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] | |
| RA | 358,685 | G→A | L2L (CTC→CTT) | cynR ← | DNA‑binding transcriptional dual regulator CynR |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| JC JC | 568,591 | IS2 (+) +5 bp | coding (277‑281/333 nt) | emrE → | multidrug/betaine/choline efflux transporter EmrE |
| JC JC | 607,765 | IS150 (+) +3 bp | noncoding (26‑28/60 nt) | sokE ← | small RNA SokE |
| RA | 708,367 | G→A | A12T (GCG→ACG) | chiP → | chitooligosaccharide outer membrane channel |
| JC JC | 770,940 | IS5 (–) +4 bp | intergenic (+329/‑515) | mngB → / → cydA | alpha‑mannosidase/cytochrome bd‑I subunit 1 |
| RA | 846,189 | A→G | L92P (CTG→CCG) | glnQ ← | L‑glutamine ABC transporter ATP binding subunit |
| RA | 987,152 | G→T | intergenic (‑170/+433) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| JC JC | 1,186,598 | IS150 (–) +3 bp | coding (755‑757/1227 nt) | pepT → | peptidase T |
| RA | 1,305,066 | C→T | Q105* (CAA→TAA) | oppD → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppD |
| RA | 1,319,381 | T→A | L136F (TTA→TTT) | trpC ← | fused indole‑3‑glycerol phosphate synthase/phosphoribosylanthranilate isomerase |
| RA | 1,325,313 | G→T | G190C (GGC→TGC) | yciQ → | DUF2207 domain‑containing protein YciQ |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| MC JC | 1,469,241 | Δ117,356 bp | IS2‑mediated | ydbA–ydeP | 100 genes ydbA, insI2, ydbA, pdxI, ydbD, ynbA, ynbB, ynbC, ynbD, azoR, hrpA, ydcF, aldA, cybB, rydC, ydcA, yncP, hokB, mokB, sokB, trg, ydcI, ydcJ, opgD, ydcH, rimL, ydcK, tehA, tehB, ydcL, insQ, ydcO, sutR, rlhA, yncJ, hicA, hicB, ydcR, ydcS, ydcT, ydcU, ydcV, patD, yncL, ortT, ydcY, ydcZ, mnaT, curA, mcbR, yncD, yncE, ansP, yncG, yncH, ydcD, yncO, ydcC, pptA, yddH, nhoA, yddE, narV, narW, narY, narZ, narU, yddK, yddL, yddG, fdnG, fdnH, fdnI, yddM, adhP, maeA, sra, bdm, osmC, ddpF, ddpD, ddpC, ddpB, ddpA, ddpX, dosP, dosC, yddY, digH, gadC, gadB, pqqL, yddB, yddA, yneP, ydeM, ydeN, ydeO, safA, ydeP |
| RA | 1,648,662 | G→A | *52* (TGA→TAA) | ydfA → | DUF1391 domain‑containing protein YdfA |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,654,049 | G→T | H365N (CAT→AAT) | rspA ← | mandelate racemase/muconate lactonizing enzyme family protein RspA |
| RA | 1,667,887 | Δ1 bp | coding (678/1221 nt) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,750,445 | A→G | L190S (TTG→TCG) | ydhX ← | putative 4Fe‑4S ferredoxin‑like protein YdhX |
| RA | 1,841,778 | G→A | E97K (GAA→AAA) | nudG → | 5‑hydroxy‑CTP diphosphatase |
| RA | 1,843,167 | G→C | G266A (GGC→GCC) | gdhA → | glutamate dehydrogenase |
| RA | 1,925,047 | C→A | intergenic (‑78/‑61) | yobA ← / → holE | copper‑binding protein/DNA polymerase III subunit theta |
| RA | 1,965,861 | C→A | G111* (GGA→TGA) | flhB ← | flagellar biosynthesis protein FlhB |
| RA | 2,003,264 | C→T | E115K (GAA→AAA) | fliC ← | flagellar filament structural protein |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,254,251 | G→A | T312T (ACC→ACT) | rihB ← | pyrimidine‑specific ribonucleoside hydrolase RihB |
| JC JC | 2,255,511 | IS5 (+) +4 bp | coding (157‑160/660 nt) | yeiL → | DNA‑binding transcriptional activator YeiL |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| RA | 2,429,061 | A→T | L393H (CTC→CAC) | purF ← | amidophosphoribosyltransferase |
| RA | 2,866,825 | C→T | E243K (GAG→AAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,866,830 | (T)5→7 | coding (722/993 nt) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,867,454 | 2 bp→AA | coding (97‑98/993 nt) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,626,168 | C→T | V212V (GTG→GTA) | yhhJ ← | ABC transporter family protein YhhJ |
| MC JC | 3,682,261 | Δ34 bp | coding (1154‑1187/1287 nt) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| JC JC | 3,737,137 | IS2 (+) +5 bp | coding (37‑41/825 nt) | bax ← | putative glycoside hydrolase Bax |
| RA | 3,888,972 | Δ1 bp | coding (243/1416 nt) | tnaA → | tryptophanase |
| JC JC | 4,123,923 | IS2 (–) +5 bp | coding (530‑534/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,314,321 | (G)5→6 | intergenic (+124/+23) | yjdP → / ← phnP | protein YjdP/5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase |
| JC JC | 4,353,815 | IS2 (–) +5 bp | coding (899‑903/1518 nt) | lysU ← | lysine‑‑tRNA ligase/Ap4A synthetase/Ap3A synthetase |
| RA | 4,542,725 | (T)6→5 | intergenic (+92/‑390) | fimE → / → fimA | regulator for fimA/type 1 fimbriae major subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1978495 | 1979270–1978503 | 9–776 | 116 [0] | [0] 127 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423807–3424234 | 3424452–3424238 | 5–646 | 32 [31] | [31] 32 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3762422–3764074 | 3765155–3764083 | 10–2734 | 33 [31] | [31] 32 | rhsA | rhs element protein RhsA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 366291 = | 70 (0.740) | 3262 (35.210) +CCAAGCTT |
314/582 | 0.0 | 97.7% | coding (15/3075 nt) | lacZ | beta‑galactosidase |
| ? | NC_000913 | 712964 = | 85 (0.890) | intergenic (‑162/‑23) | ybfF/seqA | esterase/negative modulator of initiation of replication | |||||
| * | ? | NC_000913 | 381260 = | NA (NA) | 79 (0.830) | 58/598 | 0.4 | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382183 | NA (NA) | noncoding (924/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 382179 = | NA (NA) | 39 (0.410) | 29/594 | 2.3 | NA | noncoding (920/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 679007 = | 99 (1.050) | 584 (6.180) | 212/594 | -0.0 | 85.5% | coding (400/555 nt) | ybeT | Sel1 repeat‑containing protein YbeT |
| ? | NC_000913 | = 689045 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 31 (0.330) | 58 (0.640) | 42/566 | 0.9 | 62.6% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 40 (0.440) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 35 (0.370) | 60 (0.670) | 47/566 | 0.7 | 62.1% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 40 (0.440) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 128 (1.360) | 84/590 | 0.0 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 116 (1.220) | 75/598 | 0.1 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 127 (1.330) | 93/598 | 0.0 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||