G | 6.8% | intergenic (+63/‑108) | PP_1487 → / → PP_1488 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| RA | 1,702,572 | C→T | 5.8% | Y308Y (TAC→TAT) | lysS → | lysine‑‑tRNA ligase |
| RA | 1,732,209 | A→G | 6.7% | F554S (TTC→TCC) | PP_1526 ← | beta‑(1‑3)‑glucosyl transferase |
| RA | 1,747,351 | T→G | 27.6% | E53A (GAG→GCG) | PP_5473 ← | LuxR family transcriptional regulator |
| JC | 1,780,067 | Δ62 bp | 63.7% | intergenic (+26/+19) | PP_1587 → / ← dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| RA | 1,905,088 | G→A | 6.9% | S448N (AGC→AAC) | nirB → | nitrite reductase large subunit |
| RA | 1,926,122 | A→T | 7.8% | R248R (CGT→CGA) | PP_1726 ← | ABC transporter substrate‑binding protein |
| 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 | 1,960,112 | C→G | 13.1% | intergenic (+63/‑65) | bolA → / → PP_1758 | DNA‑binding transcriptional dual regulator/rhodanese‑like domain‑containing sulfurtransferase |
| RA | 1,993,604 | A→C | 14.0% | intergenic (+42/+56) | PP_1780 → / ← PP_1781 | mannosyltransferase/acyltransferase |
| RA | 2,100,946 | T→C | 5.8% | Y285H (TAC→CAC) | PP_1876 → | AAA family ATP/GTP‑binding protein |
| RA | 2,101,751 | A→C | 24.6% | L186R (CTG→CGG) | PP_1878 ← | hypothetical protein |
| RA | 2,162,508 | A→G | 6.9% | intergenic (+190/‑632) | yceG → / → PP_5482 | septation protein/hypothetical protein |
| RA | 2,200,607 | G→A | 6.3% | V61M (GTG→ATG) | folD‑I → | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| RA | 2,278,653 | G→C | 5.7% | intergenic (‑74/‑208) | PP_2007 ← / → fadH | P‑47‑like protein/2,4‑dienoyl‑CoA reductase |
| JC | 2,282,749 | Δ66 bp | 23.1% | intergenic (‑141/+23) | PP_2010 ← / ← PP_2011 | cytochrome b561/hypothetical protein |
| RA | 2,291,752 | T→C | 5.5% | I49I (ATT→ATC) | PP_2019 → | RND family multidrug transporter |
| RA | 2,300,593 | A→G | 5.5% | I255T (ATC→ACC) | sbcD ← | exonuclease subunit SbcD |
| RA | 2,300,653 | A→G | 5.5% | V235A (GTC→GCC) | sbcD ← | exonuclease subunit SbcD |
| RA | 2,355,186 | G→T | 9.0% | A275A (GCC→GCA) | PP_2069 ← | multidrug MFS transporter outer membrane protein |
| RA | 2,535,685 | T→C | 8.7% | K33R (AAG→AGG) | mrpD ← | K(+)/H(+) antiporter subunit D |
| RA | 2,720,828 | G→A | 6.6% | L71F (CTC→TTC) | PP_2381 ← | hypothetical protein |
| RA | 2,793,755 | A→C | 17.0% | intergenic (+64/+63) | PP_2445 → / ← PP_2446 | membrane protein/hypothetical protein |
| RA | 2,823,440 | T→A | 7.8% | V338E (GTG→GAG) | curA → | NADPH‑dependent curcumin/dihydrocurcumin reductase |
| RA | 2,883,429 | C→T | 5.9% | intergenic (+115/‑12) | PP_2538 → / → PP_2539 | hypothetical protein/LysR family transcriptional regulator |
| RA | 2,892,757 | G→A | 7.3% | S4F (TCC→TTC) | PP_2547 ← | LysR family transcriptional regulator |
| RA | 2,951,341 | A→C | 11.5% | intergenic (‑120/+41) | oguA ← / ← PP_2585 | 8‑oxoguanine deaminase/alpha‑ketoglutaric semialdehyde dehydrogenase |
| RA | 2,951,342 | G→T | 17.5% | intergenic (‑121/+40) | oguA ← / ← PP_2585 | 8‑oxoguanine deaminase/alpha‑ketoglutaric semialdehyde dehydrogenase |
| JC | 2,957,081 | Δ84 bp | 24.7% | 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 |
| RA | 3,026,055 | A→G | 7.5% | V194A (GTC→GCC) | PP_2641 ← | iron‑sulfur cluster‑binding protein |
| RA | 3,128,355 | A→G | 6.0% | L21P (CTG→CCG) | PP_2745 ← | universal stress protein family protein |
| RA | 3,171,774 | A→T | 17.5% | I16F (ATT→TTT) | PP_2784 → | short‑chain dehydrogenase/reductase family oxidoreductase |
| RA | 3,447,291 | T→G | 29.3% | A19A (GCT→GCG) | PP_5556 → | bacteriophage lysis protein |
| RA | 3,492,271 | C→T | 7.4% | E50K (GAA→AAA) | PP_3096 ← | hypothetical protein |
| RA | 3,574,093 | A→G | 6.2% | W418R (TGG→CGG) | PP_3155 ← | ferric siderophore receptor |
| RA | 3,612,428 | C→T | 6.0% | G419D (GGC→GAC) | mcoA ← | Mn(II) copper oxidase A |
| RA | 3,653,438 | G→A | 11.4% | intergenic (+4/+94) | PP_3218 → / ← PP_3219 | NtaA/SnaA/SoxA family monooxygenase/alkansulfonate monooxygenase |
| RA | 3,714,009 | C→A | 6.7% | G169C (GGC→TGC) | paaK ← | phenylacetate‑CoA ligase |
| RA | 3,721,979 | C→T | 6.7% | P75P (CCG→CCA) | fnrC ← | Crp/Fnr family transcriptional regulator |
| RA | 3,791,727 | T→G | 36.9% | S531R (AGC→CGC) | PP_3354 ← | acyl‑CoA dehydrogenase |
| RA | 3,810,630 | A→G | 8.1% | P249P (CCA→CCG) | PP_3366 → | LysR family transcriptional regulator |
| 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 | 3,883,600 | G→A | 7.1% | G207S (GGC→AGC) | PP_3428 → | TPR repeat‑containing protein |
| RA | 3,891,788 | G→T | 7.0% | A258S (GCC→TCC) | PP_3435 → | hypothetical protein |
| 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 | 3,996,335 | T→G | 26.6% | intergenic (+13/+32) | PP_3523 → / ← PP_3524 | hypothetical protein/hypothetical protein |
| RA | 4,110,767 | C→T | 6.9% | Y863Y (TAC→TAT) | PP_3616 → | membrane protein |
| RA | 4,158,466 | T→G | 47.8% | L159R (CTG→CGG) | PP_3661 → | membrane protein |
| RA | 4,158,471 | A→C | 36.1% | S161R (AGC→CGC) | PP_3661 → | membrane protein |
| MC JC | 4,274,119 | 32 bp→45 bp | 100% | intergenic (‑243/‑1) | glcC ← / → glcD | transcriptional regulator GlcC/glycolate oxidase FAD‑linked subunit |
| RA | 4,322,176 | A→G | 6.1% | intergenic (‑79/‑1344) | PP_3792 ← / → PP_5631 | hypothetical protein/hypothetical protein |
| RA | 4,348,812 | A→G | 48.8% | intergenic (‑70/+404) | PP_3820 ← / ← galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| RA | 4,373,575 | A→C | 5.9% | N161T (AAC→ACC) | PP_3849 → | hemolysin‑type calcium‑binding protein |
| RA | 4,436,996 | T→A | 7.0% | Y17N (TAT→AAT) | PP_3932 → | diguanylate cyclase |
| RA | 4,442,726 | A→C | 24.1% | intergenic (‑89/+49) | nicP‑II ← / ← nicT | porin‑like protein/metabolite transport protein NicT |
| RA | 4,556,095 | T→G | 7.6% | E170A (GAG→GCG) | zwfB ← | glucose 6‑phosphate 1‑dehydrogenase |
| RA | 4,585,353 | C→T | 5.8% | C113Y (TGC→TAC) | glgE ← | alpha‑1,4‑glucan:maltose‑1‑phosphate maltosyltransferase |
| 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 | 4,598,251 | C→T | 6.6% | L555L (CTG→CTA) | PP_4071 ← | membrane protein |
| RA | 4,714,982 | C→G | 43.1% | R36G (CGC→GGC) | PP_4173 → | two‑component system sensor histidine kinase/response regulator |
| 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 | 4,741,336 | 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 | 4,745,946 | G→A | 6.1% | N56N (AAC→AAT) | PP_4200 ← | hypothetical protein |
| 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 | 4,768,243 | C→A | 59.9% | L57M (CTG→ATG) | tpaK → | probable terephthalate transporter, MFS superfamily protein |
| RA | 4,769,141 | A→T | 44.4% | N356I (AAT→ATT) | tpaK → | probable terephthalate transporter, MFS superfamily protein |
| RA | 4,795,178 | G→A | 7.0% | A122V (GCG→GTG) | pvdI ← | non‑ribosomal peptide synthetase |
| RA | 4,798,307 | A→G | 15.9% | intergenic (‑162/+56) | pvdH ← / ← PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| RA | 4,798,315 | C→T | 18.5% | intergenic (‑170/+48) | pvdH ← / ← PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| RA | 4,798,317 | G→C | 29.0% | intergenic (‑172/+46) | pvdH ← / ← PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| RA | 4,798,320 | G→C | 20.8% | intergenic (‑175/+43) | pvdH ← / ← PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| RA | 4,798,322 | A→G | 25.7% | intergenic (‑177/+41) | pvdH ← / ← PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| RA | 4,798,330 | C→T | 19.0% | intergenic (‑185/+33) | pvdH ← / ← PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| MC JC | 4,875,480 | Δ756 bp | 100% | coding (1‑756/756 nt) | PP_4283 ← | GntR family transcriptional regulator |
| RA | 4,888,972 | C→T | 7.7% | H110Y (CAC→TAC) | gcl → | glyoxylate carboligase |
| RA | 4,948,753 | C→T | 6.1% | A104T (GCG→ACG) | fliR ← | flagellar biosynthetic protein FliR |
| RA | 4,975,791 | C→T | 6.5% | A506T (GCC→ACC) | flgK ← | flagellar hook‑associated protein FlgK |
| JC | 4,982,288 | +GGC | 93.2% | intergenic (‑24/+44) | PP_4387 ← / ← flgE | hypothetical protein/flagellar hook protein FlgE |
| RA | 5,111,161 | A→G | 6.4% | Y416Y (TAT→TAC) | aroP‑II ← | aromatic amino acid transport protein |
| RA | 5,123,530 | G→C | 18.2% | A308G (GCG→GGG) | PP_4508 ← | AraC family transcriptional regulator |
| RA | 5,123,537 | G→C | 11.1% | L306V (CTG→GTG) | PP_4508 ← | AraC family transcriptional regulator |
| RA | 5,140,117 | G→C | 6.6% | D201H (GAC→CAC) | PP_4523 → | agmatinase |
| RA | 5,144,356 | A→G | 7.3% | T330A (ACC→GCC) | PP_4526 → | MFS transporter |
| RA | 5,191,670 | T→A | 7.6% | N100I (AAC→ATC) | PP_4570 ← | hypothetical protein |
| RA | 5,218,255 | G→A | 7.3% | P52S (CCC→TCC) | PP_4596 ← | putative oxidoreductase |
| RA | 5,255,511 | C→T | 6.5% | G276S (GGC→AGC) | PP_4630 ← | MerR family transcriptional regulator |
| RA | 5,279,700 | G→A | 6.3% | A320T (GCA→ACA) | PP_4652 → | membrane protein |
| RA | 5,373,996 | C→T | 6.2% | A293T (GCC→ACC) | carA ← | carbamoyl‑phosphate synthase small subunit |
| RA | 5,396,064 | A→G | 100% | V231A (GTA→GCA) | tphBII ← | 4‑hydroxythreonine‑4‑phosphate dehydrogenase |
| RA | 5,462,375 | T→G | 43.4% | intergenic (+18/‑22) | PP_4795 → / → holA | lipoprotein/DNA polymerase III subunit delta |
| RA | 5,464,465 | C→T | 9.7% | A197V (GCC→GTC) | PP_4798 → | membrane‑bound lytic murein transglycosylase |
| RA | 5,484,356 | C→T | 7.0% | P344S (CCT→TCT) | PP_4819 → | hypothetical protein |
| RA | 5,491,140 | G→A | 5.1% | A552T (GCC→ACC) | PP_4824 → | two‑component system sensor histidine kinase/response regulator |
| JC | 5,558,423 | +GCC | 94.8% | intergenic (‑84/+87) | PP_4887 ← / ← PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| RA | 5,558,463 | T→A | 20.7% | intergenic (‑124/+47) | PP_4887 ← / ← PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| RA | 5,558,464 | A→T | 15.4% | intergenic (‑125/+46) | PP_4887 ← / ← PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| RA | 5,558,465 | T→A | 13.0% | intergenic (‑126/+45) | PP_4887 ← / ← PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| RA | 5,579,540 | G→A | 6.5% | L149L (CTG→CTA) | PP_4906 → | hypothetical protein |
| RA | 5,589,364 | A→G | 8.0% | L246P (CTG→CCG) | PP_4914 ← | phytase‑like protein |
| RA | 5,668,822 | G→A | 5.3% | A7A (GCG→GCA) | nhaP → | NhaP‑type Na+(K+)/H+ antiporter |
| 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 |
| RA | 5,678,475 | T→C | 5.7% | H94R (CAC→CGC) | yceJ ← | iron‑regulated cytochrome b561 |
| JC | 5,684,230 | +CGGG | 91.9% | intergenic (‑133/+71) | PP_4986 ← / ← PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| RA | 5,778,383 | G→A | 6.6% | V479I (GTC→ATC) | betB → | NAD‑dependent betaine aldehyde dehydrogenase |
| RA | 5,911,923 | G→T | 5.2% | A38D (GCT→GAT) | spuD ← | spermidine/putrescine ABC transporter substrate‑binding protein |
| RA | 5,985,764 | G→T | 5.1% | L1198L (CTG→CTT) | PP_5242 → | GAF domain‑containing sensor histidine kinase |
| RA | 5,991,634 | T→C | 16.0% | intergenic (+113/‑433) | kefB‑III → / → PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| RA | 5,991,639 | C→T | 16.3% | intergenic (+118/‑428) | kefB‑III → / → PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| RA | 5,991,640 | G→T | 18.5% | intergenic (+119/‑427) | kefB‑III → / → PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| RA | 5,991,641 | C→T | 16.3% | intergenic (+120/‑426) | kefB‑III → / → PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| RA | 5,991,644 | A→G | 16.3% | intergenic (+123/‑423) | kefB‑III → / → PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| RA | 5,991,650 | G→C | 16.7% | intergenic (+129/‑417) | kefB‑III → / → PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| RA | 5,991,652 | C→G | 14.1% | intergenic (+131/‑415) | kefB‑III → / → PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| RA | 5,991,659 | C→G | 15.9% | intergenic (+138/‑408) | kefB‑III → / → PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| RA | 5,991,663 | C→T | 15.9% | intergenic (+142/‑404) | kefB‑III → / → PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| RA | 5,991,665 | C→T | 15.5% | intergenic (+144/‑402) | kefB‑III → / → PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| RA | 5,991,709 | C→T | 10.2% | intergenic (+188/‑358) | kefB‑III → / → PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| RA | 5,991,710 | A→G | 10.1% | intergenic (+189/‑357) | kefB‑III → / → PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| RA | 5,991,720 | T→C | 13.1% | intergenic (+199/‑347) | kefB‑III → / → PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| RA | 5,991,726 | Δ1 bp | 12.5% | 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 | 6,093,871 | A→G | 5.6% | L144S (TTG→TCG) | PP_5342 ← | GntR family transcriptional regulator |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_002947_CJ‑RC | 171367–176306 | 176306 | 1–4940 | 25 [23] | [23] 25 | PP_16SA–[PP_5SA] | PP_16SA,PP_23SA,[PP_5SA] |
| * | * | ÷ | NC_002947_CJ‑RC | 176643–181695 | 181695 | 1–5053 | 24 [23] | [21] 24 | PP_16SB–[PP_r01] | PP_16SB,PP_23SB,[PP_r01] |
| * | * | ÷ | NC_002947_CJ‑RC | 2837045 | 2837286 | 242 | 24 [23] | [23] 24 | [sad‑I]–[PP_2489] | [sad‑I],[PP_2489] |
| * | * | ÷ | NC_002947_CJ‑RC | 5509258 | 5509446 | 189 | 24 [23] | [23] 24 | [PP_4839] | [PP_4839] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 652782 | 37 (0.670) | 3 (0.060) | 3/232 | NT | 16.0% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809862 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | 3366553 = | 42 (0.760) | 3 (0.050) | 3/272 | NT | 5.7% | intergenic (+219/‑142) | PP_2962/PP_2964 | alcohol dehydrogenase/transposase |
| ? | NC_002947_CJ‑RC | = 5399071 | 58 (1.050) | coding (482/1218 nt) | hsdM | type I restriction modification system methylase | |||||
| * | ? | NC_002947_CJ‑RC | 4046130 = | 36 (0.650) | 3 (0.060) | 3/258 | NT | 8.3% | coding (590/906 nt) | PP_3567 | LysR family transcriptional regulator |
| ? | NC_002947_CJ‑RC | 4046163 = | 32 (0.610) | coding (557/906 nt) | PP_3567 | LysR family transcriptional regulator | |||||
| * | ? | NC_002947_CJ‑RC | = 4586136 | 8 (0.140) | 15 (0.290) | 11/250 | NT | 59.6% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947_CJ‑RC | = 4586216 | 13 (0.260) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 0 (0.000) | 7 (0.170) | 6/202 | NT | 37.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 23 (0.560) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 0 (0.000) | 8 (0.160) | 7/248 | NT | 28.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 40 (0.790) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 5194427 = | 22 (0.400) | 5 (0.110) | 4/222 | NT | 29.4% | intergenic (+105/‑97) | PP_4572/PP_4573 | hypothetical protein/AAA family ATPase |
| ? | NC_002947_CJ‑RC | 5194496 = | 6 (0.130) | intergenic (+174/‑28) | PP_4572/PP_4573 | hypothetical protein/AAA family ATPase | |||||
| * | ? | NC_002947_CJ‑RC | = 5197657 | 58 (1.050) | 3 (0.060) | 3/254 | NT | 5.3% | coding (561/690 nt) | ybgJ | allophanate hydrolase subunit 1 |
| ? | NC_002947_CJ‑RC | = 5197813 | 52 (1.010) | coding (405/690 nt) | ybgJ | allophanate hydrolase subunit 1 | |||||
| * | ? | NC_002947_CJ‑RC | 5655737 = | 27 (0.490) | 4 (0.080) | 4/258 | NT | 18.3% | intergenic (‑23/+138) | PP_4961/PP_4962 | lipoprotein/hypothetical protein |
| ? | NC_002947_CJ‑RC | 5655825 = | 10 (0.190) | intergenic (‑111/+50) | PP_4961/PP_4962 | lipoprotein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5991574 | 40 (0.720) | 5 (0.100) | 5/258 | NT | 13.5% | intergenic (+53/‑493) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991766 = | 26 (0.500) | intergenic (+245/‑301) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 38 (0.690) | 4 (0.080) | 4/256 | NT | 11.1% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 28 (0.540) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||