mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
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% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 263,603 | G→A | 18.8% | Q23* (CAA→TAA) | ykfI ← | CP4‑6 prophage; toxin of the YkfI‑YafW toxin‑antitoxin system |
| RA | 292,571 | G→T | 12.1% | Y126* (TAC→TAA) | yagK ← | CP4‑6 prophage; uncharacterized protein YagK |
| RA | 819,360 | G→T | 24.0% | L22L (CTG→CTT) | moaE → | molybdopterin synthase catalytic subunit |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,517,532 | C→T | 18.4% | F48F (TTC→TTT) | ortT → | orphan toxin OrtT |
| RA | 1,547,149 | C→T | 17.4% | T7T (ACG→ACA) | yddG ← | aromatic amino acid exporter |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,383,257 | Δ1 bp | 10.3% | coding (545/1212 nt) | elaD → | protease ElaD |
| RA | 3,410,763 | G→A | 16.7% | G162S (GGC→AGC) | dusB → | tRNA‑dihydrouridine synthase B |
| RA | 3,504,511 | T→C | 17.4% | Y154H (TAT→CAT) | frlR → | putative DNA‑binding transcriptional regulator FrlR |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 4,183,378 | T→C | 31.0% | S712P (TCC→CCC) | rpoB → | RNA polymerase subunit beta |
| RA | 4,186,532 | A→G | 28.6% | K395E (AAA→GAA) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,296,060 | C→T | 40.0% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 283918 | 284001 | 84 | 2 [1] | [1] 2 | yagF | CP4‑6 prophage; D‑xylonate dehydratase |
| * | * | ÷ | NC_000913 | 287638 | 287671 | 34 | 2 [1] | [1] 2 | yagH | CP4‑6 prophage; putative xylosidase/arabinosidase |
| * | * | ÷ | NC_000913 | 776779 | 776799 | 21 | 2 [1] | [1] 2 | tolA | Tol‑Pal system protein TolA |
| * | * | ÷ | NC_000913 | 913735 | 913755 | 21 | 2 [1] | [1] 2 | hcp | protein S‑nitrosylase |
| * | * | ÷ | NC_000913 | 980657 | 980669 | 13 | 3 [0] | [0] 4 | mukB | chromosome partitioning protein MukB |
| * | * | ÷ | NC_000913 | 1043866 | 1043897 | 32 | 2 [1] | [1] 3 | etk | protein‑tyrosine kinase Etk |
| * | * | ÷ | NC_000913 | 1137575 | 1137582 | 8 | 3 [0] | [0] 2 | flgJ | putative peptidoglycan hydrolase FlgJ |
| * | * | ÷ | NC_000913 | 1393303 | 1393315 | 13 | 2 [1] | [1] 2 | mppA | murein tripeptide ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 2098515 | 2098533 | 19 | 2 [1] | [1] 2 | ugd | UDP‑glucose 6‑dehydrogenase |
| * | * | ÷ | NC_000913 | 2164409 | 2164420 | 12 | 4 [1] | [1] 2 | baeR | DNA‑binding transcriptional activator BaeR |
| * | * | ÷ | NC_000913 | 2178606 | 2178608 | 3 | 3 [0] | [0] 3 | fbaB/yegT | fructose‑bisphosphate aldolase class I/putative transporter YegT |
| * | * | ÷ | NC_000913 | 2183220 | 2183250 | 31 | 2 [1] | [1] 2 | yegX | putative hydrolase |
| * | * | ÷ | NC_000913 | 2271801 | 2271804 | 4 | 2 [0] | [0] 2 | pdeN | putative c‑di‑GMP phosphodiesterase PdeN |
| * | * | ÷ | NC_000913 | 2619127 | 2619143 | 17 | 2 [1] | [0] 3 | uraA | hypothetical protein |
| * | * | ÷ | NC_000913 | 3043656 | 3043668 | 13 | 3 [0] | [0] 5 | [bglA] | [bglA] |
| * | * | ÷ | NC_000913 | 3423824–3424234 | 3424404–3424239 | 6–581 | 2 [1] | [1] 2 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3468868 | 3468881 | 14 | 2 [1] | [0] 2 | chiA | endochitinase |
| * | * | ÷ | NC_000913 | 3556145 | 3556156 | 12 | 2 [1] | [1] 7 | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | * | ÷ | NC_000913 | 4003241 | 4003245 | 5 | 2 [0] | [1] 2 | yigG/rarD | inner membrane protein/putative transporter RarD |
| * | * | ÷ | NC_000913 | 4511478 | 4511490 | 13 | 2 [1] | [1] 2 | fecD | ferric citrate ABC transporter membrane subunit FecD |
| * | * | ÷ | NC_000913 | 4565643 | 4565676 | 34 | 2 [1] | [1] 3 | yjiM | putative dehydratase subunit |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 7 (0.390) | 16 (1.020) | 13/232 | NT | 75.9% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 4 (0.250) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 7 (0.390) | 16 (1.020) | 16/232 | NT | 75.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 4 (0.250) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||