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 | 100,078 | G→T | 6.7% | M145I (ATG→ATT) | murG → | N‑acetylglucosaminyl transferase |
| RA | 238,497 | G→T | 22.1% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,523 | G→T | 31.5% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 28.2% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| RA | 253,169 | T→C | 7.4% | intergenic (+8/‑298) | yafP → / → ykfJ | putative acyltransferase with acyl‑CoA N‑acyltransferase domain/conserved protein YkfJ |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 287,496 | G→C | 11.9% | W236C (TGG→TGC) | yagH → | CP4‑6 prophage; putative xylosidase/arabinosidase |
| RA | 360,147 | G→A | 6.4% | A52A (GCG→GCA) | cynX → | cyanate transporter |
| RA | 408,470 | C→T | 11.0% | intergenic (+9/‑139) | ppnP → / → ykiA | nucleoside phosphorylase PpnP/DUF2773 domain‑containing protein YkiA |
| RA | 498,557 | A→T | 8.5% | Y168F (TAC→TTC) | hemH → | ferrochelatase |
| RA | 588,945 | T→C | 7.7% | E670E (GAA→GAG) | nfrA ← | bacteriophage N4 receptor, outer membrane protein |
| RA | 777,853 | T→C | 6.8% | G38G (GGT→GGC) | tolB → | Tol‑Pal system periplasmic protein TolB |
| RA | 820,626 | A→T | 23.1% | intergenic (+38/‑167) | ybhL → / → ybhM | Bax1‑I family protein YbhL/Bax1‑I family protein YbhM |
| RA | 820,638 | C→A | 30.2% | intergenic (+50/‑155) | ybhL → / → ybhM | Bax1‑I family protein YbhL/Bax1‑I family protein YbhM |
| RA | 1,162,060 | A→G | 8.5% | E59G (GAG→GGG) | hinT → | purine nucleoside phosphoramidase |
| RA | 1,331,576 | T→A | 13.7% | Y177N (TAT→AAT) | topA → | DNA topoisomerase 1 |
| RA | 1,426,335 | A→G | 6.2% | intergenic (+355/‑119) | ydaY → / → ynaA | Rac prophage; putative uncharacterized protein YdaY/Rac prophage; putative prophage tail length tape measure domain‑containing protein YnaA |
| RA | 1,924,559 | A→G | 7.5% | F11F (TTT→TTC) | yebZ ← | putative inner membrane protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,040,756 | T→C | 11.2% | L92L (TTA→CTA) | msrQ → | periplasmic protein‑L‑methionine sulfoxide reductase heme binding subunit |
| RA | 2,046,213 | C→A | 6.1% | R426S (CGC→AGC) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,060,890 | Δ1 bp | 9.8% | coding (25/951 nt) | cbl ← | DNA‑binding transcriptional activator Cbl |
| RA | 2,126,354 | G→A | 7.5% | G279G (GGC→GGT) | fcl ← | GDP‑L‑fucose synthase |
| RA | 2,136,605 | C→T | 10.5% | V213V (GTG→GTA) | wza ← | outer membrane polysaccharide export protein Wza |
| RA | 2,162,165 | C→T | 6.9% | G234G (GGC→GGT) | mdtD → | putative multidrug efflux pump MdtD |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,177,245 | G→T | 61.2% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,299,509 | A→C | 7.4% | W24G (TGG→GGG) | napH ← | ferredoxin‑type protein NapH |
| RA | 2,383,318 | Δ1 bp | 7.5% | coding (606/1212 nt) | elaD → | protease ElaD |
| RA | 2,470,436 | C→A | 34.4% | Q436K (CAA→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,502,093 | T→C | 8.8% | Q798R (CAG→CGG) | fryA ← | putative PTS multiphosphoryl transfer protein FryA |
| RA | 2,505,459 | G→A | 6.8% | A30V (GCG→GTG) | ypdE ← | broad‑specificity exoaminopeptidase |
| RA | 2,525,321 | C→T | 5.5% | N65N (AAC→AAT) | yfeN → | conserved outer membrane protein YfeN |
| RA | 2,781,053 | T→A | 6.1% | E558D (GAA→GAT) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,924,592 | C→A | 18.0% | intergenic (‑68/+143) | csrB ← / ← syd | small regulatory RNA CsrB/SecY‑interacting protein |
| RA | 2,924,597 | G→T | 14.1% | intergenic (‑73/+138) | csrB ← / ← syd | small regulatory RNA CsrB/SecY‑interacting protein |
| RA | 3,069,655 | C→T | 5.9% | A51A (GCG→GCA) | mscS ← | small conductance mechanosensitive channel MscS |
| RA | 3,105,096 | C→T | 7.0% | P222S (CCG→TCG) | mltC → | membrane‑bound lytic murein transglycosylase C |
| RA | 3,119,536 | Δ1 bp | 5.6% | intergenic (‑424/+61) | yghJ ← / ← glcA | putative lipoprotein YghJ/glycolate/lactate:H(+) symporter GlcA |
| RA | 3,124,764 | G→A | 6.7% | A232A (GCC→GCT) | glcF ← | glycolate dehydrogenase, putative iron‑sulfur subunit |
| RA | 3,264,802 | A→C | 12.6% | R72R (CGT→CGG) | tdcC ← | threonine/serine:H(+) symporter |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,714,619 | C→T | 7.4% | P592P (CCG→CCA) | bisC ← | biotin sulfoxide reductase |
| RA | 3,828,979 | A→C | 33.3% | Q12P (CAA→CCA) ‡ | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,828,980 | A→C | 36.4% | Q12H (CAA→CAC) ‡ | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,886,015 | C→T | 5.9% | Q314* (CAG→TAG) | yidC → | membrane protein insertase YidC |
| RA | 3,905,022 | G→A | 9.0% | N192N (AAC→AAT) | bglF ← | beta‑glucoside specific PTS enzyme II/BglG kinase/BglG phosphatase |
| RA | 3,932,689 | G→C | 6.0% | L458L (CTG→CTC) | kup → | K(+):H(+) symporter Kup |
| RA | 4,108,823 | A→T | 9.9% | intergenic (+309/‑11) | pfkA → / → sbp | 6‑phosphofructokinase I/sulfate/thiosulfate ABC transporter periplasmic binding protein Sbp |
| RA | 4,114,767 | A→G | 6.2% | D271D (GAT→GAC) | glpX ← | fructose‑1,6‑bisphosphatase 2 |
| MC JC | 4,123,449 | Δ990 bp | 100% | coding (19‑1008/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,128,868 | G→A | 9.1% | G66D (GGT→GAT) | metB → | O‑succinylhomoserine(thiol)‑lyase/O‑ succinylhomoserine lyase |
| JC | 4,186,098 | +TCCGCTGGT | 80.9% | coding (749/4224 nt) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,296,060 | C→T | 28.8% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,314,598 | G→A | 6.3% | P169S (CCG→TCG) | phnP ← | 5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase |
| RA | 4,337,269 | C→T | 6.0% | G221S (GGC→AGC) | adiY ← | DNA‑binding transcriptional activator AdiY |
| RA | 4,393,459 | G→C | 6.4% | C203W (TGC→TGG) | queG ← | epoxyqueuosine reductase |
| RA | 4,399,191 | A→C | 8.3% | T594P (ACG→CCG) | mutL → | DNA mismatch repair protein MutL |
| RA | 4,485,718 | G→A | 6.9% | C78C (TGC→TGT) | pepA ← | aminopeptidase A/I |
| RA | 4,510,602 | C→A | 6.9% | intergenic (+469/+88) | yjhV → / ← fecE | KpLE2 phage‑like element; putative uncharacterized protein YjhV/ferric citrate ABC transporter ATP binding subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423780–3424525 | 3424525 | 1–746 | 14 [13] | [13] 14 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 258675 | NA (NA) | 3 (0.060) | 3/236 | NT | 5.2% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1293015 = | 55 (1.130) | intergenic (‑93/‑512) | hns/tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 1207790 = | 26 (0.530) | 43 (1.020) | 31/204 | NT | 63.0% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 28 (0.660) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 24 (0.490) | 25 (0.590) | 19/204 | NT | 50.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 28 (0.660) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1293038 | 46 (0.940) | 5 (0.100) | 5/236 | NT | 9.8% | intergenic (‑116/‑489) | hns/tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| ? | NC_000913 | = 1469240 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 60 (1.270) | 42/228 | NT | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3720633 = | NA (NA) | 53 (1.090) | 39/234 | NT | 48.4% | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | = 3824324 | 57 (1.170) | coding (1925/2109 nt) | spoT | bifunctional (p)ppGpp synthase/hydrolase SpoT | |||||