mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 2,154 | C→T | 75.0% | D606D (GAC→GAT) | thrA → | fused aspartokinase I and homoserine dehydrogenase I |
| RA | 70,434 | C→T | 66.1% | N16N (AAC→AAT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,581 | C→T | 61.5% | V65V (GTC→GTT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,740 | T→G | 60.4% | G118G (GGT→GGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,079 | C→T | 62.3% | R231R (CGC→CGT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,082 | T→C | 62.1% | I232I (ATT→ATC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,085 | T→C | 57.7% | S233S (AGT→AGC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,109 | T→C | 60.8% | T241T (ACT→ACC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,175 | A→G | 42.9% | R263R (CGA→CGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,214 | T→C | 65.4% | F276F (TTT→TTC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 155,463 | A→T | 100% | *247K (TAA→AAA) | ecpD ← | predicted periplasmic pilin chaperone |
| RA | 236,101 | A→C | 60.0% | D12A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 236,107 | A→C | 52.3% | E14A (GAA→GCA) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 547,694 | A→G | 100% | pseudogene (114/261 nt) pseudogene (114/1259 nt) |
ylbE → ylbE → |
ECK0512:JW0507:b4507; hypothetical protein, N‑ter fragment ECK0512:JW0508+JW0507:b4572; hypothetical protein |
| RA | 547,831:1 | +G | 100% | pseudogene (251/261 nt) pseudogene (251/1259 nt) |
ylbE → ylbE → |
ECK0512:JW0507:b4507; hypothetical protein, N‑ter fragment ECK0512:JW0508+JW0507:b4572; hypothetical protein |
| RA | 556,858 | A→T | 100% | L36Q (CTG→CAG) | folD ← | bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase and 5,10‑methylene‑tetrahydrofolate cyclohydrolase |
| MC JC | 654,214 | Δ1,199 bp | 100% | [dcuC]–[dcuC] | [dcuC], insH, [dcuC] | |
| RA | 713,690 | G→A | 10.0% | L94L (CTG→CTA) | seqA → | regulatory protein for replication initiation |
| RA | 907,713 | G→A | 100% | T331I (ACC→ATC) | ybjT ← | conserved hypothetical protein with NAD(P)‑binding Rossmann‑fold domain |
| RA | 1,093,686 | T→C | 100% | V130A (GTA→GCA) | ycdT → | predicted diguanylate cyclase |
| RA | 1,151,925 | A→C | 58.5% | P207P (CCA→CCC) | fabD → | malonyl‑CoA‑[acyl‑carrier‑protein] transacylase |
| MC JC | 1,301,041 | Δ1,336 bp | 100% | insC–insD | insC, insD | |
| RA | 1,303,631 | C→T | 100% | Q246Y (CAG→TAT) | oppA → | oligopeptide transporter subunit |
| RA | 1,303,633 | G→T | 100% | Q246Y (CAG→TAT) | oppA → | oligopeptide transporter subunit |
| RA | 2,058,034 | C→T | 100% | G279G (GGC→GGT) | amn → | AMP nucleosidase |
| MC JC | 2,176,983 | Δ1,199 bp | 100% | [gatA]–[gatA] | [gatA], insH, [gatA] | |
| RA | 2,286,501 | C→A | 60.0% | A261S (GCG→TCG) | yejK ← | nucleotide associated protein |
| MC JC | 2,320,795 | Δ1,336 bp | 100% | insD–[rcsC] | insD, insC, [rcsC] | |
| RA | 2,809,581 | G→A | 58.3% | G52G (GGG→GGA) | mprA → | DNA‑binding transcriptional regulator |
| RA | 2,855,731 | G→T | 20.9% | intergenic (‑269/‑18) | ygbA ← / → mutS | hypothetical protein/methyl‑directed mismatch repair protein |
| RA | 2,855,732 | G→A | 20.9% | intergenic (‑270/‑17) | ygbA ← / → mutS | hypothetical protein/methyl‑directed mismatch repair protein |
| RA | 2,866,110 | T→A | 100% | intergenic (‑20/+160) | rpoS ← / ← nlpD | RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein |
| RA | 3,053,471 | A→G | 100% | F9S (TTT→TCT) | pepP ← | proline aminopeptidase P II |
| RA | 3,141,782 | G→T | 16.6% | P347T (CCG→ACG) | hybB ← | predicted hydrogenase 2 cytochrome b type component |
| MC JC | 3,261,134 | Δ1,199 bp | 100% | insH–[tdcD] | insH, [tdcD] | |
| RA | 3,315,139 | T→A | 100% | D244V (GAT→GTT) | infB ← | fused protein chain initiation factor 2, IF2 |
| RA | 3,688,001 | A→G | 66.7% | S440G (AGT→GGT) | yifB → | predicted bifunctional protein, enzyme and transcriptional regulator |
| MC JC | 3,742,938 | Δ1,336 bp | 100% | insD–insC | insD, insC | |
| MC JC | 3,746,913 | Δ1,199 bp | 100% | [tnaB]–[tnaB] | [tnaB], insH, [tnaB] | |
| MC JC | 3,750,593 | Δ1,199 bp | 100% | insH | insH | |
| RA | 3,824,280 | T→C | 100% | pseudogene (413/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,326 | T→C | 100% | pseudogene (459/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,362 | A→T | 100% | pseudogene (495/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,368 | G→A | 100% | pseudogene (501/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,374 | C→T | 100% | pseudogene (507/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,380 | 2 bp→AA | 100% | pseudogene (513‑514/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,410 | T→A | 100% | pseudogene (543/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,514 | T→C | 100% | pseudogene (647/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,524 | T→G | 100% | pseudogene (657/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,533:1 | +G | 100% | pseudogene (666/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 4,195,173 | A→G | 100% | *118* (TAA→TGA) | rplR → | 50S ribosomal subunit protein L18 |
| RA | 4,246,990 | C→T | 100% | R40H (CGT→CAT) | malG ← | maltose transporter subunit |
| MC JC | 4,310,365 | Δ1,199 bp | 100% | insH–[alsK] | insH, [alsK] | |
| RA | 4,340,671 | G→A | 100% | T347T (ACC→ACT) | adiC ← | arginine:agmatin |
| RA | 4,371,273 | Δ2 bp | 100% | intergenic (‑6/+299) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,416,062 | A→G | 100% | N27D (AAT→GAT) | yjfK → | conserved hypothetical protein |
| RA | 4,434,349 | T→A | 100% | intergenic (+112/‑197) | fklB → / → cycA | FKBP‑type peptidyl‑prolyl cis‑trans isomerase/D‑alanine/D‑serine/glycine transporter |
| RA | 4,539,733 | C→G | 16.7% | P13A (CCA→GCA) | yjhR → | predicted frameshift suppressor |
| RA | 4,563,589 | T→A | 100% | K207M (AAG→ATG) | iadA ← | isoaspartyl dipeptidase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | W3110S.gb | 90745 | 90746 | 2 | 3 [0] | [0] 4 | mraW | S‑adenosyl‑dependent methyltransferase activity on membrane‑located substrates |
| * | * | ÷ | W3110S.gb | 94871 | 94885 | 15 | 2 [0] | [1] 2 | murF | UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase |
| * | * | ÷ | W3110S.gb | 127566 | 127596 | 31 | 3 [1] | [0] 2 | [aceF] | [aceF] |
| * | * | ÷ | W3110S.gb | 164568 | 164583 | 16 | 2 [1] | [0] 3 | hrpB/mrcB | predicted ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| * | * | ÷ | W3110S.gb | 171662 | 171695 | 34 | 2 [0] | [1] 2 | fhuB | fused subunits of iron‑hydroxamate transporter and membrane components of ABC superfamily transporter |
| * | * | ÷ | W3110S.gb | 174056 | 174073 | 18 | 3 [0] | [1] 7 | hemL | glutamate‑1‑semialdehyde aminotransferase |
| * | * | ÷ | W3110S.gb | 280338 | 280419 | 82 | 3 [1] | [1] 3 | yagA | predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 280811 | 280858 | 48 | 2 [0] | [1] 3 | yagA | predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 283032 | 283256 | 225 | 5 [1] | [1] 2 | yagF | predicted dehydratase |
| * | * | ÷ | W3110S.gb | 285741 | 285743 | 3 | 2 [1] | [0] 2 | yagG | predicted sugar transporter |
| * | * | ÷ | W3110S.gb | 286872 | 286902 | 31 | 2 [0] | [1] 2 | yagH | predicted xylosidase/arabinosidase |
| * | * | ÷ | W3110S.gb | 409769 | 409786 | 18 | 4 [0] | [1] 2 | mak | manno(fructo)kinase |
| * | * | ÷ | W3110S.gb | 422758 | 422796 | 39 | 4 [0] | [1] 3 | malZ | maltodextrin glucosidase |
| * | * | ÷ | W3110S.gb | 497094 | 497099 | 6 | 3 [1] | [1] 4 | adk/hemH | adenylate kinase/ferrochelatase |
| * | * | ÷ | W3110S.gb | 522929 | 522987 | 59 | 2 [1] | [1] 3 | rhsD | rhsD element protein |
| * | * | ÷ | W3110S.gb | 523105 | 523162 | 58 | 2 [1] | [0] 3 | rhsD | rhsD element protein |
| * | * | ÷ | W3110S.gb | 573871–575008 | 575999 | 992–2129 | 2 [1] | [0] 68 | insH–[nmpC] | insH,[nmpC] |
| * | * | ÷ | W3110S.gb | 598771 | 598830 | 60 | 2 [1] | [1] 2 | cusA | copper/silver efflux system, membrane component |
| * | * | ÷ | W3110S.gb | 600188 | 600198 | 11 | 2 [0] | [1] 5 | cusA | copper/silver efflux system, membrane component |
| * | * | ÷ | W3110S.gb | 632563 | 632566 | 4 | 2 [0] | [1] 3 | ybdH | predicted oxidoreductase |
| * | * | ÷ | W3110S.gb | 640624 | 640628 | 5 | 2 [0] | [0] 2 | ahpF/uspG | alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding/universal stress protein UP12 |
| * | * | ÷ | W3110S.gb | 668606 | 668612 | 7 | 2 [0] | [0] 2 | mrdA | transpeptidase involved in peptidoglycan synthesis |
| * | * | ÷ | W3110S.gb | 684360 | 684378 | 19 | 2 [1] | [0] 4 | rihA | ribonucleoside hydrolase 1 |
| * | * | ÷ | W3110S.gb | 695085 | 695095 | 11 | 3 [0] | [0] 3 | miaB | isopentenyl‑adenosine A37 tRNA methylthiolase |
| * | * | ÷ | W3110S.gb | 721524 | 721543 | 20 | 2 [0] | [0] 3 | kdpE | DNA‑binding response regulator in two‑component regulatory system with KdpD |
| * | * | ÷ | W3110S.gb | 730222 | 730503–730237 | 16–282 | 3 [1] | [1] 2 | rhsC | rhsC element core protein RshC |
| * | * | ÷ | W3110S.gb | 730613–730713 | 730901–730729 | 17–289 | 3 [0] | [0] 2 | rhsC | rhsC element core protein RshC |
| * | * | ÷ | W3110S.gb | 744427 | 744438 | 12 | 2 [1] | [0] 4 | ybgJ | predicted enzyme subunit |
| * | * | ÷ | W3110S.gb | 754093 | 754142 | 50 | 3 [1] | [1] 6 | gltA | citrate synthase |
| * | * | ÷ | W3110S.gb | 762366 | 762366 | 1 | 2 [0] | [0] 2 | sucB | dihydrolipoyltranssuccinase |
| * | * | ÷ | W3110S.gb | 765217 | 765236 | 20 | 2 [1] | [1] 2 | sucD | succinyl‑CoA synthetase, NAD(P)‑binding, alpha subunit |
| * | * | ÷ | W3110S.gb | 794073 | 794099 | 27 | 3 [0] | [1] 2 | modF | fused subunits of molybdate transporter and ATP‑binding components of ABC superfamily |
| * | * | ÷ | W3110S.gb | 794830 | 794837 | 8 | 3 [0] | [0] 7 | modE | DNA‑binding transcriptional dual regulator |
| * | * | ÷ | W3110S.gb | 836155 | 836170 | 16 | 2 [0] | [0] 2 | ybiB | predicted transferase/phosphorylase |
| * | * | ÷ | W3110S.gb | 907996 | 908009 | 14 | 3 [1] | [1] 2 | ybjT | conserved hypothetical protein with NAD(P)‑binding Rossmann‑fold domain |
| * | * | ÷ | W3110S.gb | 915634 | 915659 | 26 | 2 [1] | [1] 2 | ybjE/aqpZ | predicted transporter/aquaporin |
| * | * | ÷ | W3110S.gb | 935065 | 935072 | 8 | 2 [1] | [1] 2 | ftsK | DNA‑binding membrane protein required for chromosome resolution and partitioning |
| * | * | ÷ | W3110S.gb | 936022 | 936068 | 47 | 2 [0] | [1] 2 | ftsK | DNA‑binding membrane protein required for chromosome resolution and partitioning |
| * | * | ÷ | W3110S.gb | 995453 | 995456 | 4 | 2 [0] | [0] 3 | ssuD | alkanesulfonate monooxygenase, FMNH(2)‑dependent |
| * | * | ÷ | W3110S.gb | 1002688 | 1002716 | 29 | 9 [0] | [1] 3 | ycbT | predicted fimbrial‑like adhesin protein |
| * | * | ÷ | W3110S.gb | 1039453 | 1039472 | 20 | 2 [0] | [1] 3 | appC | cytochrome bd‑II oxidase, subunit I |
| * | * | ÷ | W3110S.gb | 1041159 | 1041184 | 26 | 2 [1] | [0] 3 | appA | phosphoanhydride phosphorylase |
| * | * | ÷ | W3110S.gb | 1041892 | 1041917 | 26 | 2 [0] | [1] 3 | appA | phosphoanhydride phosphorylase |
| * | * | ÷ | W3110S.gb | 1081344 | 1081346 | 3 | 2 [1] | [0] 4 | putP/ycdN | proline:sodium symporter/ECK1007:JW5141:b1016; hypothetical protein, N‑ter fragment |
| * | * | ÷ | W3110S.gb | 1083338 | 1083343 | 6 | 2 [1] | [0] 4 | ycdO | conserved hypothetical protein |
| * | * | ÷ | W3110S.gb | 1157345 | 1157351 | 7 | 6 [1] | [0] 6 | holB | DNA polymerase III, delta prime subunit |
| * | * | ÷ | W3110S.gb | 1164313 | 1164326 | 14 | 2 [0] | [0] 4 | ycfM | predicted outer membrane lipoprotein |
| * | * | ÷ | W3110S.gb | 1173156 | 1173204 | 49 | 2 [1] | [0] 2 | mfd | transcription‑repair coupling factor |
| * | * | ÷ | W3110S.gb | 1174535 | 1174598 | 64 | 3 [0] | [1] 4 | mfd | transcription‑repair coupling factor |
| * | * | ÷ | W3110S.gb | 1227303 | 1227350 | 48 | 2 [1] | [1] 2 | minC | cell division inhibitor |
| * | * | ÷ | W3110S.gb | 1240113 | 1240136 | 24 | 2 [0] | [1] 3 | dadA | D‑amino acid dehydrogenase |
| * | * | ÷ | W3110S.gb | 1248617 | 1248622 | 6 | 2 [1] | [0] 5 | treA | periplasmic trehalase |
| * | * | ÷ | W3110S.gb | 1251022 | 1251032 | 11 | 2 [1] | [1] 2 | dhaL | dihydroxyacetone kinase, C‑terminal domain |
| * | * | ÷ | W3110S.gb | 1266982 | 1267008 | 27 | 2 [0] | [1] 4 | prfA | peptide chain release factor RF‑1 |
| * | * | ÷ | W3110S.gb | 1306860 | 1306863 | 4 | 4 [0] | [0] 5 | oppD | oligopeptide transporter subunit |
| * | * | ÷ | W3110S.gb | 1328301 | 1328346 | 46 | 2 [0] | [0] 2 | yciQ | predicted inner membrane protein |
| * | * | ÷ | W3110S.gb | 1338214 | 1338226 | 13 | 5 [0] | [0] 2 | acnA | aconitate hydratase 1 |
| * | * | ÷ | W3110S.gb | 1371182 | 1371225 | 44 | 2 [0] | [1] 3 | pspD | peripheral inner membrane phage‑shock protein |
| * | * | ÷ | W3110S.gb | 1410000 | 1410010 | 11 | 5 [1] | [1] 3 | ydaN | predicted Zn(II) transporter |
| * | * | ÷ | W3110S.gb | 1421315 | 1421327 | 13 | 5 [0] | [1] 4 | ydaG/racR | hypothetical protein/predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 1423357 | 1423388 | 32 | 5 [1] | [1] 2 | ydaU | conserved hypothetical protein |
| * | * | ÷ | W3110S.gb | 1431926 | 1431935 | 10 | 2 [1] | [1] 2 | stfR | predicted tail fiber protein |
| * | * | ÷ | W3110S.gb | 1457957 | 1457978 | 22 | 3 [0] | [0] 2 | paaD | predicted multicomponent oxygenase/reductase subunit for phenylacetic acid degradation |
| * | * | ÷ | W3110S.gb | 1487479 | 1487483 | 5 | 3 [1] | [0] 2 | hrpA | ATP‑dependent helicase |
| * | * | ÷ | W3110S.gb | 1495209 | 1495235 | 27 | 2 [1] | [1] 2 | trg | methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor |
| * | * | ÷ | W3110S.gb | 1569591 | 1569620 | 30 | 2 [0] | [0] 8 | yddW | predicted liprotein |
| * | * | ÷ | W3110S.gb | 1760937 | 1760959 | 23 | 2 [1] | [1] 2 | sufE | sulfur acceptor protein |
| * | * | ÷ | W3110S.gb | 1822221 | 1822226 | 6 | 3 [0] | [1] 2 | chbC | N,N'‑diacetylchitobiose‑specific enzyme IIC component of PTS |
| * | * | ÷ | W3110S.gb | 1831634 | 1831639 | 6 | 5 [1] | [1] 2 | astA | arginine succinyltransferase |
| * | * | ÷ | W3110S.gb | 1878895 | 1878902 | 8 | 2 [1] | [0] 5 | yeaO | conserved hypothetical protein |
| * | * | ÷ | W3110S.gb | 1922893 | 1922931 | 39 | 6 [1] | [1] 2 | yebU | predicted methyltransferase |
| * | * | ÷ | W3110S.gb | 1928946 | 1928960 | 15 | 6 [1] | [1] 3 | ptrB | protease II |
| * | * | ÷ | W3110S.gb | 1997975 | 1997996 | 22 | 3 [0] | [0] 4 | yecF | hypothetical protein |
| * | * | ÷ | W3110S.gb | 2041777 | 2041786 | 10 | 3 [0] | [0] 2 | yedY | predicted reductase |
| * | * | ÷ | W3110S.gb | 2051214 | 2051227 | 14 | 3 [1] | [1] 4 | yeeJ | adhesin |
| * | * | ÷ | W3110S.gb | 2095252 | 2095283 | 32 | 3 [0] | [1] 2 | hisC | histidinol‑phosphate aminotransferase |
| * | * | ÷ | W3110S.gb | 2193311 | 2193333 | 23 | 3 [1] | [0] 2 | yehB | predicted outer membrane protein |
| * | * | ÷ | W3110S.gb | 2232524 | 2232585–2232535 | 12–62 | 2 [0] | [1] 3 | yohH/dusC | conserved hypothetical protein/tRNA‑dihydrouridine synthase C |
| * | * | ÷ | W3110S.gb | 2296393 | 2296419 | 27 | 2 [0] | [1] 2 | ccmF | heme lyase, CcmF subunit |
| * | * | ÷ | W3110S.gb | 2381728 | 2381728 | 1 | 4 [0] | [0] 3 | yfbB | predicted peptidase |
| * | * | ÷ | W3110S.gb | 2381947 | 2381984 | 38 | 2 [1] | [1] 3 | yfbB | predicted peptidase |
| * | * | ÷ | W3110S.gb | 2383575 | 2383591 | 17 | 4 [0] | [1] 2 | menD | bifunctional 2‑oxoglutarate decarboxylase and SHCHC synthase |
| * | * | ÷ | W3110S.gb | 2545802 | 2545836 | 35 | 3 [1] | [1] 4 | cysA | sulfate/thiosulfate transporter subunit |
| * | * | ÷ | W3110S.gb | 2547904 | 2547907 | 4 | 2 [0] | [0] 2 | cysU | sulfate/thiosulfate transporter subunit |
| * | * | ÷ | W3110S.gb | 2569104 | 2569128 | 25 | 2 [1] | [1] 3 | eutE | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| * | * | ÷ | W3110S.gb | 2679367 | 2679394 | 28 | 2 [1] | [1] 4 | yphG | conserved hypothetical protein |
| * | * | ÷ | W3110S.gb | 2768288 | 2768289 | 2 | 2 [0] | [0] 6 | yfjQ/yfjR | hypothetical protein/predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 2777813 | 2777827 | 15 | 4 [1] | [0] 5 | ypjA | adhesin‑like autotransporter |
| * | * | ÷ | W3110S.gb | 2790485 | 2790491 | 7 | 2 [0] | [1] 3 | gabD | succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
| * | * | ÷ | W3110S.gb | 2827366 | 2827421 | 56 | 4 [1] | [1] 2 | gutM | DNA‑binding transcriptional activator |
| * | * | ÷ | W3110S.gb | 2846562 | 2846571 | 10 | 4 [0] | [1] 4 | hycC | hydrogenase 3, membrane subunit |
| * | * | ÷ | W3110S.gb | 2876788 | 2876811 | 24 | 2 [1] | [0] 2 | iap/ygbF | aminopeptidase in alkaline phosphatase isozyme conversion/hypothetical protein |
| * | * | ÷ | W3110S.gb | 2893895 | 2893917 | 23 | 2 [0] | [1] 4 | ygcQ | predicted flavoprotein |
| * | * | ÷ | W3110S.gb | 2902946 | 2902962 | 17 | 5 [1] | [1] 2 | ygcE/ygcF | predicted kinase/conserved hypothetical protein |
| * | * | ÷ | W3110S.gb | 2905211 | 2905216 | 6 | 6 [1] | [0] 2 | ygcG | hypothetical protein |
| * | * | ÷ | W3110S.gb | 3044664 | 3044733 | 70 | 4 [1] | [1] 2 | ygfF/gcvP | predicted NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex |
| * | * | ÷ | W3110S.gb | 3124980 | 3124987 | 8 | 2 [0] | [0] 2 | glcE | glycolate oxidase FAD binding subunit |
| * | * | ÷ | W3110S.gb | 3178745 | 3178786 | 42 | 2 [1] | [1] 2 | ygiB | conserved outer membrane protein |
| * | * | ÷ | W3110S.gb | 3209432 | 3209436 | 5 | 2 [1] | [0] 2 | ygjD/rpsU | predicted peptidase/30S ribosomal subunit protein S21 |
| * | * | ÷ | W3110S.gb | 3252434 | 3252477 | 44 | 2 [1] | [1] 3 | yhaJ | predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 3488817 | 3488821 | 5 | 4 [1] | [1] 3 | yijO | predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 3503622 | 3503628 | 7 | 2 [1] | [0] 2 | metF | 5,10‑methylenetetrahydrofolate reductase |
| * | * | ÷ | W3110S.gb | 3514041 | 3514052 | 12 | 2 [1] | [1] 3 | ftsN | essential cell division protein |
| * | * | ÷ | W3110S.gb | 3651005 | 3651005 | 1 | 3 [0] | [0] 2 | aslA | acrylsulfatase‑like enzyme |
| * | * | ÷ | W3110S.gb | 3799039 | 3799042 | 4 | 2 [0] | [0] 2 | yicM | predicted transporter |
| * | * | ÷ | W3110S.gb | 3859267 | 3859301 | 35 | 4 [1] | [0] 2 | yibK/lldD | predicted rRNA methylase/L‑lactate dehydrogenase, FMN‑linked |
| * | * | ÷ | W3110S.gb | 4023709 | 4023727 | 19 | 3 [0] | [1] 2 | nikC | nickel transporter subunit |
| * | * | ÷ | W3110S.gb | 4029777 | 4029790 | 14 | 2 [0] | [1] 2 | yhhS | predicted transporter |
| * | * | ÷ | W3110S.gb | 4083754 | 4083833 | 80 | 2 [1] | [1] 4 | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | * | ÷ | W3110S.gb | 4090497 | 4090500 | 4 | 4 [0] | [1] 3 | malQ | 4‑alpha‑glucanotransferase |
| * | * | ÷ | W3110S.gb | 4157464 | 4157484 | 21 | 2 [1] | [0] 4 | yheS | fused predicted transporter subunits and ATP‑binding components of ABC superfamily |
| * | * | ÷ | W3110S.gb | 4213636–4215887 | 4216721–4215891 | 5–3086 | 2 [0] | [0] 2 | [rrlE]–[rrfE] | [rrlE],[rrfE] |
| * | * | ÷ | W3110S.gb | 4266870 | 4266883 | 14 | 2 [1] | [1] 6 | qor | quinone oxidoreductase, NADPH‑dependent |
| * | * | ÷ | W3110S.gb | 4320906 | 4320956 | 51 | 3 [1] | [1] 2 | phnM | carbon‑phosphorus lyase complex subunit |
| * | * | ÷ | W3110S.gb | 4326154 | 4326181 | 28 | 2 [0] | [1] 4 | phnG | carbon‑phosphorus lyase complex subunit |
| * | * | ÷ | W3110S.gb | 4344046 | 4344062 | 17 | 4 [1] | [0] 2 | adiA | biodegradative arginine decarboxylase |
| * | * | ÷ | W3110S.gb | 4393966 | 4393991 | 26 | 2 [1] | [1] 9 | yjeP | predicted mechanosensitive channel |
| * | * | ÷ | W3110S.gb | 4401144 | 4401163 | 20 | 3 [1] | [0] 3 | amiB | N‑acetylmuramoyl‑l‑alanine amidase II |
| * | * | ÷ | W3110S.gb | 4403349 | 4403367 | 19 | 2 [1] | [0] 3 | mutL | methyl‑directed mismatch repair protein |
| * | * | ÷ | W3110S.gb | 4406885 | 4406891 | 7 | 3 [1] | [0] 2 | hflK | modulator for HflB protease specific for phage lambda cII repressor |
| * | * | ÷ | W3110S.gb | 4601184 | 4601225 | 42 | 3 [1] | [1] 4 | yjjN | predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | W3110S.gb | 70061 = | 22 (1.160) | 29 (1.950) +CGCGTACAACT |
11/80 | NT | 65.0% | intergenic (‑13/‑326) | araB/araC | L‑ribulokinase/DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 236044 = | 18 (0.950) | intergenic (‑42/‑23) | rnhA/dnaQ | ribonuclease HI, degrades RNA of DNA‑RNA hybrids/DNA polymerase III epsilon subunit | |||||
| * | ? | W3110S.gb | = 71265 | 23 (1.210) | 21 (1.530) +AGGGTCCCTAAGTC |
13/74 | NT | 70.0% | coding (879/879 nt) | araC | DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 3464879 = | 2 (0.110) | intergenic (‑255/+46) | murB/rrfB | UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding/5S ribosomal RNA | |||||
| * | ? | W3110S.gb | = 274373 | NA (NA) | 17 (0.890) | 5/102 | NT | 100% | intergenic (‑32/‑176) | insH/mmuP | IS5 transposase and trans‑activator/predicted S‑methylmethionine transporter |
| ? | W3110S.gb | 576000 = | 0 (0.000) | pseudogene (109/1128 nt) | nmpC | DLP12 prophage region; ECK0544:JW5078:b0553; truncated outer membrane porin | |||||
| * | ? | W3110S.gb | 314453 = | 14 (0.740) | 13 (0.710) +TC |
10/98 | NT | 65.9% | coding (873/888 nt) | eaeH | attaching and effacing protein, pathogenesis factor |
| ? | W3110S.gb | 3932930 = | 0 (0.000) | coding (219/1608 nt) | dppA | dipeptide transporter | |||||
| * | ? | W3110S.gb | = 315707 | NA (NA) | 29 (1.520) | 13/102 | NT | 100% | coding (654/687 nt) | ykgA | predicted DNA‑binding transcriptional regulator |
| ? | W3110S.gb | 576911 = | 0 (0.000) | coding (76/498 nt) | ybcS | predicted lysozyme | |||||
| * | ? | W3110S.gb | 566000 = | NA (NA) | 57 (3.000) | 20/102 | NT | 100% | intergenic (+90/‑56) | ybcD/insE | DLP12 prophage region; ECK0532:JW0527:b4508; predicted replication protein fragment/IS3 element protein InsE |
| ? | W3110S.gb | = 576913 | 0 (0.000) | coding (78/498 nt) | ybcS | predicted lysozyme | |||||
| * | ? | W3110S.gb | 713380 = | 21 (1.100) | 37 (2.110) | 14/94 | NT | 69.0% | intergenic (‑156/‑29) | ybfF/seqA | conserved hypothetical protein/regulatory protein for replication initiation |
| ? | W3110S.gb | = 4125340 | 14 (0.800) | coding (836/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 713954 | 16 (0.840) | 45 (2.370) | 20/102 | NT | 57.7% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | W3110S.gb | 2809398 = | 50 (2.630) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | W3110S.gb | 1209367 = | 9 (0.470) | 10 (0.770) | 5/70 | NT | 66.4% | coding (290/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | 1211196 = | 4 (0.310) | pseudogene (37/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | = 1209382 | 8 (0.420) | 7 (0.540) | 4/70 | NT | 59.7% | coding (305/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | = 1211179 | 4 (0.310) | pseudogene (54/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | 2018571 = | 0 (0.000) | 8 (0.450) | 5/96 | NT | 100% | coding (567/687 nt) | fliH | flagellar biosynthesis protein |
| ? | W3110S.gb | 2519723 = | NA (NA) | intergenic (+33/‑54) | nupC/insL | nucleoside (except guanosine) transporter/predicted transposase | |||||
| * | ? | W3110S.gb | = 2018583 | 0 (0.000) | 10 (0.550) | 7/98 | NT | 100% | coding (579/687 nt) | fliH | flagellar biosynthesis protein |
| ? | W3110S.gb | = 2521059 | NA (NA) | intergenic (+170/+30) | insL/yfeA | predicted transposase/predicted diguanylate cyclase | |||||
| * | ? | W3110S.gb | 2172308 = | NA (NA) | 40 (2.150) | 17/100 | NT | 100% | pseudogene (1563/2041 nt) | gatR | DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 |
| ? | W3110S.gb | = 3920281 | 0 (0.000) | coding (88/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | = 2173564 | NA (NA) | 28 (1.500) | 13/100 | NT | 100% | pseudogene (307/2041 nt) pseudogene (307/339 nt) |
gatR gatR |
DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 DNA‑binding transcriptional regulator, C‑ter fragment; ECK2083:JW2074:b2090 |
| ? | W3110S.gb | 3920278 = | 0 (0.000) | coding (91/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | = 2173565 | NA (NA) | 15 (0.790) | 9/102 | NT | 100% | pseudogene (306/2041 nt) pseudogene (306/339 nt) |
gatR gatR |
DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 DNA‑binding transcriptional regulator, C‑ter fragment; ECK2083:JW2074:b2090 |
| ? | W3110S.gb | = 3932933 | 0 (0.000) | coding (222/1608 nt) | dppA | dipeptide transporter | |||||
| * | ? | W3110S.gb | = 2412225 | NA (NA) | 17 (0.890) | 9/102 | NT | 70.8% | intergenic (‑55/‑782) | insA/yfbQ | IS1 element protein/predicted aminotransferase |
| ? | W3110S.gb | = 3748807 | 7 (0.370) | coding (176/984 nt) | tnaB | tryptophan transporter of low affinity | |||||
| * | ? | W3110S.gb | = 2855747 | 27 (1.420) | 15 (0.800) | 6/100 | NT | 40.3% | intergenic (‑285/‑2) | ygbA/mutS | hypothetical protein/methyl‑directed mismatch repair protein |
| ? | W3110S.gb | 4124505 = | 18 (0.970) | coding (1/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | W3110S.gb | 3748799 = | 3 (0.160) | 19 (1.000) | 10/102 | NT | 86.4% | coding (184/984 nt) | tnaB | tryptophan transporter of low affinity |
| ? | W3110S.gb | 4056222 = | NA (NA) | intergenic (‑564/+15) | yrhB/insB | hypothetical protein/IS1 transposase InsAB' | |||||
| * | ? | W3110S.gb | 4547364 = | 26 (1.370) | 9 (0.580) | 5/84 | NT | 40.6% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | 4547678 = | 5 (0.320) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||