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 | annotation | gene | description |
| MC JC | 1,385,534 | Δ69 bp | coding (861‑929/1266 nt) | oprD ← | basic amino acid specific porin OprD |
| RA | 1,843,613 | T→C | N408S (AAC→AGC) | gacS ← | sensor protein GacS |
| JC | 1,852,168 | (TGGCC)2→3 | coding (1212/2241 nt) | relA → | ATP:GTP 3'‑pyrophosphotransferase |
| MC JC | 3,866,612 | Δ6 bp | coding (305‑310/1020 nt) | PP_3415 ← | LacI family transcriptional regulator |
| RA | 4,741,273 | +C | intergenic (+464/+288) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,275 | A→G | intergenic (+466/+286) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,277 | C→T | intergenic (+468/+284) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,280 | C→T | intergenic (+471/+281) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,283 | C→G | intergenic (+474/+278) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,741,285 | 2 bp→CT | intergenic (+476/+275) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 5,610,676 | G→A | E14K (GAA→AAA) | emrE → | small multidrug resistance protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_002947 | 171364–176271 | 176271 | 1–4908 | 4 [3] | [3] 4 | PP_16SA–[PP_5SA] | PP_16SA,PP_23SA,[PP_5SA] |
| * | * | ÷ | NC_002947 | 176665–181681 | 181681 | 1–5017 | 4 [3] | [3] 4 | PP_16SB–[PP_r01] | PP_16SB,PP_23SB,[PP_r01] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 176399 | NA (NA) | 10 (0.410) +CGAAA |
8/262 | 1.7 | 27.1% | intergenic (+43/‑420) | PP_5SA/PP_16SB | 5S ribosomal RNA/16S ribosomal RNA |
| ? | NC_002947 | = 182013 | 28 (1.100) | intergenic (+2/+63) | PP_5SB/PP_0160 | 5S ribosomal RNA/ferrioxamine receptor | |||||
| * | ? | NC_002947 | 441138 = | 21 (0.830) | 5 (0.200) | 5/268 | 2.4 | 20.1% | coding (16/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase |
| ? | NC_002947 | 441167 = | 19 (0.760) | coding (45/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase | |||||
| * | ? | NC_002947 | = 612084 | NA (NA) | 4 (0.170) | 4/258 | 2.7 | NA | intergenic (+12/+205) | PP_0526/dxs | transposase/1‑deoxyxylulose‑5‑phosphate synthase |
| ? | NC_002947 | = 612087 | NA (NA) | intergenic (+15/+202) | PP_0526/dxs | transposase/1‑deoxyxylulose‑5‑phosphate synthase | |||||
| * | ? | NC_002947 | = 1298172 | NA (NA) | 4 (0.160) | 4/264 | 2.7 | NA | intergenic (+25/+404) | PP_1133/PP_1134 | transposase/hypothetical protein |
| ? | NC_002947 | = 1298230 | NA (NA) | intergenic (+83/+346) | PP_1133/PP_1134 | transposase/hypothetical protein | |||||
| * | ? | NC_002947 | 1419553 = | 11 (0.430) | 6 (0.310) | 6/208 | 1.6 | 33.9% | intergenic (‑36/+101) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | 1419647 = | 15 (0.770) | intergenic (‑130/+7) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 1419584 | 11 (0.430) | 6 (0.310) | 6/208 | 1.6 | 33.9% | intergenic (‑67/+70) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | = 1419614 | 15 (0.770) | intergenic (‑97/+40) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | 1967188 = | 2 (0.080) | 7 (0.360) | 6/206 | 1.6 | 57.1% | intergenic (+15/+104) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | 1967284 = | 9 (0.470) | intergenic (+111/+8) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | = 1967220 | 2 (0.080) | 6 (0.310) | 6/206 | 1.6 | 53.3% | intergenic (+47/+72) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | = 1967250 | 9 (0.470) | intergenic (+77/+42) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | 2033789 = | 5 (0.200) | 8 (0.330) | 8/262 | 1.7 | 57.5% | coding (1227/1665 nt) | pgi‑I | glucose 6‑phosphate isomerase |
| ? | NC_002947 | 5344023 = | 7 (0.290) | coding (1215/1665 nt) | pgi‑II | glucose 6‑phosphate isomerase | |||||
| * | ? | NC_002947 | 2464301 = | 14 (0.550) | 4 (0.170) | 4/254 | 2.6 | 25.8% | intergenic (+13/+27) | lolE/PP_2157 | lipoprotein releasing system permease/sensor histidine kinase |
| ? | NC_002947 | 2464329 = | 10 (0.420) | coding (1352/1353 nt) | PP_2157 | sensor histidine kinase | |||||
| * | ? | NC_002947 | = 3464323 | 10 (0.390) | 5 (0.240) | 5/224 | 2.0 | 34.2% | coding (78/1929 nt) | PP_3078 | ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 3464362 | 11 (0.530) | coding (39/1929 nt) | PP_3078 | ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | 3989028 = | 19 (0.750) | 5 (0.200) | 4/262 | 2.7 | 21.6% | coding (1502/2085 nt) | oplA | 5‑oxoprolinase A |
| ? | NC_002947 | 3989083 = | 18 (0.740) | coding (1557/2085 nt) | oplA | 5‑oxoprolinase A | |||||
| * | ? | NC_002947 | 4253573 = | 14 (0.550) | 4 (0.160) | 4/264 | 2.7 | 24.6% | coding (150/1407 nt) | rocE | amino acid permease RocE |
| ? | NC_002947 | 4253600 = | 11 (0.450) | coding (123/1407 nt) | rocE | amino acid permease RocE | |||||
| * | ? | NC_002947 | = 4328080 | 11 (0.430) | 4 (0.160) | 4/262 | 2.7 | 28.0% | coding (1004/1194 nt) | PP_3797 | membrane protein |
| ? | NC_002947 | = 4328111 | 10 (0.410) | coding (1035/1194 nt) | PP_3797 | membrane protein | |||||
| * | ? | NC_002947 | = 4808224 | 3 (0.120) | 21 (0.910) | 16/248 | 0.5 | 55.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5988821 = | 31 (1.340) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4861197 | 20 (0.790) | 7 (0.340) | 7/222 | 1.5 | 29.6% | intergenic (‑103/+134) | ligA/PP_4275 | DNA ligase/cell division protein ZipA |
| ? | NC_002947 | = 4861238 | 17 (0.820) | intergenic (‑144/+93) | ligA/PP_4275 | DNA ligase/cell division protein ZipA | |||||
| * | ? | NC_002947 | 5216577 = | 22 (0.870) | 8 (0.330) | 8/262 | 1.7 | 28.0% | coding (177/2331 nt) | PP_4596 | putative oxidoreductase |
| ? | NC_002947 | 5216608 = | 20 (0.820) | coding (146/2331 nt) | PP_4596 | putative oxidoreductase | |||||
| * | ? | NC_002947 | 5914213 = | 29 (1.140) | 5 (0.250) | 5/216 | 2.0 | 20.8% | intergenic (+49/+104) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947 | 5914309 = | 15 (0.740) | intergenic (+145/+8) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||