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 |
| RA | 1,843,140 | G→A | Q566* (CAG→TAG) | gacS ← | sensor protein GacS |
| RA | 1,852,005 | G→A | R350H (CGT→CAT) | relA → | ATP:GTP 3'‑pyrophosphotransferase |
| 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 | 5,610,048 | C→A | S173I (AGC→ATC) | PP_4929 ← | LysR family transcriptional regulator |
| RA | 5,912,914 | G→A | E43K (GAG→AAG) | spuI → | glutamylpolyamine synthetase |
| RA | 5,914,046 | +A | coding (1259/1377 nt) | spuI → | glutamylpolyamine synthetase |
| RA | 6,180,730 | C→G | W258S (TGG→TCG) | atpB ← | ATP synthase subunit a |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_002947 | 171382–176286 | 176286 | 1–4905 | 9 [8] | [8] 9 | PP_16SA–[PP_5SA] | PP_16SA,PP_23SA,[PP_5SA] |
| * | * | ÷ | NC_002947 | 176674–181686 | 181686 | 1–5013 | 9 [8] | [8] 9 | PP_16SB–[PP_r01] | PP_16SB,PP_23SB,[PP_r01] |
| * | * | ÷ | NC_002947 | 1131767 | 1131831 | 65 | 9 [7] | [7] 10 | PP_0992 | hypothetical protein |
| * | * | ÷ | NC_002947 | 4808205 | 4808218 | 14 | 21 [0] | [0] 27 | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 90374 | 33 (0.940) | 10 (0.320) | 9/240 | 2.3 | 24.4% | intergenic (+49/+73) | PP_0079/PP_0080 | transcriptional regulator/hypothetical protein |
| ? | NC_002947 | = 90397 | 33 (1.060) | intergenic (+72/+50) | PP_0079/PP_0080 | transcriptional regulator/hypothetical protein | |||||
| * | ? | NC_002947 | = 176399 | NA (NA) | 22 (0.650) +CGAAA |
14/262 | 1.6 | 30.5% | intergenic (+43/‑420) | PP_5SA/PP_16SB | 5S ribosomal RNA/16S ribosomal RNA |
| ? | NC_002947 | = 182013 | 52 (1.470) | intergenic (+2/+63) | PP_5SB/PP_0160 | 5S ribosomal RNA/ferrioxamine receptor | |||||
| * | ? | NC_002947 | 413997 = | 18 (0.510) | 12 (0.430) | 10/216 | 1.8 | 45.0% | intergenic (+14/‑189) | glnE/waaF | glutamate‑ammonia‑ligase adenylyltransferase/ADP‑heptose:LPS heptosyltransferase II |
| ? | NC_002947 | 414083 = | 15 (0.540) | intergenic (+100/‑103) | glnE/waaF | glutamate‑ammonia‑ligase adenylyltransferase/ADP‑heptose:LPS heptosyltransferase II | |||||
| * | ? | NC_002947 | = 414024 | 18 (0.510) | 9 (0.320) | 8/216 | 2.2 | 38.1% | intergenic (+41/‑162) | glnE/waaF | glutamate‑ammonia‑ligase adenylyltransferase/ADP‑heptose:LPS heptosyltransferase II |
| ? | NC_002947 | = 414054 | 15 (0.540) | intergenic (+71/‑132) | glnE/waaF | glutamate‑ammonia‑ligase adenylyltransferase/ADP‑heptose:LPS heptosyltransferase II | |||||
| * | ? | NC_002947 | = 652785 | 23 (0.650) | 15 (0.500) | 13/232 | 1.4 | 60.5% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4808204 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | 1296580 = | NA (NA) | 13 (0.390) | 12/254 | 1.8 | NA | intergenic (‑327/‑239) | nhaA‑I/PP_1133 | Na(+)/H(+) antiporter NhaA/transposase |
| ? | NC_002947 | 1296616 = | NA (NA) | intergenic (‑363/‑203) | nhaA‑I/PP_1133 | Na(+)/H(+) antiporter NhaA/transposase | |||||
| * | ? | NC_002947 | 1731205 = | 28 (0.790) | 7 (0.250) | 7/216 | 2.5 | 26.8% | intergenic (‑76/+115) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase |
| ? | NC_002947 | 1731297 = | 16 (0.570) | intergenic (‑168/+23) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase | |||||
| * | ? | NC_002947 | 1967188 = | 7 (0.200) | 9 (0.340) | 7/206 | 2.4 | 52.5% | intergenic (+15/+104) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | 1967284 = | 11 (0.410) | intergenic (+111/+8) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | = 1967220 | 7 (0.200) | 8 (0.300) | 6/206 | 2.7 | 49.5% | intergenic (+47/+72) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947 | = 1967250 | 11 (0.410) | intergenic (+77/+42) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947 | 4074203 = | NA (NA) | 15 (0.440) | 9/262 | 2.6 | 69.0% | coding (1256/1329 nt) | PP_3586 | transposase |
| ? | NC_002947 | 5545215 = | 7 (0.200) | intergenic (‑307/+570) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB | |||||
| * | ? | NC_002947 | 4340085 = | 13 (0.370) | 10 (0.380) | 8/204 | 2.1 | 65.0% | intergenic (+26/‑305) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| ? | NC_002947 | 4340169 = | 1 (0.040) | intergenic (+110/‑221) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein | |||||
| * | ? | NC_002947 | = 4586100 | 16 (0.450) | 15 (0.590) | 10/196 | 1.5 | 52.1% | intergenic (+139/+78) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586128 | 16 (0.630) | intergenic (+167/+50) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | 4808219 = | 0 (0.000) | 18 (0.690) | 16/202 | 0.7 | 57.1% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988991 | 27 (1.030) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4896443 | 29 (0.820) | 14 (0.470) | 9/230 | 2.2 | 35.7% | intergenic (+31/‑177) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947 | = 4896490 | 26 (0.870) | intergenic (+78/‑130) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947 | = 5903825 | 24 (0.680) | 11 (0.340) | 8/252 | 2.7 | 34.2% | intergenic (+25/+82) | PP_5176/spuH | hypothetical protein/spermidine/putrescine ABC transporter permease |
| ? | NC_002947 | = 5903887 | 20 (0.610) | intergenic (+87/+20) | PP_5176/spuH | hypothetical protein/spermidine/putrescine ABC transporter permease | |||||
| * | ? | NC_002947 | 5903827 = | 24 (0.680) | 11 (0.350) | 7/240 | 2.8 | 34.8% | intergenic (+27/+80) | PP_5176/spuH | hypothetical protein/spermidine/putrescine ABC transporter permease |
| ? | NC_002947 | 5903887 = | 20 (0.640) | intergenic (+87/+20) | PP_5176/spuH | hypothetical protein/spermidine/putrescine ABC transporter permease | |||||
| * | ? | NC_002947 | = 5914240 | 17 (0.480) | 7 (0.250) | 7/216 | 2.5 | 39.4% | intergenic (+76/+77) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947 | = 5914280 | 8 (0.290) | intergenic (+116/+37) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947 | = 6006630 | 14 (0.400) | 9 (0.350) | 7/200 | 2.3 | 40.6% | intergenic (+42/+57) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator |
| ? | NC_002947 | = 6006642 | 16 (0.620) | intergenic (+54/+45) | ydcJ/PP_5261 | metalloprotein/LysR family transcriptional regulator | |||||
| * | ? | NC_002947 | = 6060500 | 29 (0.820) | 7 (0.220) | 7/244 | 2.9 | 20.6% | intergenic (+80/+101) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein |
| ? | NC_002947 | = 6060559 | 28 (0.880) | intergenic (+139/+42) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||