mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 37,693 | A→C | N44K (AAT→AAG) | caiC ← | putative crotonobetaine/carnitine‑CoA ligase |
| RA | 100,657 | T→G | I338M (ATT→ATG) | murG → | N‑acetylglucosaminyl transferase |
| JC | 111,028 | +46 bp | intergenic (+44/‑16) | secA → / → mutT | preprotein translocase subunit, ATPase/dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase |
| RA | 140,169 | T→G | T353P (ACC→CCC) | gcd ← | glucose dehydrogenase |
| RA | 146,136 | T→G | F352L (TTT→TTG) | yadE → | putative polysaccharide deacetylase lipoprotein |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 522,892 | A→C | intergenic (+62/‑369) | ybbP → / → rhsD | putative ABC transporter permease/Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 532,886 | A→C | N146H (AAC→CAC) | allA → | ureidoglycolate lyase, releasing urea |
| RA | 707,238 | T→G | F382L (TTT→TTG) | glnS → | glutamyl‑tRNA synthetase |
| RA | 943,261 | T→G | L768R (CTG→CGG) | dmsA → | dimethyl sulfoxide reductase, anaerobic, subunit A |
| RA | 1,343,574 | T→G | intergenic (‑246/+23) | osmB ← / ← yciT | osmotically and stress inducible lipoprotein/global regulator of transcription; DeoR family |
| RA | 1,356,671 | T→G | Y147S (TAC→TCC) | sapA ← | antimicrobial peptide transport ABC transporter periplasmic binding protein |
| JC JC | 1,425,236 | IS5 (–) +4 bp | coding (1455‑1458/1458 nt) | trkG → | Rac prophage; potassium transporter subunit |
| RA | 1,502,324 | T→G | intergenic (+169/‑133) | tehB → / → ydcL | tellurite, selenium methyltransferase, SAM‑dependent; tellurite, selenium resistance protein/lipoprotein |
| RA | 1,583,769 | T→G | Q64P (CAA→CCA) | safA ← | two‑component system connector membrane protein, EvgSA to PhoQP |
| RA | 1,614,214 | T→G | N164H (AAT→CAT) | sad ← | succinate semialdehyde dehydrogenase, NAD(P)+‑dependent |
| RA | 1,756,083 | T→C | L129P (CTG→CCG) | pykF → | pyruvate kinase I |
| RA | 1,821,514 | T→G | I36L (ATT→CTT) | chbB ← | N,N'‑diacetylchitobiose‑specific enzyme IIB component of PTS |
| RA | 1,903,203 | T→G | I41S (ATC→AGC) | manY → | mannose‑specific enzyme IIC component of PTS |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,085,510 | A→C | L6V (TTA→GTA) | yeeE ← | UPF0394 family inner membrane protein |
| RA | 2,133,868 | A→C | A595A (GCT→GCG) | wzc ← | colanic acid production tyrosine‑protein kinase; autokinase; Ugd phosphorylase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,173,468 | A→C | pseudogene (811/914 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,343,454 | T→G | Y239S (TAT→TCT) | yfaL ← | adhesin |
| RA | 2,406,260 | A→C | L128V (TTA→GTA) | lrhA ← | transcriptional repressor of flagellar, motility and chemotaxis genes |
| RA | 2,495,641 | A→C | intergenic (‑349/‑4) | yfdY ← / → lpxP | DUF2545 family putative inner membrane protein/palmitoleoyl‑acyl carrier protein (ACP)‑dependent acyltransferase |
| RA | 2,511,580 | A→C | L376W (TTG→TGG) | mntH ← | manganese/divalent cation transporter |
| RA | 2,583,262 | T→G | N73H (AAT→CAT) | nudK ← | GDP‑mannose pyrophosphatase |
| RA | 2,591,492 | A→C | L82F (TTA→TTC) | yffB → | putative ArsC family reductase |
| RA | 2,751,315 | T→G | F162C (TTC→TGC) | nadK → | NAD kinase |
| RA | 2,828,281 | T→G | L182R (CTG→CGG) | srlD → | sorbitol‑6‑phosphate dehydrogenase |
| RA | 3,000,850 | A→C | Q169P (CAG→CCG) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| RA | 3,021,392 | T→G | L26W (TTG→TGG) | xdhD → | putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding |
| RA | 3,067,245 | T→G | intergenic (‑72/+95) | ygfI ← / ← yggE | putative DNA‑binding transcriptional regulator/oxidative stress defense protein |
| RA | 3,378,200 | T→G | E3A (GAA→GCA) | rpsI ← | 30S ribosomal subunit protein S9 |
| RA | 3,560,455 | +G | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,927,462 | A→C | E103A (GAA→GCA) | asnA → | asparagine synthetase A |
| RA | 3,989,853 | T→G | E305A (GAA→GCA) | hemC ← | hydroxymethylbilane synthase |
| RA | 4,032,395 | A→C | E412A (GAA→GCA) | pepQ → | proline dipeptidase |
| RA | 4,153,955 | A→C | L298R (CTG→CGG) | argE ← | acetylornithine deacetylase |
| RA | 4,180,393 | A→C | E133A (GAA→GCA) | rplJ → | 50S ribosomal subunit protein L10 |
| RA | 4,182,313 | A→C | N357H (AAC→CAC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,187,214 | A→T | D622V (GAC→GTC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,586,506 | A→C | L86V (TTA→GTA) | hsdR ← | endonuclease R Type I restriction enzyme |
| RA | 4,609,163 | T→G | M173R (ATG→AGG) | yjjG → | dUMP phosphatase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423693–3424234 | 3424588–3424238 | 5–896 | 38 [35] | [37] 38 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 6 (0.080) | 50 (0.770) | 42/266 | 1.0 | 87.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 9 (0.140) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 6 (0.080) | 55 (0.850) | 43/266 | 0.9 | 88.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 9 (0.140) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 64 (0.910) | 54/290 | 0.5 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||