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 |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| MC JC | 260,173 | Δ13,782 bp | IS5‑mediated | proB–[ykfC] | 19 genes proB, proA, thrW, ykfI, yafW, ykfH, ykfG, yafX, ykfF, ykfB, yafY, yafZ, ykfA, perR, insN, insI1, insN, eyeA, [ykfC] |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 635,355 | G→A | R8* (CGA→TGA) N405N (AAC→AAT) |
ybdM ← ybdN ← |
ParB‑like nuclease domain‑containing protein YbdM putative PAPS reductase/DUF3440 domain‑containing protein YbdN |
| RA | 696,582 | C→T | noncoding (35/75 nt) | glnV ← | tRNA‑Gln |
| RA | 811,531 | G→A | G384D (GGT→GAT) V4I (GTT→ATT) |
bioF → bioC → |
8‑amino‑7‑oxononanoate synthase malonyl‑acyl carrier protein methyltransferase |
| RA | 1,097,494 | T→A | intergenic (+665/+71) | ycdU → / ← serX | uncharacterized protein YcdU/tRNA‑Ser |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,705,108 | G→A | G54R (GGG→AGG) | cnu → | H‑NS‑ and StpA‑binding protein |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,406,142 | IS1 (+) +9 bp | coding (492‑500/939 nt) | lrhA ← | DNA‑binding transcriptional dual regulator LrhA |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 4,132,697 | G→A | E28K (GAG→AAG) | metF → | 5,10‑methylenetetrahydrofolate reductase |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,566,642 | G→A | S202L (TCG→TTG) | yjiN ← | DUF445 domain‑containing protein YjiN |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423764–3424233 | 3424477–3424238 | 6–714 | 27 [26] | [25] 27 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 146734 = | 81 (0.890) | 28 (0.310) | 26/598 | 2.3 | 25.7% | intergenic (‑40/‑234) | panD/rpnC | aspartate 1‑decarboxylase proenzyme/recombination‑promoting nuclease RpnC |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 146735 | 82 (0.900) | 24 (0.260) | 22/598 | 2.9 | 22.6% | intergenic (‑41/‑233) | panD/rpnC | aspartate 1‑decarboxylase proenzyme/recombination‑promoting nuclease RpnC |
| ? | NC_000913 | 270541 = | NA (NA) | noncoding (1/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 273955 = | NA (NA) | 69 (0.760) | 45/598 | 0.8 | 66.3% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 679345 = | 35 (0.390) | coding (62/555 nt) | ybeT | Sel1 repeat‑containing protein YbeT | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 65 (0.720) | 46/598 | 0.7 | 62.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 679348 | 39 (0.430) | coding (59/555 nt) | ybeT | Sel1 repeat‑containing protein YbeT | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 34 (0.370) | 28/598 | 2.1 | 27.4% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 691806 = | 90 (0.990) | intergenic (‑22/+68) | ybeX/ybeY | CorC‑HlyC family protein YbeX/endoribonuclease YbeY | |||||
| * | ? | NC_000913 | = 1096852 | 128 (1.410) | 33 (0.360) | 25/596 | 2.4 | 20.5% | intergenic (+23/+713) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| ? | NC_000913 | 1467910 = | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 76 (0.840) | 50 (0.580) | 38/566 | 1.1 | 38.2% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 90 (1.050) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 79 (0.870) | 58 (0.670) | 41/566 | 0.9 | 41.3% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 90 (1.050) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 1 (0.010) | 94 (1.080) | 63/574 | 0.2 | 99.0% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | = 1300693 | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1299498 | 1 (0.010) | 33 (0.380) | 26/574 | 2.2 | 97.1% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1427599 = | NA (NA) | noncoding (1196/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1299499 = | NA (NA) | 107 (1.230) | 67/574 | 0.1 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1300694 = | 0 (0.000) | intergenic (+147/‑488) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1300694 = | 0 (0.000) | 21 (0.240) | 21/572 | 2.9 | 100% | intergenic (+147/‑488) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | = 1428794 | NA (NA) | noncoding (1/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 24 (0.260) | 23/598 | 2.7 | 26.1% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1996011 = | 68 (0.750) | coding (194/225 nt) | yecF | DUF2594 domain‑containing protein YecF | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 64 (0.700) | 53/598 | 0.5 | 73.6% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2176309 = | 23 (0.250) | coding (13/1263 nt) | gatZ | putative tagatose‑1,6‑bisphosphate aldolase 2 chaperone | |||||
| * | ? | NC_000913 | 1399590 = | 68 (0.750) | 32 (0.350) | 29/598 | 2.0 | 32.0% | intergenic (‑64/+131) | fnr/ogt | DNA‑binding transcriptional dual regulator FNR/methylated‑DNA‑‑[protein]‑cysteine S‑methyltransferase |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1399593 | 66 (0.730) | 30 (0.330) | 26/596 | 2.3 | 31.2% | intergenic (‑67/+128) | fnr/ogt | DNA‑binding transcriptional dual regulator FNR/methylated‑DNA‑‑[protein]‑cysteine S‑methyltransferase |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1996014 | 68 (0.750) | 33 (0.360) | 30/596 | 1.9 | 32.7% | coding (197/225 nt) | yecF | DUF2594 domain‑containing protein YecF |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 2070271 | NA (NA) | 73 (0.800) | 50/598 | 0.6 | 68.2% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 2389243 | 34 (0.370) | coding (128/849 nt) | yfbP | uncharacterized protein YfbP | |||||
| * | ? | NC_000913 | = 2176312 | 23 (0.250) | 64 (0.700) | 43/598 | 0.9 | 73.6% | coding (10/1263 nt) | gatZ | putative tagatose‑1,6‑bisphosphate aldolase 2 chaperone |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 29 (0.320) | 25/598 | 2.5 | 30.9% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2492975 = | 65 (0.720) | coding (280/1251 nt) | frc | formyl‑CoA transferase | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 30 (0.330) | 26/596 | 2.3 | 31.6% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2492978 | 65 (0.720) | coding (277/1251 nt) | frc | formyl‑CoA transferase | |||||
| * | ? | NC_000913 | 2389239 = | 33 (0.360) | 57 (0.630) | 50/598 | 0.6 | 63.3% | coding (124/849 nt) | yfbP | uncharacterized protein YfbP |
| ? | NC_000913 | 2996361 = | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||