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] | |
| JC JC | 562,624 | IS5 (–) +4 bp | 12.0% | coding (289‑292/984 nt) | sfmH → | FimA homolog, function unknown |
| RA | 1,097,158 | C→T | 11.3% | intergenic (+329/+407) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,196,220 | C→T | 24.9% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,232 | C→T | 23.2% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,245 | T→C | 20.6% | L375L (TTA→CTA) ‡ | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,247 | A→G | 20.5% | L375L (TTA→TTG) ‡ | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,277 | C→T | 17.6% | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,280 | G→C | 17.8% | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,283 | A→G | 17.5% | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,292 | C→T | 14.2% | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,304 | G→A | 12.6% | E394E (GAG→GAA) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,316 | T→A | 12.0% | D398E (GAT→GAA) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,325 | A→G | 10.1% | K401K (AAA→AAG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,352 | C→A | 6.7% | D410E (GAC→GAA) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,261,430 | C→A | 5.1% | S149I (AGC→ATC) | prs ← | phosphoribosylpyrophosphate synthase |
| RA | 1,290,656 | C→T | 13.9% | L139F (CTT→TTT) | rssB → | PcnB‑degradosome interaction factor; response regulator |
| 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 | 1,333,383 | T→A | 10.3% | V779E (GTG→GAG) | topA → | DNA topoisomerase I, omega subunit |
| RA | 1,335,283 | G→T | 11.7% | G54* (GGA→TGA) | ymiA → | uncharacterized protein |
| RA | 1,351,222 | T→G | 6.8% | intergenic (‑183/+185) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,351,227 | A→T | 5.2% | intergenic (‑188/+180) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,351,234 | C→A | 5.5% | intergenic (‑195/+173) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,354,220 | C→A | 5.5% | G100V (GGT→GTT) | sapC ← | antimicrobial peptide transport ABC transporter permease |
| JC | 1,686,126 | +CAGCAG | 6.9% | coding (463/1404 nt) | fumC ← | fumarate hydratase (fumarase C),aerobic Class II |
| RA | 1,878,015 | G→T | 5.2% | A101S (GCA→TCA) | yeaP → | diguanylate cyclase |
| RA | 1,882,635 | G→A | 100% | A242T (GCG→ACG) | dmlA → | D‑malate oxidase, NAD‑dependent; putative tartrate dehydrogenase |
| MC JC | 1,905,253 | Δ36,755 bp | 100% | [yobD]–[znuA] | 41 genes [yobD], mntP, rlmA, cspC, yobF, yebO, mgrB, yobH, kdgR, yebQ, htpX, prc, proQ, msrC, yebS, yebT, rsmF, yebV, yebW, pphA, ryeA, sdsR, yebY, yebZ, yobA, holE, yobB, exoX, ptrB, yebE, yebF, yebG, purT, eda, edd, zwf, yebK, pykA, lpxM, mepM, [znuA] |
|
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,171,814 | A→G | 5.2% | intergenic (‑87/+19) | gatR ← / ← gatD | pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted/galactitol‑1‑phosphate dehydrogenase, Zn‑dependent and NAD(P)‑binding |
| RA | 2,171,816 | C→G | 5.2% | intergenic (‑89/+17) | gatR ← / ← gatD | pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted/galactitol‑1‑phosphate dehydrogenase, Zn‑dependent and NAD(P)‑binding |
| RA | 2,171,818 | C→T | 5.2% | intergenic (‑91/+15) | gatR ← / ← gatD | pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted/galactitol‑1‑phosphate dehydrogenase, Zn‑dependent and NAD(P)‑binding |
| 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 | 2,252,812 | A→T | 5.1% | intergenic (+24/+83) | yeiI → / ← nupX | putative kinase/nucleoside permease |
| JC JC | 2,601,785 | Δ1 bp :: IS186 (+) +5 bp | 7.1% | coding (585‑589/618 nt) | hyfA → | hydrogenase 4, 4Fe‑4S subunit |
| RA | 2,653,695 | A→T | 5.2% | intergenic (+356/‑160) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,653,698 | A→T | 5.0% | intergenic (+359/‑157) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,698,428:1 | +A | 93.7% | coding (123/636 nt) | pgpC ← | phosphatidylglycerophosphatase C, membrane bound |
| RA | 2,698,428:2 | +C | 93.7% | coding (123/636 nt) | pgpC ← | phosphatidylglycerophosphatase C, membrane bound |
| RA | 2,850,749 | G→A | 5.5% | A35T (GCA→ACA) | hypA → | protein involved in nickel insertion into hydrogenases 3 |
| RA | 2,860,761 | C→T | 17.1% | A158A (GCG→GCA) ‡ | ygbI ← | DeoR family putative transcriptional regulator |
| RA | 2,860,762 | G→T | 17.1% | A158E (GCG→GAG) ‡ | ygbI ← | DeoR family putative transcriptional regulator |
| RA | 2,980,746 | C→T | 5.1% | intergenic (‑111/+18) | ygeA ← / ← araE | Asp/Glu_racemase family protein/arabinose transporter |
| RA | 3,241,795 | A→G | 5.5% | intergenic (‑51/+32) | ygjV ← / ← uxaA | Imp‑YgjV family inner membrane protein/altronate hydrolase |
| RA | 3,439,588 | G→C | 5.1% | intergenic (‑79/+28) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| RA | 3,439,589 | G→C | 5.0% | intergenic (‑80/+27) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| 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 | 3,815,809 | Δ1 bp | 14.2% | intergenic (‑41/+25) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,815,812 | G→T | 19.6% | intergenic (‑44/+22) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,951,543 | Δ1 bp | 35.5% | pseudogene (984/984 nt)|pseudogene (2/663 nt) | ilvG → ilvG → |
pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
| RA | 4,296,190 | A→G | 28.1% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 26.7% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 29.1% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 17.4% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 7.5% | intergenic (+509/+133) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 8.0% | 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 | 3423792–3424234 | 3424516–3424238 | 5–725 | 81 [80] | [79] 81 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 32 (0.220) | 44 (0.320) | 41/532 | NT | 61.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 26 (0.190) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 33 (0.220) | 37 (0.270) | 37/532 | NT | 56.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 26 (0.190) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 2731065 = | 126 (0.860) | 6 (0.040) | 6/558 | NT | 5.0% | noncoding (93/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | 3428688 = | 102 (0.700) | noncoding (75/1542 nt) | rrsD | 16S ribosomal RNA of rrnD operon | |||||