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 | 20,724 | G→A | 5.1% | intergenic (‑216/+91) | insA ← / ← rpsT | IS1 repressor TnpA/30S ribosomal subunit protein S20 |
| RA | 27,126 | C→A | 6.1% | Q284K (CAG→AAG) | ispH → | 4‑hydroxy‑3‑methylbut‑2‑enyl diphosphate reductase, 4Fe‑4S protein |
| RA | 218,831 | C→A | 5.5% | G101V (GGC→GTC) | metN ← | DL‑methionine transporter subunit |
| RA | 235,769 | G→T | 5.2% | pseudogene (177/273 nt) | yafF → | pseudogene, H repeat‑associated protein |
| RA | 249,908 | A→G | 6.8% | intergenic (+260/‑58) | yafP → / → ykfJ | putative acyl‑CoA transferase/pseudogene |
| RA | 249,918 | T→A | 8.0% | intergenic (+270/‑48) | yafP → / → ykfJ | putative acyl‑CoA transferase/pseudogene |
| RA | 249,924 | T→C | 7.9% | intergenic (+276/‑42) | yafP → / → ykfJ | putative acyl‑CoA transferase/pseudogene |
| RA | 259,937 | T→G | 5.9% | R8R (AGG→CGG) | ykfH ← | uncharacterized protein |
| RA | 274,938 | T→A | 5.8% | Q152L (CAG→CTG) | insB1 ← | IS1 transposase B |
| RA | 277,658 | T→G | 5.3% | M13L (ATG→CTG) | yagA ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| RA | 345,384 | G→C | 5.6% | intergenic (+101/‑339) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 345,387 | G→A | 5.1% | intergenic (+104/‑336) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 345,428 | T→C | 5.1% | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 353,317 | C→T | 6.0% | intergenic (+152/+185) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| RA | 372,807 | Δ1 bp | 7.4% | intergenic (+40/+184) | yaiL → / ← frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| RA | 372,808 | G→A | 7.5% | intergenic (+41/+183) | yaiL → / ← frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| RA | 513,343 | G→A | 6.8% | T131T (ACC→ACT) | ybbN ← | DnaK co‑chaperone, thioredoxin‑like protein |
| RA | 656,982 | A→G | 9.1% | intergenic (‑148/+111) | ybeF ← / ← lipB | LysR family putative transcriptional regulator/octanoyltransferase; octanoyl‑[ACP]:protein N‑octanoyltransferase |
| RA | 657,031 | T→C | 9.5% | intergenic (‑197/+62) | ybeF ← / ← lipB | LysR family putative transcriptional regulator/octanoyltransferase; octanoyl‑[ACP]:protein N‑octanoyltransferase |
| RA | 692,593 | Δ1 bp | 100% | intergenic (‑4/+376) | metT ← / ← asnB | tRNA‑Met/asparagine synthetase B |
| RA | 694,919 | G→T | 8.8% | intergenic (‑286/+111) | asnB ← / ← umpH | asparagine synthetase B/UMP phosphatase |
| RA | 694,921 | A→G | 5.6% | intergenic (‑288/+109) | asnB ← / ← umpH | asparagine synthetase B/UMP phosphatase |
| RA | 694,922 | T→C | 9.1% | intergenic (‑289/+108) | asnB ← / ← umpH | asparagine synthetase B/UMP phosphatase |
| RA | 694,942 | G→C | 5.5% | intergenic (‑309/+88) | asnB ← / ← umpH | asparagine synthetase B/UMP phosphatase |
| RA | 694,943 | G→C | 5.5% | intergenic (‑310/+87) | asnB ← / ← umpH | asparagine synthetase B/UMP phosphatase |
| RA | 694,945 | G→T | 6.7% | intergenic (‑312/+85) | asnB ← / ← umpH | asparagine synthetase B/UMP phosphatase |
| RA | 694,947 | T→C | 6.6% | intergenic (‑314/+83) | asnB ← / ← umpH | asparagine synthetase B/UMP phosphatase |
| RA | 694,948 | G→T | 6.7% | intergenic (‑315/+82) | asnB ← / ← umpH | asparagine synthetase B/UMP phosphatase |
| RA | 726,100 | A→G | 5.6% | R354R (CGA→CGG) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 726,110 | T→C | 6.7% | C358R (TGT→CGT) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,369 | A→G | 5.1% | A777A (GCA→GCG) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,375 | A→G | 5.1% | G779G (GGA→GGG) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 811,097 | G→A | 8.2% | intergenic (+94/+98) | uvrB → / ← ybhK | excinulease of nucleotide excision repair, DNA damage recognition component/putative NAD(P)‑binding transferase |
| RA | 811,098 | C→A | 6.5% | intergenic (+95/+97) | uvrB → / ← ybhK | excinulease of nucleotide excision repair, DNA damage recognition component/putative NAD(P)‑binding transferase |
| RA | 811,100:1 | +A | 5.8% | intergenic (+97/+95) | uvrB → / ← ybhK | excinulease of nucleotide excision repair, DNA damage recognition component/putative NAD(P)‑binding transferase |
| RA | 811,146 | C→A | 6.6% | intergenic (+143/+49) | uvrB → / ← ybhK | excinulease of nucleotide excision repair, DNA damage recognition component/putative NAD(P)‑binding transferase |
| RA | 859,422 | A→C | 7.0% | T109P (ACC→CCC) | fsaA → | fructose‑6‑phosphate aldolase 1 |
| RA | 893,516:1 | +C | 8.6% | coding (72/489 nt) | ybjO → | DUF2593 family inner membrane protein |
| RA | 893,516:2 | +A | 8.6% | coding (72/489 nt) | ybjO → | DUF2593 family inner membrane protein |
| RA | 893,517:1 | +A | 8.6% | coding (73/489 nt) | ybjO → | DUF2593 family inner membrane protein |
| RA | 893,520 | C→G | 7.8% | Q26E (CAG→GAG) ‡ | ybjO → | DUF2593 family inner membrane protein |
| RA | 893,521 | A→C | 8.3% | Q26P (CAG→CCG) ‡ | ybjO → | DUF2593 family inner membrane protein |
| RA | 893,522:1 | +C | 8.3% | coding (78/489 nt) | ybjO → | DUF2593 family inner membrane protein |
| RA | 893,522:2 | +T | 8.3% | coding (78/489 nt) | ybjO → | DUF2593 family inner membrane protein |
| RA | 910,671 | T→G | 11.5% | intergenic (‑358/+137) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 910,682 | T→G | 11.8% | intergenic (‑369/+126) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 920,106 | C→T | 8.0% | Q463* (CAG→TAG) | clpA → | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity |
| RA | 931,037 | G→A | 6.4% | A786A (GCG→GCA) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| RA | 931,040 | A→G | 6.5% | P787P (CCA→CCG) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| RA | 946,743 | G→T | 6.3% | F756L (TTC→TTA) | pflB ← | formate C‑acetyltransferase 1, anaerobic; pyruvate formate‑lyase 1 |
| RA | 981,924 | C→A | 6.9% | G172V (GGC→GTC) | ompF ← | outer membrane porin 1a (Ia;b;F) |
| RA | 988,636 | G→T | 5.6% | G853G (GGG→GGT) | pepN → | aminopeptidase N |
| RA | 1,020,092 | G→T | 5.2% | E56* (GAG→TAG) | helD → | DNA helicase IV |
| RA | 1,042,210 | A→C | 6.7% | S398A (TCA→GCA) | gfcD ← | putative O‑antigen capsule production periplasmic protein |
| RA | 1,062,549 | C→T | 6.2% | intergenic (‑2/+19) | yccJ ← / ← wrbA | uncharacterized protein/NAD(P)H:quinone oxidoreductase |
| RA | 1,140,403 | C→T | 5.9% | T3I (ACA→ATA) | rluC → | 23S rRNA pseudouridine(955,2504,2580) synthase |
| RA | 1,218,978 | C→T | 6.5% | intergenic (+73/‑42) | ymgJ → / → ycgI | uncharacterized protein/pseudogene |
| RA | 1,250,869 | G→T | 8.8% | N180K (AAC→AAA) | ycgV ← | putative adhesin |
| RA | 1,254,694 | G→T | 5.5% | R522R (CGC→CGA) | dauA ← | C4‑dicarboxylic acid transporter |
| RA | 1,264,818 | G→T | 12.2% | noncoding (40/67 nt) | rdlA → | sRNA antisense regulator affects LdrA translation; proposed addiction module in LDR‑A repeat, with toxic peptide LdrA |
| RA | 1,264,930 | A→T | 8.9% | intergenic (+85/+229) | rdlA → / ← ldrB | sRNA antisense regulator affects LdrA translation; proposed addiction module in LDR‑A repeat, with toxic peptide LdrA/toxic polypeptide, small |
| RA | 1,264,932 | T→G | 6.9% | intergenic (+87/+227) | rdlA → / ← ldrB | sRNA antisense regulator affects LdrA translation; proposed addiction module in LDR‑A repeat, with toxic peptide LdrA/toxic polypeptide, small |
| RA | 1,266,001 | G→T | 7.5% | intergenic (+85/+204) | rdlC → / ← chaA | sRNA antisense regulator affects LdrC translation; proposed addiction module in LDR‑C repeat, with toxic peptide LdrC/calcium/sodium:proton antiporter |
| RA | 1,276,748 | C→A | 5.8% | L477M (CTG→ATG) | narG → | nitrate reductase 1, alpha subunit |
| RA | 1,282,249 | A→G | 10.2% | intergenic (+267/+273) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,430 | C→T | 5.1% | intergenic (+448/+92) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,283,577 | C→A | 5.7% | K168N (AAG→AAT) | purU ← | formyltetrahydrofolate hydrolase |
| RA | 1,301,313 | G→A | 6.7% | P32L (CCA→CTA) | yciU ← | UPF0263 family protein |
| RA | 1,302,193 | G→T | 5.2% | T237N (ACC→AAC) | clsA ← | cardiolipin synthase 1 |
| RA | 1,342,844 | G→A | 5.9% | A109V (GCC→GTC) | rnb ← | ribonuclease II |
| RA | 1,344,548 | C→T | 6.5% | G250D (GGT→GAT) | fabI ← | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent |
| RA | 1,382,083 | G→A | 5.3% | P369P (CCG→CCA) | tyrR → | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase |
| RA | 1,417,757 | C→G | 8.6% | pseudogene (300/444 nt) P34R (CCG→CGG) |
rzpR → rzoR → |
pseudogene, Rac prophage; Bacteriophage Rz lysis protein family;Phage or Prophage Related; putative Rac prophage endopeptidase; completely contained in another CDS Rac prophage; putative lipoprotein |
| RA | 1,422,040 | A→G | 8.2% | pseudogene (944/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,060 | G→C | 11.9% | pseudogene (924/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,648 | G→C | 5.9% | pseudogene (336/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,440,280 | T→C | 8.7% | A48A (GCT→GCC) | ydbL → | DUF1318 family protein |
| RA | 1,460,458 | T→C | 5.7% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,467 | G→A | 5.8% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,515 | G→C | 8.5% | pseudogene (867/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,527 | C→T | 6.7% | pseudogene (879/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,689 | A→G | 6.6% | pseudogene (1041/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,695 | T→G | 7.2% | pseudogene (1047/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,752 | C→T | 9.9% | pseudogene (1104/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,761 | A→G | 9.6% | pseudogene (1113/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,887 | G→C | 9.2% | pseudogene (1239/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,896 | C→T | 9.4% | pseudogene (1248/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,498,535 | C→T | 5.9% | Q188* (CAG→TAG) | insQ → | IS609 transposase B |
| RA | 1,503,183 | C→A | 10.1% | E47* (GAA→TAA) | yncJ ← | uncharacterized protein |
| RA | 1,505,066 | C→A | 8.0% | L269L (CTC→CTA) | ydcR → | putative DNA‑binding transcriptional regulator/putative amino transferase |
| RA | 1,566,159 | G→A | 9.2% | D48D (GAC→GAT) | gadB ← | glutamate decarboxylase B, PLP‑dependent |
| RA | 1,571,757 | A→G | 5.0% | P40P (CCT→CCC) | yddB ← | putative TonB‑dependent outer membrane receptor |
| RA | 1,620,254 | Δ1 bp | 6.9% | coding (1384/2046 nt) | dcp ← | dipeptidyl carboxypeptidase II |
| RA | 1,622,276 | C→T | 9.3% | T168M (ACG→ATG) | ydfG → | NADP‑dependent 3‑hydroxy acid dehydrogenase; malonic semialdehyde reductase |
| RA | 1,629,745 | T→A | 5.2% | A120A (GCA→GCT) | stfQ ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,665,932 | C→A | 5.7% | P100P (CCC→CCA) | asr → | acid shock‑inducible periplasmic protein |
| RA | 1,702,919 | C→G | 6.7% | Q582E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,702,966 | T→A | 7.0% | R597R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,705,034 | C→A | 5.7% | Q192K (CAG→AAG) | rsxG → | SoxR iron‑sulfur cluster reduction factor component; putative membrane protein of electron transport complex |
| RA | 1,710,601 | G→T | 5.3% | S293R (AGC→AGA) | tyrS ← | tyrosyl‑tRNA synthetase |
| RA | 1,792,383 | C→A | 8.7% | G273W (GGG→TGG) | pheS ← | phenylalanine tRNA synthetase, alpha subunit |
| RA | 1,797,963 | G→A | 5.5% | pseudogene (189/1476 nt) | arpB → | pseudogene, ankyrin repeats |
| RA | 1,879,439 | C→A | 8.1% | A173E (GCG→GAG) | yeaW → | putative YeaWX dioxygenase alpha subunit; 2Fe‑2S cluster |
| RA | 2,060,781 | C→T | 7.3% | G8R (GGA→AGA) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 2,086,677 | G→T | 5.2% | E267* (GAA→TAA) | hisC → | histidinol‑phosphate aminotransferase |
| RA | 2,113,323 | A→G | 6.0% | L106P (CTG→CCG) | wzxC ← | putative colanic acid exporter |
| RA | 2,175,459 | G→T | 7.9% | V295V (GTG→GTT) | yegV → | putative kinase |
| RA | 2,298,159 | T→C | 5.4% | intergenic (+287/+428) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,298,241 | T→C | 5.7% | intergenic (+369/+346) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,356,748 | G→A | 7.8% | P122L (CCT→CTT) | yfaY ← | inactive PncC family protein |
| RA | 2,465,527 | C→T | 13.5% | pseudogene (75/579 nt) | yfdL ← | pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related |
| RA | 2,546,408 | C→A | 8.9% | S233* (TCA→TAA) | amiA → | N‑acetylmuramoyl‑l‑alanine amidase I |
| RA | 2,707,492 | A→C | 13.1% | K413T (AAG→ACG) | srmB → | ATP‑dependent RNA helicase |
| RA | 2,707,699 | C→T | 7.5% | intergenic (+110/+99) | srmB → / ← yfiE | ATP‑dependent RNA helicase/putative DNA‑binding transcriptional regulator |
| RA | 2,707,703 | C→T | 16.3% | intergenic (+114/+95) | srmB → / ← yfiE | ATP‑dependent RNA helicase/putative DNA‑binding transcriptional regulator |
| RA | 2,719,426 | T→C | 100% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,730,346 | G→T | 10.9% | intergenic (+104/‑167) | bamD → / → raiA | BamABCDE complex OM biogenesis lipoprotein/cold shock protein associated with 30S ribosomal subunit |
| RA | 2,732,681 | C→T | 5.1% | A250T (GCG→ACG) | tyrA ← | fused chorismate mutase T/prephenate dehydrogenase |
| RA | 2,739,692 | C→T | 8.9% | intergenic (‑148/+101) | rpsP ← / ← ffh | 30S ribosomal subunit protein S16/Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) |
| RA | 2,740,209 | C→T | 6.7% | A316T (GCA→ACA) | ffh ← | Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) |
| RA | 2,754,049 | G→T | 6.1% | M48I (ATG→ATT) | yfjJ → | CP4‑57 prophage; uncharacterized protein |
| RA | 2,755,783 | G→A | 5.9% | Q373* (CAG→TAG) | yfjK ← | DEAD/H helicase‑like protein, CP4‑57 putative defective prophage |
| RA | 2,771,529 | T→C | 9.0% | V1519V (GTA→GTG) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,776,199 | A→G | 9.1% | intergenic (‑114/+225) | ypjA ← / ← pinH | adhesin‑like autotransporter/pseudogene, invertase resolvase family |
| RA | 2,776,221 | T→C | 9.2% | intergenic (‑136/+203) | ypjA ← / ← pinH | adhesin‑like autotransporter/pseudogene, invertase resolvase family |
| RA | 2,863,882 | C→A | 6.4% | G261V (GGC→GTC) | truD ← | tRNA(Glu) pseudouridine(13) synthase |
| RA | 3,023,253 | G→A | 7.3% | G346G (GGC→GGT) | ygfT ← | putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit |
| RA | 3,024,674 | C→A | 5.2% | intergenic (‑384/‑52) | ygfT ← / → uacT | putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit/uric acid permease |
| RA | 3,051,396 | C→T | 7.6% | R125H (CGC→CAC) | serA ← | D‑3‑phosphoglycerate dehydrogenase |
| RA | 3,084,347 | C→A | 6.0% | R214R (CGC→CGA) | endA → | DNA‑specific endonuclease I |
| RA | 3,237,983 | G→T | 8.0% | Q40K (CAG→AAG) | uxaC ← | uronate isomerase |
| RA | 3,243,351 | C→A | 6.8% | L104I (CTA→ATA) | yqjE → | DUF1469 family inner membrane protein |
| RA | 3,286,442 | G→T | 5.0% | Q85K (CAA→AAA) | rsmI ← | 16S rRNA C1402 2'‑O‑ribose methyltransferase, SAM‑dependent |
| RA | 3,302,464 | G→T | 6.0% | S688R (AGC→AGA) | pnp ← | polynucleotide phosphorylase/polyadenylase |
| RA | 3,313,029 | G→T | 6.1% | R345L (CGT→CTT) | argG → | argininosuccinate synthetase |
| RA | 3,323,804 | G→T | 5.1% | intergenic (+49/+137) | dacB → / ← obgE | D‑alanyl‑D‑alanine carboxypeptidase/GTPase involved in cell partioning and DNA repair |
| RA | 3,323,813 | G→A | 5.5% | intergenic (+58/+128) | dacB → / ← obgE | D‑alanyl‑D‑alanine carboxypeptidase/GTPase involved in cell partioning and DNA repair |
| RA | 3,323,815 | T→G | 5.5% | intergenic (+60/+126) | dacB → / ← obgE | D‑alanyl‑D‑alanine carboxypeptidase/GTPase involved in cell partioning and DNA repair |
| RA | 3,323,817 | Δ1 bp | 5.5% | intergenic (+62/+124) | dacB → / ← obgE | D‑alanyl‑D‑alanine carboxypeptidase/GTPase involved in cell partioning and DNA repair |
| RA | 3,384,766 | A→C | 9.2% | F208V (TTT→GTT) | tldD ← | putative peptidase |
| RA | 3,385,662:1 | +G | 8.2% | intergenic (‑275/+155) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
| RA | 3,416,890 | T→G | 6.3% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,416,899 | A→G | 12.1% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,422,276 | Δ1 bp | 10.3% | intergenic (‑155/‑319) | rrsD ← / → yrdA | 16S ribosomal RNA of rrnD operon/bacterial transferase hexapeptide domain protein |
| RA | 3,422,282 | Δ1 bp | 9.1% | intergenic (‑161/‑313) | rrsD ← / → yrdA | 16S ribosomal RNA of rrnD operon/bacterial transferase hexapeptide domain protein |
| RA | 3,422,286 | T→G | 9.5% | intergenic (‑165/‑309) | rrsD ← / → yrdA | 16S ribosomal RNA of rrnD operon/bacterial transferase hexapeptide domain protein |
| RA | 3,498,220 | T→G | 12.9% | intergenic (+78/+74) | frlR → / ← yhfS | putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| RA | 3,498,239 | A→C | 6.7% | intergenic (+97/+55) | frlR → / ← yhfS | putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| RA | 3,515,842 | G→T | 5.5% | S90* (TCG→TAG) | hofM ← | DNA catabolic putative pilus assembly protein |
| RA | 3,524,578:1 | +T | 5.1% | coding (1221/1725 nt) | yhgE ← | DUF4153 family putative inner membrane protein |
| RA | 3,524,578:2 | +G | 5.1% | coding (1221/1725 nt) | yhgE ← | DUF4153 family putative inner membrane protein |
| RA | 3,524,578:3 | +C | 5.1% | coding (1221/1725 nt) | yhgE ← | DUF4153 family putative inner membrane protein |
| RA | 3,615,780 | G→A | 5.4% | A1077T (GCC→ACC) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,630,389 | G→A | 5.8% | R128C (CGT→TGT) | yhiN ← | putative oxidoreductase |
| RA | 3,634,142 | C→T | 6.0% | intergenic (+237/‑80) | uspA → / → dtpB | universal stress global response regulator/dipeptide and tripeptide permease B |
| RA | 3,669,589 | A→G | 6.1% | intergenic (+121/+61) | yhjE → / ← yhjG | MFS superfamily sugar transport 1 family protein/putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,669,597 | C→T | 6.1% | intergenic (+129/+53) | yhjE → / ← yhjG | MFS superfamily sugar transport 1 family protein/putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,758,716 | A→G | 5.1% | R1058R (AGA→AGG) | rhsA → | Rhs family protein, putative polymorphic toxin; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| RA | 3,935,371 | G→T | 6.9% | noncoding (204/1542 nt) | rrsC → | 16S ribosomal RNA of rrnC operon |
| RA | 3,961,292 | T→C | 5.8% | V6A (GTG→GCG) | wecA → | UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
| RA | 3,991,416 | T→G | 17.8% | L25R (CTT→CGT) | uvrD → | DNA‑dependent ATPase I and helicase II |
| RA | 4,014,141 | C→A | 5.2% | R186S (CGT→AGT) | ubiB → | regulator of octaprenylphenol hydroxylation, ubiquinone synthesis; regulator of 2'‑N‑acetyltransferase; putative ABC1 family protein kinase |
| RA | 4,033,888 | A→C | 20.1% | noncoding (12/120 nt) | rrfA → | 5S ribosomal RNA of rrnA operon |
| RA | 4,054,006 | G→A | 6.8% | G67E (GGG→GAG) | yihL → | putative DNA‑binding transcriptional regulator |
| RA | 4,098,583 | G→A | 6.8% | intergenic (+141/‑179) | pfkA → / → sbp | 6‑phosphofructokinase I/sulfate transporter subunit |
| RA | 4,165,449 | C→T | 19.0% | noncoding (50/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,450 | A→C | 19.0% | noncoding (51/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,167,038 | A→T | 5.7% | V389V (GTA→GTT) | tufB → | translation elongation factor EF‑Tu 2 |
| RA | 4,167,041 | A→T | 5.6% | A390A (GCA→GCT) | tufB → | translation elongation factor EF‑Tu 2 |
| RA | 4,178,500 | C→T | 91.3% | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,202,979 | A→C | 40.0% | noncoding (12/120 nt) | rrfE → | 5S ribosomal RNA of rrnE operon |
| RA | 4,285,988 | C→T | 5.2% | intergenic (+266/+265) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,375,474 | G→T | 14.8% | D89Y (GAT→TAT) | yjeN → | uncharacterized protein |
| RA | 4,454,076 | G→T | 5.7% | R151S (CGC→AGC) | treC ← | trehalose‑6‑P hydrolase |
| RA | 4,467,949 | T→A | 6.5% | R60R (CGA→CGT) | argI ← | ornithine carbamoyltransferase 1 |
| RA | 4,471,348 | G→A | 5.7% | C769C (TGC→TGT) | valS ← | valyl‑tRNA synthetase |
| RA | 4,498,906 | T→C | 6.4% | pseudogene (81/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,498,909 | G→T | 6.8% | pseudogene (84/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,604,111 | T→C | 5.6% | intergenic (+34/+386) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,604,253 | T→G | 7.4% | intergenic (+176/+244) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,604,311 | G→A | 7.9% | intergenic (+234/+186) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,604,316 | C→T | 6.9% | intergenic (+239/+181) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,604,320 | T→C | 12.8% | intergenic (+243/+177) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,604,321 | A→G | 6.4% | intergenic (+244/+176) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,604,341 | Δ1 bp | 5.4% | intergenic (+264/+156) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| RA | 4,604,397 | G→A | 7.7% | intergenic (+320/+100) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 2027296 | 2027390 | 95 | 17 [8] | [16] 18 | rseX/yedS | sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology; putative outer membrane protein |
| * | * | ÷ | CP009273 | 2897085 | 2897256 | 172 | 19 [15] | [12] 17 | ygcE/queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| * | * | ÷ | CP009273 | 3432085 | 3432507 | 423 | 17 [10] | [15] 18 | [zntR]–[yhdN] | [zntR],[yhdN] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 69011 = | 136 (1.360) | 11 (0.130) | 5/206 | NT | 6.1% | coding (404/699 nt) | thiQ | thiamine, thiamine pyrophosphate ABC transporter ATPase; ThiBPQ thiamine, thiamine pyrophosphate importer |
| ? | CP009273 | = 3582121 | 226 (2.740) | coding (420/1071 nt) | ugpC | glycerol‑3‑phosphate transporter subunit | |||||
| * | ? | CP009273 | 360104 = | 96 (0.960) | 114 (1.140) | 42/250 | NT | 54.3% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | 370378 = | NA (NA) | 14 (0.150) | 4/234 | NT | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| ? | CP009273 | 372785 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | CP009273 | = 370385 | 129 (1.770) | 14 (0.210) | 6/164 | NT | 10.8% | intergenic (+48/‑530) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| ? | CP009273 | = 372977 | NA (NA) | noncoding (187/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | 370386 = | NA (NA) | 18 (0.280) | 8/164 | NT | 13.9% | noncoding (1/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | 372978 = | 124 (1.710) | intergenic (+211/+13) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | CP009273 | = 370414 | 129 (1.290) | 5 (0.070) | 4/176 | NT | 5.8% | noncoding (29/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | = 372848 | 72 (1.020) | noncoding (58/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | 370580 = | 100 (1.000) | 6 (0.090) | 4/166 | NT | 5.9% | noncoding (195/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | 372986 = | 124 (1.870) | intergenic (+219/+5) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | CP009273 | = 370587 | 101 (1.390) | 10 (0.150) | 7/166 | NT | 9.8% | noncoding (202/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | = 372977 | NA (NA) | noncoding (187/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | 1203246 = | 49 (0.490) | 23 (0.260) | 13/218 | NT | 43.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 16 (0.180) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 43 (0.430) | 23 (0.260) | 20/218 | NT | 46.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 16 (0.180) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1972777 | 41 (0.410) | 12 (0.120) | 5/250 | NT | 22.6% | intergenic (‑323/‑457) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||
| * | ? | CP009273 | 1972854 = | 10 (0.100) | 63 (0.630) | 35/250 | NT | 86.3% | intergenic (‑400/‑380) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | 3576788 = | NA (NA) | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA | |||||
| * | ? | CP009273 | = 1972861 | 13 (0.130) | 62 (0.620) | 28/250 | NT | 82.7% | intergenic (‑407/‑373) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||
| * | ? | CP009273 | = 2298543 | NA (NA) | 3 (0.040) | 3/188 | NT | NA | noncoding (648/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences |
| ? | CP009273 | = 4478328 | NA (NA) | noncoding (7/36 nt) | REP343 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP343 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | CP009273 | = 3323818 | 68 (0.960) | 8 (0.120) | 3/174 | NT | 10.7% | intergenic (+63/+123) | dacB/obgE | D‑alanyl‑D‑alanine carboxypeptidase/GTPase involved in cell partioning and DNA repair |
| ? | CP009273 | = 3591855 | NA (NA) | noncoding (99/99 nt) | RIP259 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP259 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||