mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.26.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| JC JC | 573,890 | IS5 (–) +4 bp | 50.8% | intergenic (+20/‑63) | ylcG → / → quuD | uncharacterized protein, DLP12 prophage/DLP12 prophage; putative antitermination protein |
| RA | 657,541 | G→T | 53.9% | intergenic (+40/+14) | cspE → / ← flc | constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein/fluoride efflux channel, dual topology membrane protein |
| RA | 1,519,739 | T→C | 6.0% | L238P (CTT→CCT) | curA → | curcumin/dihydrocurcumin reductase, NADPH‑dependent |
| RA | 1,529,218 | C→T | 100% | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,907,258 | C→T | 6.6% | G60S (GGT→AGT) | cspC ← | stress protein, member of the CspA‑family |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 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 | 2,186,771 | C→A | 5.6% | intergenic (+30/‑189) | rcnA → / → rcnB | membrane protein conferring nickel and cobalt resistance/periplasmic modulator of Ni and Co efflux |
| RA | 2,911,534 | Δ1 bp | 45.8% | coding (2118/2235 nt) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 3,560,455 | +G | 100% | 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 | 3,815,809 | +A | 8.7% | intergenic (‑41/+25) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,952,371 | C→T | 6.0% | V57V (GTC→GTT) | ilvM → | acetolactate synthase 2 small subunit |
| RA | 4,187,507 | A→C | 100% | N720H (AAC→CAC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,190 | A→G | 11.0% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 12.9% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 32.8% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 22.6% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 13.6% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 14.4% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380 | +C | 92.6% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380 | +G | 92.6% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,326,088 | T→G | 9.4% | intergenic (‑347/+311) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,141 | T→C | 5.4% | intergenic (‑400/+258) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 83979 | 84294 | 316 | 39 [37] | [32] 42 | leuL/leuO | leu operon leader peptide/global transcription factor |
| * | * | ÷ | NC_000913 | 583056 | 584241 | 1186 | 40 [38] | [37] 39 | [tfaX]–[appY] | [tfaX], [appY] |
| * | * | ÷ | NC_000913 | 720795 | 721197 | 403 | 47 [37] | [38] 40 | [ybfK]–[kdpE] | [ybfK], [kdpE] |
| * | * | ÷ | NC_000913 | 1978493 | 1979676 | 1184 | 40 [38] | [37] 41 | insB1–insA | insB1, insA |
| Unassigned new junction evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 37 (0.390) | 20 (0.220) | 19/514 | NT | 38.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 28 (0.310) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 32 (0.340) | 32 (0.360) | 29/514 | NT | 52.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 28 (0.310) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 29 (0.310) | 24/538 | NT | 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 | |||||
| * | ? | NC_000913 | 1907448 = | 130 (1.390) | 5 (0.050) | 4/538 | NT | 3.7% | coding (144/144 nt) | yobF | DUF2527 family heat‑induced protein |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 35 (0.380) | 32/530 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||