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 | 38,145 | G→A | T324I (ACC→ATC) | caiB ← | gamma‑butyrobetainyl‑CoA:carnitine CoA transferase |
| RA | 38,163 | G→A | A318V (GCC→GTC) | caiB ← | gamma‑butyrobetainyl‑CoA:carnitine CoA transferase |
| RA | 42,108 | G→A | intergenic (‑177/‑295) | caiT ← / → fixA | L‑carnitine:gamma‑butyrobetaine antiporter/putative electron transfer flavoprotein FixA |
| RA | 75,070 | C→T | P137P (CCG→CCA) | thiB ← | thiamine ABC transporter periplasmic binding protein |
| RA | 81,498 | C→T | G154D (GGT→GAT) | leuB ← | 3‑isopropylmalate dehydrogenase |
| RA | 226,027 | C→T | noncoding (269/2904 nt) | rrlH → | 23S ribosomal RNA |
| RA | 246,747 | G→T | S12S (TCG→TCT) | yafL → | NlpC/P60 family protein YafL |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 260,015 | C→T | G29D (GGT→GAT) | phoE ← | outer membrane porin PhoE |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 299,256 | G→A | A560V (GCC→GTC) | paoC ← | aldehyde dehydrogenase: molybdenum cofactor‑binding subunit |
| RA | 300,585 | G→A | A117V (GCC→GTC) | paoC ← | aldehyde dehydrogenase: molybdenum cofactor‑binding subunit |
| RA | 300,645 | G→A | A97V (GCC→GTC) | paoC ← | aldehyde dehydrogenase: molybdenum cofactor‑binding subunit |
| RA | 303,911 | C→T | G91E (GGA→GAA) | ykgJ ← | putative metal‑chelating domain‑containing protein YkgJ |
| RA | 305,596 | G→A | L408F (CTC→TTC) | ecpD ← | fimbrial adhesin EcpD |
| RA | 306,474 | C→T | G115D (GGC→GAC) | ecpD ← | fimbrial adhesin EcpD |
| RA | 313,543 | G→A | intergenic (‑301/‑1748) | ykgR ← / → insE1 | putative membrane protein YkgR/IS3 element protein InsE |
| RA | 337,418 | G→A | G214D (GGC→GAC) | yahF → | putative acyl‑CoA synthetase YahF |
| RA | 342,413 | A→G | D430G (GAC→GGC) | yahJ → | amidohydrolase family protein YahJ |
| RA | 363,362 | C→T | G982S (GGC→AGC) | lacZ ← | beta‑galactosidase |
| MC JC | 402,391 | Δ723 bp | coding (645‑1367/1416 nt) | phoA → | alkaline phosphatase |
| RA | 426,428 | C→T | L98F (CTT→TTT) | tgt → | tRNA‑guanine transglycosylase |
| RA | 429,132 | C→T | L496L (CTG→TTG) | secD → | Sec translocon accessory complex subunit SecD |
| RA | 435,272 | C→T | L46L (CTG→TTG) | nusB → | transcription antitermination protein NusB |
| RA | 446,642 | C→T | G9S (GGT→AGT) | yajR ← | putative transport protein YajR |
| RA | 456,645 | C→T | intergenic (+214/‑32) | tig → / → clpP | trigger factor/ATP‑dependent Clp protease proteolytic subunit |
| RA | 458,220 | C→T | G265G (GGC→GGT) | clpX → | ATP‑dependent Clp protease ATP‑binding subunit ClpX |
| RA | 460,036 | C→T | G383G (GGC→GGT) | lon → | Lon protease |
| RA | 466,776 | C→T | G179G (GGG→GGA) | ybaE ← | uncharacterized protein YbaE |
| RA | 472,585 | C→T | intergenic (+168/‑13) | mdlB → / → glnK | ABC transporter family protein MdlB/nitrogen regulatory protein PII‑2 |
| RA | 474,379 | C→T | V261V (GTG→GTA) | tesB ← | acyl‑CoA thioesterase II |
| RA | 480,295 | 2 bp→AA | coding (13‑14/219 nt) | hha ← | hemolysin expression‑modulating protein Hha |
| RA | 480,686 | C→T | R8K (AGA→AAA) | tomB ← | Hha toxicity modulator TomB |
| RA | 487,802 | C→T | L423L (CTG→TTG) | mscK → | potassium dependent, small conductance mechanosensitive channel |
| RA | 492,215 | C→T | L42F (CTT→TTT) L42F (CTT→TTT) |
dnaX → dnaX → |
DNA polymerase III subunit tau DNA polymerase III subunit tau |
| RA | 496,241 | C→T | F374F (TTC→TTT) | htpG → | chaperone protein HtpG |
| RA | 500,069 | C→T | intergenic (‑96/‑56) | aes ← / → gsk | acetylesterase/inosine/guanosine kinase |
| RA | 500,641 | C→T | Q173* (CAG→TAG) | gsk → | inosine/guanosine kinase |
| RA | 501,193 | G→A | G357R (GGG→AGG) | gsk → | inosine/guanosine kinase |
| RA | 508,652 | C→T | intergenic (+93/+223) | ybaQ → / ← copA | DNA‑binding transcriptional regulator YbaQ/Cu(+) exporting P‑type ATPase |
| RA | 511,602 | G→A | intergenic (‑223/‑39) | copA ← / → glsA | Cu(+) exporting P‑type ATPase/glutaminase 1 |
| RA | 512,904 | C→T | A110V (GCC→GTC) | ybaT → | putative transporter YbaT |
| RA | 518,704 | C→T | G149E (GGA→GAA) | ybbO ← | NADP(+)‑dependent aldehyde reductase YbbO |
| RA | 518,989 | C→T | R54H (CGC→CAC) | ybbO ← | NADP(+)‑dependent aldehyde reductase YbbO |
| RA | 519,280 | C→T | L162L (CTG→CTA) | tesA ← | multifunctional acyl‑CoA thioesterase I and protease I and lysophospholipase L1 |
| RA | 606,604 | G→A | T260T (ACC→ACT) | ybdK ← | putative glutamate‑‑cysteine ligase 2 |
| RA | 690,948 | G→A | V279V (GTC→GTT) | ybeX ← | CorC‑HlyC family protein YbeX |
| RA | 700,038 | G→A | H97Y (CAT→TAT) | umpH ← | UMP phosphatase |
| RA | 789,597 | C→T | S128N (AGT→AAT) | galK ← | galactokinase |
| RA | 809,217 | 2 bp→AG | coding (40‑41/1290 nt) | bioA ← | adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase |
| RA | 891,983 | T→A | L6* (TTG→TAG) | rimK → | ribosomal protein S6 modification protein |
| RA | 908,760 | A→T | C179S (TGC→AGC) | ltaE ← | low‑specificity L‑threonine aldolase |
| RA | 968,837 | G→A | D158N (GAT→AAT) | lpxK → | tetraacyldisaccharide 4'‑kinase |
| RA | 1,005,503 | A→G | N246D (AAT→GAT) | pyrD → | dihydroorotate dehydrogenase, type 2 |
| RA | 1,040,126 | G→T | L277L (CTG→CTT) | appB → | cytochrome bd‑II subunit 2 |
| RA | 1,061,935 | G→A | S46N (AGC→AAC) | torD → | trimethylamine‑N‑oxide reductase‑specific chaperone |
| RA | 1,111,727 | 2 bp→TT | coding (865‑866/2544 nt) | opgH → | osmoregulated periplasmic glucans biosynthesis protein H |
| RA | 1,115,233 | C→T | M86I (ATG→ATA) | mdtG ← | efflux pump MdtG |
| RA | 1,129,324 | C→T | L496L (CTG→TTG) | murJ → | lipid II flippase MurJ |
| RA | 1,133,668 | C→T | V365V (GTC→GTT) | flgE → | flagellar hook protein FlgE |
| RA | 1,155,389 | C→T | A89V (GCT→GTT) | tmk → | Tmk |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,180,426 | T→A | intergenic (+67/+53) | cobB → / ← ycfZ | protein‑lysine deacetylase/desuccinylase/lipoamidase/putative inner membrane protein YcfZ |
| RA | 1,181,285 | C→T | R147R (AGG→AGA) | ymfA ← | putative inner membrane protein YmfA |
| RA | 1,186,294 | G→A | A151T (GCG→ACG) | pepT → | peptidase T |
| RA | 1,189,296 | C→T | V161I (GTA→ATA) | phoQ ← | sensor histidine kinase PhoQ |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| 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 | 1,278,991 | C→T | G345G (GGC→GGT) | narK → | nitrate:nitrite antiporter NarK |
| JC JC | 1,293,268 | IS5 (–) +4 bp | intergenic (‑346/‑256) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| RA | 1,301,998 | A→G | S273G (AGC→GGC) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,302,268 | C→T | Q363* (CAG→TAG) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,357,202 | C→T | intergenic (‑92/+221) | sapA ← / ← ymjA | putative periplasmic binding protein SapA/DUF2543 domain‑containing protein YmjA |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,397,802 | G→A | T274I (ACC→ATC) | uspE ← | universal stress protein E |
| JC JC | 1,431,062 | IS2 (–) +5 bp | coding (2014‑2018/3363 nt) | stfR → | putative prophage side tail fiber protein StfR |
| RA | 1,479,799 | C→T | P221L (CCC→CTC) | ynbC → | hydrolase/methyltransferase domain‑containing protein YnbC |
| RA | 1,553,310 | C→T | A177T (GCC→ACC) | adhP ← | ethanol dehydrogenase/alcohol dehydrogenase |
| RA | 1,600,234 | C→T | intergenic (‑25/+54) | lsrK ← / ← lsrR | autoinducer‑2 kinase/DNA‑binding transcriptional repressor LsrR |
| RA | 1,601,098 | C→A | S48S (TCG→TCT) | lsrR ← | DNA‑binding transcriptional repressor LsrR |
| RA | 1,601,103 | C→T | V47M (GTG→ATG) | lsrR ← | DNA‑binding transcriptional repressor LsrR |
| RA | 1,632,712 | A→G | intergenic (‑427/‑178) | ydfJ ← / → ynfT | putative transporter YdfJ/protein YnfT |
| RA | 1,632,735 | G→A | intergenic (‑450/‑155) | ydfJ ← / → ynfT | putative transporter YdfJ/protein YnfT |
| RA | 1,641,002 | T→C | intergenic (+27/+337) | ynfU → / ← cspB | putative zinc‑binding protein YnfU/cold shock‑like protein CspB |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,649,971 | C→T | P60S (CCG→TCG) | ydfD → | lysis protein |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,702,757 | C→T | F175F (TTC→TTT) | add → | adenosine deaminase |
| MC JC | 1,757,529 | Δ63 bp | coding (109‑171/237 nt) | lpp → | murein lipoprotein |
| RA | 1,793,377 | Δ1 bp | coding (182/750 nt) | btuD ← | vitamin B12 ABC transporter ATP binding subunit |
| RA | 1,861,311 | C→T | G8S (GGC→AGC) | ydjL ← | putative zinc‑binding dehydrogenase YdjL |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| RA | 1,964,254 | A→C | V266G (GTC→GGC) | flhA ← | flagellar biosynthesis protein FlhA |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| JC | 2,092,996 | (TGGC)4→3 | coding (599‑602/1071 nt) | hisC → | histidinol‑phosphate aminotransferase |
| RA | 2,099,525 | A→T | I30N (ATT→AAT) | ugd ← | UDP‑glucose 6‑dehydrogenase |
| RA | 2,111,259 | Δ1 bp | coding (718/900 nt) | rfbD ← | dTDP‑4‑dehydrorhamnose reductase |
| RA | 2,155,880 | C→T | L206L (CTC→CTT) | mdtB → | multidrug efflux pump RND permease subunit MdtB |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,173,448 | C→T | intergenic (‑575/+834) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,224,169 | A→G | F234F (TTT→TTC) | pbpG ← | peptidoglycan DD‑endopeptidase PbpG |
| RA | 2,237,105 | G→T | P217T (CCG→ACG) | mglC ← | D‑galactose/methyl‑galactoside ABC transporter membrane subunit |
| JC JC | 2,237,684 | IS5 (+) +4 bp | coding (67‑70/1011 nt) | mglC ← | D‑galactose/methyl‑galactoside ABC transporter membrane subunit |
| RA | 2,264,460 | 2 bp→AT | coding (598‑599/1182 nt) | setB → | sugar exporter SetB |
| RA | 2,319,078 | C→A | D267Y (GAT→TAT) | rcsC ← | histidine kinase RcsC |
| RA | 2,360,550 | Δ1 bp | coding (865/1206 nt) | rhmD ← | L‑rhamnonate dehydratase |
| RA | 2,392,233 | C→G | G270A (GGT→GCT) | nuoM ← | NADH:quinone oxidoreductase subunit M |
| RA | 2,423,891 | C→T | V207I (GTA→ATA) | hisP ← | lysine/arginine/ornithine ABC transporter/histidine ABC transporter, ATP binding subunit |
| RA | 2,443,447 | G→A | A562T (GCG→ACG) | mnmC → | fused tRNA 5‑aminomethyl‑2‑thiouridylate methyltransferase and tRNA 5‑aminomethyl‑2‑thiouridylate synthase |
| RA | 2,473,392 | G→A | intergenic (‑146/‑212) | yfdO ← / → yfdP | protein YdfO/uncharacterized protein YfdP |
| RA | 2,473,397 | +T | intergenic (‑151/‑207) | yfdO ← / → yfdP | protein YdfO/uncharacterized protein YfdP |
| RA | 2,510,609 | C→T | P327L (CCG→CTG) | yfeO → | putative transport protein YfeO |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,587,112 | C→T | A461V (GCA→GTA) | narQ → | sensor histidine kinase NarQ |
| RA | 2,630,852 | G→A | S176N (AGC→AAC) | yfgI → | nalidixic acid resistance protein YfgI |
| RA | 2,732,992 | G→A | I394I (ATC→ATT) I394I (ATC→ATT) |
clpB ← clpB ← |
chaperone protein ClpB chaperone protein ClpB |
| RA | 2,745,565 | G→T | T118T (ACC→ACA) | rimM ← | ribosome maturation factor RimM |
| RA | 2,804,133 | C→T | S211F (TCT→TTT) | nrdF → | ribonucleoside‑diphosphate reductase 2 subunit beta |
| RA | 2,814,459 | Δ1 bp | coding (275/516 nt) | luxS ← | S‑ribosylhomocysteine lyase |
| RA | 2,814,461 | C→T | L91L (CTG→CTA) | luxS ← | S‑ribosylhomocysteine lyase |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,871,153 | T→G | N51T (AAC→ACC) | truD ← | tRNA pseudouridine(13) synthase |
| JC JC | 2,913,392 | IS2 (–) +5 bp | coding (256‑260/2235 nt) | relA ← | GDP/GTP pyrophosphokinase |
| RA | 2,920,153 | G→A | Y198Y (TAC→TAT) | gudX ← | glucarate dehydratase‑related protein |
| RA | 2,954,158 | G→A | L616L (CTG→TTG) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 2,955,385 | C→T | V207I (GTT→ATT) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 3,010,122 | G→A | G32D (GGC→GAC) | hyuA → | phenylhydantoinase |
| RA | 3,019,751 | C→T | I197I (ATC→ATT) | ssnA → | putative aminohydrolase SsnA |
| RA | 3,063,827 | C→T | Q281* (CAG→TAG) | argK → | methylmalonyl‑CoA mutase‑interacting GTPase YgfD |
| RA | 3,076,531 | G→A | T309M (ACG→ATG) | yggP ← | putative zinc‑binding dehydrogenase YggP |
| RA | 3,127,435 | G→T | S196* (TCG→TAG) | glcD ← | glycolate dehydrogenase, putative FAD‑linked subunit |
| RA | 3,175,234 | C→T | V55M (GTG→ATG) | parE ← | DNA topoisomerase IV subunit B |
| RA | 3,208,066 | G→A | A15T (GCG→ACG) | ttdT → | L‑tartrate:succinate antiporter |
| RA | 3,220,571 | G→A | E360K (GAG→AAG) | patA → | putrescine aminotransferase |
| RA | 3,221,786 | C→T | S107S (AGC→AGT) | ebgR → | DNA‑binding transcriptional repressor EbgR |
| RA | 3,230,486 | C→T | D533D (GAC→GAT) | ygjK → | glycoside hydrolase |
| RA | 3,243,050 | G→A | Q89* (CAG→TAG) | uxaA ← | D‑altronate dehydratase |
| MC JC | 3,258,933 | (ACGGC)2→1 | coding (713‑717/1365 nt) | tdcG ← | L‑serine deaminase III |
| RA | 3,329,743 | G→T | D261Y (GAT→TAT) | dacB → | peptidoglycan DD‑endopeptidase DacB |
| MC JC | 3,349,206 | Δ16,350 bp | IS5‑mediated | [mtgA]–[yhcE] | [mtgA], elbB, arcZ, arcB, yhcC, gltB, gltD, gltF, yhcA, yhcD, [yhcE] |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,432,105 | C→T | L120L (CTG→CTA) | smg ← | DUF494 domain‑containing protein Smg |
| RA | 3,443,961 | G→A | A46V (GCC→GTC) | secY ← | Sec translocon subunit SecY |
| RA | 3,443,980 | G→A | P40S (CCG→TCG) | secY ← | Sec translocon subunit SecY |
| RA | 3,452,022 | G→A | P89S (CCG→TCG) | rplD ← | 50S ribosomal subunit protein L4 |
| RA | 3,452,218 | G→A | F23F (TTC→TTT) | rplD ← | 50S ribosomal subunit protein L4 |
| RA | 3,457,378 | C→T | L334L (CTC→CTT) | gspD → | Type II secretion system protein GspD |
| RA | 3,458,245 | A→C | S623S (TCA→TCC) | gspD → | Type II secretion system protein GspD |
| RA | 3,474,425 | T→G | K43T (AAA→ACA) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,492,293 | A→G | F2S (TTC→TCC) | ppiA ← | peptidyl‑prolyl cis‑trans isomerase A |
| RA | 3,506,393 | T→C | D315G (GAC→GGC) | yhfT ← | uncharacterized protein YhfT |
| RA | 3,560,455 | 1 bp→TG | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,562,125 | C→T | A38V (GCT→GTT) | glpD → | aerobic glycerol 3‑phosphate dehydrogenase |
| RA | 3,563,255 | C→T | R415C (CGT→TGT) | glpD → | aerobic glycerol 3‑phosphate dehydrogenase |
| RA | 3,586,657 | G→A | A56V (GCC→GTC) | ggt ← | glutathione hydrolase proenzyme |
| RA | 3,626,067 | C→T | G246D (GGT→GAT) | yhhJ ← | ABC transporter family protein YhhJ |
| RA | 3,638,300 | G→A | G220D (GGC→GAC) | pitA → | metal phosphate:H(+) symporter PitA |
| RA | 3,682,515 | C→T | M311I (ATG→ATA) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| RA | 3,692,114 | C→T | S165N (AGC→AAC) | bcsB ← | cellulose synthase periplasmic subunit |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,725,176 | T→G | E48A (GAG→GCG) | glyQ ← | glycine‑‑tRNA ligase subunit alpha |
| RA | 3,729,955 | 2 bp→AA | coding (810‑811/1323 nt) | xylA ← | xylose isomerase |
| JC JC | 3,731,420 | IS1 (–) +9 bp | coding (290‑298/993 nt) | xylF → | xylose ABC transporter periplasmic binding protein |
| RA | 3,769,447 | G→A | E35K (GAA→AAA) | yibV → | PF15596 family protein YibV |
| RA | 3,773,040 | (G)6→4 | coding (760‑761/1914 nt) | mtlA → | mannitol‑specific PTS enzyme IICBA component |
| RA | 3,783,983 | G→A | S49F (TCC→TTC) | secB ← | protein export chaperone SecB |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| JC | 3,822,651 | (CAGGAT)1→2 | coding (252/2109 nt) | spoT → | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| RA | 3,823,162 | C→T | H255Y (CAC→TAC) | spoT → | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| RA | 3,835,828 | G→A | F34F (TTC→TTT) | yicJ ← | putative xyloside transporter YicJ |
| RA | 3,837,106 | G→A | V52I (GTA→ATA) | setC → | putative arabinose exporter |
| RA | 3,837,362 | G→A | G137D (GGC→GAC) | setC → | putative arabinose exporter |
| RA | 3,889,668 | C→T | G313G (GGC→GGT) | tnaA → | tryptophanase |
| RA | 3,894,233 | C→T | P118L (CCC→CTC) | yieE → | putative phosphopantetheinyl transferase |
| RA | 3,896,888 | C→T | P39S (CCT→TCT) | yieH → | 6‑phosphogluconate phosphatase |
| RA | 3,899,297 | C→T | A33T (GCA→ACA) | yieK ← | putative glucosamine‑6‑phosphate deaminase YieK |
| RA | 3,907,444 | G→A | N45N (AAC→AAT) | phoU ← | negative regulator of the pho regulon |
| JC JC | 3,931,171 | IS4 (–) +12 bp | intergenic (‑78/‑134) | ravA ← / → kup | regulatory ATPase RavA/K(+):H(+) symporter Kup |
| RA | 3,953,043 | A→G | D187G (GAT→GGT) | ilvE → | branched‑chain‑amino‑acid aminotransferase |
| RA | 3,993,531 | T→C | R793R (CGT→CGC) | cyaA → | adenylate cyclase |
| RA | 4,057,150 | C→T | A295A (GCG→GCA) | glnA ← | glutamine synthetase |
| RA | 4,058,473 | G→A | D23N (GAC→AAC) | bipA → | 50S ribosomal subunit assembly factor BipA |
| RA | 4,058,823 | G→A | W139* (TGG→TGA) | bipA → | 50S ribosomal subunit assembly factor BipA |
| RA | 4,085,516 | G→A | H103Y (CAC→TAC) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,110,415 | C→T | S162S (AGC→AGT) | cdh → | CDP‑diacylglycerol diphosphatase |
| RA | 4,116,753 | C→T | R157H (CGT→CAT) | glpK ← | glycerol kinase |
| RA | 4,117,060 | C→T | A55T (GCC→ACC) | glpK ← | glycerol kinase |
| RA | 4,117,270 | G→A | P274L (CCT→CTT) | glpF ← | glycerol facilitator |
| JC JC | 4,117,984 | IS30 (+) +2 bp | coding (106‑107/846 nt) | glpF ← | glycerol facilitator |
| RA | 4,119,767 | C→T | A195T (GCA→ACA) | menA ← | 1,4‑dihydroxy‑2‑naphthoate octaprenyltransferase |
| RA | 4,179,329 | G→A | E151K (GAA→AAA) | rplA → | 50S ribosomal subunit protein L1 |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,242,914 | C→T | Q201Q (CAG→CAA) | malG ← | maltose ABC transporter membrane subunit MalG |
| RA | 4,259,611 | G→A | A131A (GCC→GCT) | zur ← | DNA‑binding transcriptional repressor Zur |
| RA | 4,270,596 | G→A | G120E (GGG→GAG) | yjbQ → | PF01894 family protein YjbQ |
| RA | 4,278,574 | G→A | G32G (GGG→GGA) | ghxP → | guanine/hypoxanthine transporter GhxP |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,327,494 | G→A | L120L (CTG→CTA) | rdcA → | regulator of diguanylate cyclase RdcA |
| RA | 4,359,314 | G→A | Q240* (CAG→TAG) | cadB ← | lysine:cadaverine antiporter |
| RA | 4,392,997 | G→A | V357V (GTC→GTT) | queG ← | epoxyqueuosine reductase |
| RA | 4,393,552 | G→A | F172F (TTC→TTT) | queG ← | epoxyqueuosine reductase |
| RA | 4,396,373 | C→T | T103T (ACC→ACT) | amiB → | N‑acetylmuramoyl‑L‑alanine amidase B |
| RA | 4,396,772 | T→C | F236F (TTT→TTC) | amiB → | N‑acetylmuramoyl‑L‑alanine amidase B |
| RA | 4,400,119 | G→A | E290K (GAA→AAA) | miaA → | tRNA dimethylallyltransferase |
| RA | 4,413,535 | G→A | E170K (GAA→AAA) | yjfC → | putative acid‑‑amine ligase YjfC |
| RA | 4,416,177 | C→T | G39D (GGT→GAT) | yjfN ← | protease activator YjfN |
| RA | 4,420,399 | G→A | Q140Q (CAG→CAA) | ulaA → | L‑ascorbate specific PTS enzyme IIC component |
| RA | 4,425,688 | C→A | H57N (CAC→AAC) | priB → | primosomal replication protein N |
| RA | 4,425,696 | C→A | N59K (AAC→AAA) | priB → | primosomal replication protein N |
| RA | 4,436,956 | 2 bp→TT | coding (202‑203/741 nt) | cysQ → | 3'(2'),5'‑bisphosphate nucleotidase |
| RA | 4,472,406 | C→T | R43K (AGG→AAG) | pyrL ← | pyrBI operon leader peptide |
| RA | 4,486,636 | G→A | G140D (GGC→GAC) | lptF → | lipopolysaccharide transport system protein LptF |
| RA | 4,501,834 | C→T | intergenic (+245/+269) | yjgZ → / ← insG | uncharacterized protein YjgZ/IS4 family putative transposase |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,532,409 | T→G | intergenic (‑758/+28) | sgcX ← / ← yjhP | putative endoglucanase with Zn‑dependent exopeptidase domain/putative methyltransferase YjhP |
| RA | 4,546,601 | C→T | I502I (ATC→ATT) | fimD → | type I fimbriae usher protein |
| RA | 4,578,548 | G→A | Q264* (CAG→TAG) Q264* (CAG→TAG) |
mcrB ← mcrB ← |
5‑methylcytosine‑specific restriction enzyme subunit McrB 5‑methylcytosine‑specific restriction enzyme subunit McrB |
| RA | 4,604,109 | G→T | A211A (GCG→GCT) | yjjQ → | DNA‑binding transcriptional repressor YjjQ |
| RA | 4,615,345 | C→T | G67S (GGC→AGC) | yjjW ← | putative glycyl‑radical enzyme activating enzyme YjjW |
| RA | 4,631,788 | G→A | Q352Q (CAG→CAA) | slt → | soluble lytic murein transglycosylase |
| RA | 4,636,925 | G→C | R77P (CGC→CCC) | creC → | sensory histidine kinase CreC |
| RA | 4,638,240 | G→A | L21L (TTG→TTA) | creD → | putative inner membrane protein CreD |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 168355 | 168703 | 349 | 102 [0] | [0] 124 | fhuA | ferrichrome outer membrane transporter/phage receptor |
| * | * | ÷ | NC_000913 | 182569 | 182988 | 420 | 103 [1] | [3] 127 | cdaR | DNA‑binding transcriptional activator CdaR |
| * | * | ÷ | NC_000913 | 1196277 | 1211460 | 15184 | 36 [32] | [33] 42 | [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 | 1632754–1632847 | 1633399–1632956 | 110–646 | 34 [33] | [29] 34 | ynfT–ydfK | ynfT,ydfK |
| * | * | ÷ | NC_000913 | 1978495 | 1979270 | 776 | 130 [0] | [0] 136 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423902–3424234 | 3424457–3424238 | 5–556 | 34 [33] | [33] 36 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 3762431–3764074 | 3765125–3764076 | 3–2695 | 35 [33] | [33] 35 | rhsA | rhs element protein RhsA |
| * | * | ÷ | NC_000913 | 4166501–4168219 | 4171439–4168540 | 322–4939 | 35 [33] | [27] 40 | rrsB–[rrlB] | rrsB,gltT,[rrlB] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 168354 | 0 (0.000) | 102 (0.930) | 65/566 | 0.3 | 100% | coding (871/2244 nt) | fhuA | ferrichrome outer membrane transporter/phage receptor |
| ? | NC_000913 | = 182568 | 0 (0.000) | coding (106/1158 nt) | cdaR | DNA‑binding transcriptional activator CdaR | |||||
| * | ? | NC_000913 | 168704 = | 0 (0.000) | 124 (1.120) | 68/572 | 0.2 | 100% | coding (1221/2244 nt) | fhuA | ferrichrome outer membrane transporter/phage receptor |
| ? | NC_000913 | 182989 = | 0 (0.000) | coding (527/1158 nt) | cdaR | DNA‑binding transcriptional activator CdaR | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 140 (1.250) | 83/580 | 0.1 | 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) | 129 (1.130) | 75/588 | 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) | 136 (1.200) | 71/588 | 0.2 | 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 | = 4542690 | 174 (1.530) | 49 (0.440) | 33/570 | 1.9 | 24.5% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 133 (1.210) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||