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 |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 300,689 | G→T | 5.3% | T82T (ACC→ACA) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 300,692 | A→C | 5.5% | I81M (ATT→ATG) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 300,695 | G→T | 5.6% | V80V (GTC→GTA) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| JC JC | 302,732 | IS2 (–) +5 bp | 12.9% | intergenic (‑159/‑255) | paoA ← / → yagU | PaoABC aldehyde oxidoreductase, 2Fe‑2S subunit/DUF1440 family inner membrane acid resistance protein |
| RA | 374,688 | G→C | 5.4% | R274P (CGA→CCA) | mhpE → | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I |
| RA | 1,097,158 | C→T | 11.4% | intergenic (+329/+407) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,196,220 | C→T | 18.2% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,232 | C→T | 17.8% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,245 | T→C | 15.5% | L375L (TTA→CTA) ‡ | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,247 | A→G | 15.6% | L375L (TTA→TTG) ‡ | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,277 | C→T | 10.7% | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,280 | G→C | 10.8% | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,283 | A→G | 10.9% | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,292 | C→T | 11.0% | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,304 | G→A | 9.8% | E394E (GAG→GAA) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,316 | T→A | 9.7% | D398E (GAT→GAA) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,325 | A→G | 8.5% | K401K (AAA→AAG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,352 | C→A | 6.0% | D410E (GAC→GAA) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,367,335 | A→G | 5.2% | F193S (TTT→TCT) | pspF ← | psp operon transcriptional activator |
| RA | 1,367,337 | G→A | 5.1% | Y192Y (TAC→TAT) | pspF ← | psp operon transcriptional activator |
| RA | 1,367,340 | T→C | 5.1% | E191E (GAA→GAG) ‡ | pspF ← | psp operon transcriptional activator |
| RA | 1,367,342 | C→T | 5.0% | E191K (GAA→AAA) ‡ | pspF ← | psp operon transcriptional activator |
| RA | 1,514,951 | G→T | 10.4% | A64S (GCC→TCC) | ydcV → | putative ABC transporter permease |
| MC JC | 1,867,235 | Δ4 bp | 100% | coding (328‑331/1935 nt) | yeaG → | protein kinase, endogenous substrate unidentified; autokinase |
| RA | 1,881,844 | T→G | 100% | intergenic (‑35/‑68) | dmlR ← / → dmlA | transcriptional activator of dmlA/D‑malate oxidase, NAD‑dependent; putative tartrate dehydrogenase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| 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 | 2,416,674 | C→A | 18.8% | S643Y (TCT→TAT) | pta → | phosphate acetyltransferase |
| RA | 2,416,823 | Δ1 bp | 46.1% | coding (2077/2145 nt) | pta → | phosphate acetyltransferase |
| RA | 2,416,854 | T→G | 25.1% | I703S (ATC→AGC) | pta → | phosphate acetyltransferase |
| RA | 2,846,490 | C→T | 6.9% | *308* (TGA→TAA) | hycD ← | hydrogenase 3, membrane subunit |
| MC JC | 2,860,769 | Δ20 bp | 100% | coding (447‑466/768 nt) | ygbI ← | DeoR family putative transcriptional regulator |
| RA | 3,560,455:1 | +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 | 3,688,287 | A→C | 7.6% | V296G (GTG→GGG) | bcsC ← | cellulose synthase subunit |
| RA | 3,781,132 | C→G | 5.3% | intergenic (+115/‑83) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,809,191 | G→A | 5.5% | A218T (GCT→ACT) | waaA → | 3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase) |
| RA | 3,815,809 | Δ1 bp | 13.2% | intergenic (‑41/+25) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,815,810 | G→T | 9.6% | intergenic (‑42/+24) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| JC | 3,815,859 | Δ82 bp | 57.9% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,941,891 | T→A | 6.0% | noncoding (84/1542 nt) | rrsC → | 16S ribosomal RNA of rrnC operon |
| RA | 3,941,892 | T→A | 6.0% | noncoding (85/1542 nt) | rrsC → | 16S ribosomal RNA of rrnC operon |
| RA | 3,951,538 | Δ1 bp | 94.0% | pseudogene (979/984 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
| RA | 3,991,184 | G→T | 6.5% | R11I (AGA→ATA) | cyaA → | adenylate cyclase |
| RA | 4,001,885 | G→T | 8.2% | D154Y (GAC→TAC) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,296,190 | A→G | 28.0% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 31.9% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 26.2% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 19.9% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 12.5% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 12.1% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423784–3424234 | 3424533–3424238 | 5–750 | 84 [83] | [82] 84 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 40 (0.270) | 66 (0.470) | 58/532 | NT | 62.6% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 41 (0.290) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 38 (0.260) | 77 (0.550) | 74/532 | NT | 66.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 41 (0.290) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 156 (1.060) | 137/556 | 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 | = 3304484 | NA (NA) | 4 (0.030) | 3/542 | NT | NA | intergenic (+29/+89) | yhbW/mtr | putative luciferase‑like monooxygenase/tryptophan transporter of high affinity |
| ? | NC_000913 | = 3304553 | NA (NA) | intergenic (+98/+20) | yhbW/mtr | putative luciferase‑like monooxygenase/tryptophan transporter of high affinity | |||||
| * | ? | NC_000913 | = 3621583 | NA (NA) | 3 (0.020) | 3/552 | NT | 100% | coding (2392/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | = 3621667 | 0 (0.000) | coding (2476/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 3815900 = | 40 (0.270) | 31 (0.210) | 31/564 | NT | 43.7% | pseudogene (650/669 nt) | rph | ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| ? | NC_000913 | = 3815925 | NA (NA) | pseudogene (625/669 nt) | rph | ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH | |||||