mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 16,923 | T→G | 5.2% | K13T (AAG→ACG) | mokC ← | regulatory protein for HokC, overlaps CDS of hokC |
| RA | 83,587 | A→C | 5.7% | intergenic (‑58/+35) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 143,533 | T→C | 5.7% | L252P (CTG→CCG) | yadG → | putative ABC transporter ATPase |
| RA | 151,519 | A→C | 6.6% | I27M (ATT→ATG) | yadK ← | putative fimbrial‑like adhesin protein |
| RA | 151,522 | G→T | 6.8% | A26A (GCC→GCA) | yadK ← | putative fimbrial‑like adhesin protein |
| RA | 246,771 | G→A | 5.1% | P20P (CCG→CCA) | yafL → | putative lipoprotein and C40 family peptidase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 810,569 | G→A | 11.5% | Q63Q (CAG→CAA) | bioF → | 8‑amino‑7‑oxononanoate synthase |
| RA | 1,041,937 | T→G | 7.0% | intergenic (+22/+93) | appA → / ← etk | phosphoanhydride phosphorylase/tyrosine‑protein kinase, role in O‑antigen capsule formation |
| RA | 1,181,724 | A→G | 5.4% | M1T (ATG→ACG) † | ymfA ← | DUF3592 family inner membrane protein |
| RA | 1,240,929 | T→C | 7.2% | T381T (ACA→ACG) | cvrA ← | putative cation/proton antiporter |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,413,542 | A→T | 100% | Y67N (TAT→AAT) | ydaC ← | DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein |
| RA | 1,793,897 | Δ1 bp | 100% | coding (213/552 nt) | btuE ← | glutathione peroxidase |
| RA | 1,883,027 | C→G | 7.2% | intergenic (+30/‑161) | dmlA → / → yeaV | D‑malate oxidase, NAD‑dependent; putative tartrate dehydrogenase/putative transporter |
| RA | 1,901,435 | A→C | 7.1% | L51V (TTA→GTA) | yoaE ← | putative membrane protein/conserved protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,093,040 | G→A | 100% | A215T (GCT→ACT) | hisC → | histidinol‑phosphate aminotransferase |
| RA | 2,291,234 | C→G | 5.0% | intergenic (+89/+122) | narP → / ← ccmH | response regulator in two‑component regulatory system with NarQ/heme lyase, CcmH subunit |
| RA | 3,156,588 | C→A | 7.1% | intergenic (+72/‑33) | yqhD → / → dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| RA | 3,156,589 | T→G | 7.1% | intergenic (+73/‑32) | yqhD → / → dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| RA | 3,368,171 | C→G | 6.2% | P116R (CCG→CGG) | yhcG → | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| RA | 3,456,014 | C→A | 5.5% | H147N (CAT→AAT) | gspC → | general secretory pathway component, cryptic |
| RA | 3,569,436 | T→C | 6.2% | H628R (CAC→CGC) | glgX ← | glycogen debranching enzyme |
| RA | 3,833,667 | G→T | 5.6% | I290I (ATC→ATA) | yicI ← | putative alpha‑glucosidase |
| RA | 3,835,243 | T→C | 5.2% | Q229R (CAG→CGG) | yicJ ← | putative transporter |
| RA | 4,094,414 | T→G | 5.4% | intergenic (‑143/+308) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,117,004 | T→A | 100% | D73V (GAT→GTT) | glpK ← | glycerol kinase |
| MC JC | 4,188,484 | Δ27 bp | 100% | coding (3136‑3162/4224 nt) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,307,295 | A→T | 7.5% | L169Q (CTG→CAG) | alsK ← | D‑allose kinase |
| RA | 4,307,299 | G→A | 7.8% | P168S (CCC→TCC) | alsK ← | D‑allose kinase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 399794 = | 48 (0.740) | 3 (0.050) | 3/262 | NT | 5.9% | coding (202/213 nt) | yaiZ | DUF2754 family putative inner membrane protein |
| ? | NC_000913 | 399823 = | 51 (0.830) | intergenic (+18/+6) | yaiZ/ddlA | DUF2754 family putative inner membrane protein/D‑alanine‑D‑alanine ligase A | |||||
| * | ? | NC_000913 | 1207790 = | 37 (0.570) | 22 (0.380) | 21/244 | NT | 43.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 24 (0.420) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 38 (0.580) | 26 (0.450) | 24/244 | NT | 47.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 24 (0.420) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 2304469 = | 56 (0.860) | 3 (0.050) | 3/262 | NT | 6.1% | noncoding (55/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences |
| ? | NC_000913 | 2304953 = | 39 (0.630) | noncoding (539/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | |||||
| * | ? | NC_000913 | 3750789 = | 85 (1.310) | 4 (0.070) | 4/260 | NT | 5.1% | intergenic (+9/+23) | sgbE/ysaC | L‑ribulose‑5‑phosphate 4‑epimerase/pseudogene |
| ? | NC_000913 | 3750811 = | 70 (1.140) | intergenic (+31/+1) | sgbE/ysaC | L‑ribulose‑5‑phosphate 4‑epimerase/pseudogene | |||||
| * | ? | NC_000913 | = 3944977 | NA (NA) | 7 (0.110) | 7/264 | NT | 15.2% | noncoding (1275/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| ? | NC_000913 | = 4038810 | 41 (0.630) | noncoding (1293/2905 nt) | rrlA | 23S ribosomal RNA of rrnA operon | |||||
| * | ? | NC_000913 | = 4171802 | 56 (0.860) | 7 (0.110) | 5/272 | NT | 12.2% | intergenic (+47/‑254) | rrfB/murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding |
| ? | NC_000913 | = 4213161 | 46 (0.720) | intergenic (+3/‑72) | rrfE/yjaA | 5S ribosomal RNA of rrnE operon/stress‑induced protein | |||||