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 |
| Marginal read alignment evidence (highest frequency 20 of 137 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,327,121 | 0 | C | T | 64.0% | 39.9 / 101.1 | 116 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,732,885 | 0 | G | A | 58.4% | 40.4 / 80.1 | 78 | A917V (GCT→GTT) | sucA | 2‑oxoglutarate dehydrogenase subunit E1 |
| * | NC_002947 | 699,722 | 0 | A | G | 56.1% | 12.1 / 95.1 | 82 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 5,948,139 | 0 | G | A | 55.1% | 16.9 / 78.4 | 70 | A112V (GCC→GTC) | rho | transcription termination factor Rho |
| * | NC_002947 | 2,772,369 | 0 | C | T | 51.9% | ‑3.2 / 66.2 | 52 | R149R (CGG→CGA) | PP_2425 | AraC family transcriptional regulator |
| * | NC_002947 | 1,843,535 | 0 | C | T | 48.3% | 1.0 / 75.4 | 60 | G420D (GGC→GAC) | gacS | sensor protein GacS |
| * | NC_002947 | 4,348,705 | 0 | A | G | 46.4% | 36.4 / 102.9 | 84 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 4,621,021 | 0 | A | . | 45.1% | 90.0 / 87.4 | 51 | coding (31/417 nt) | PP_5654 | phosphotriesterase |
| * | NC_002947 | 195,634 | 0 | C | T | 38.9% | 91.3 / 113.9 | 114 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,340,089 | 0 | G | C | 37.9% | 13.9 / 23.5 | 30 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 5,256,864 | 0 | T | A | 35.5% | 28.1 / 18.8 | 31 | intergenic (+16/+29) | PP_5703/PP_4634 | type III effector protein HopJ/alpha/beta family hydrolase |
| * | NC_002947 | 4,340,083 | 0 | A | G | 34.5% | 26.1 / 19.2 | 30 | intergenic (+68/‑263) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 441,326 | 0 | G | . | 34.4% | 62.4 / 37.1 | 33 | coding (207/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase |
| * | NC_002947 | 4,340,090 | 0 | A | T | 33.3% | 26.5 / 14.9 | 30 | intergenic (+75/‑256) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 5,256,865 | 0 | T | A | 32.3% | 29.0 / 20.1 | 31 | intergenic (+17/+28) | PP_5703/PP_4634 | type III effector protein HopJ/alpha/beta family hydrolase |
| * | NC_002947 | 5,256,866 | 0 | T | A | 32.3% | 28.5 / 21.5 | 31 | intergenic (+18/+27) | PP_5703/PP_4634 | type III effector protein HopJ/alpha/beta family hydrolase |
| * | NC_002947 | 4,340,082 | 0 | C | T | 32.1% | 30.2 / 17.1 | 30 | intergenic (+67/‑264) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947 | 1,506,930 | 0 | T | C | 31.6% | 65.2 / 40.4 | 58 | intergenic (+51/‑66) | petC/sspA | ubiquinol‑‑cytochrome c reductase cytochrome c1 subunit/stringent starvation protein A |
| * | NC_002947 | 1,544,489 | 0 | C | A | 31.1% | 55.4 / 33.3 | 45 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 4,340,084 | 0 | C | T | 31.0% | 33.2 / 17.2 | 30 | intergenic (+69/‑262) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 527 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 4586029 | 11 (0.160) | 30 (0.480) | 21/258 | 3.1 | 53.5% | intergenic (+112/+103) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586109 | 42 (0.670) | intergenic (+192/+23) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | 4808174 = | 4 (0.060) | 22 (0.430) | 14/210 | 3.6 | 61.1% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988935 | 25 (0.490) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4073915 | NA (NA) | 21 (0.320) | 19/272 | 3.8 | 30.6% | intergenic (‑453/+171) | mdtA/PP_3586 | multidrug transporter membrane fusion protein/transposase |
| ? | NC_002947 | = 4302585 | 49 (0.720) | intergenic (+1075/‑225) | PP_3774/PP_5627 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | 1298266 = | NA (NA) | 21 (0.320) | 19/272 | 3.8 | NA | intergenic (+125/+304) | PP_1133/PP_1134 | transposase/hypothetical protein |
| ? | NC_002947 | 1298312 = | NA (NA) | intergenic (+171/+258) | PP_1133/PP_1134 | transposase/hypothetical protein | |||||
| * | ? | NC_002947 | = 5545666 | NA (NA) | 18 (0.270) | 18/274 | 4.0 | 41.4% | intergenic (‑806/+71) | rpsF/rlmB | 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB |
| ? | NC_002947 | 5621244 = | 26 (0.380) | coding (20/774 nt) | PP_4939 | hypothetical protein | |||||
| * | ? | NC_002947 | 4537544 = | 0 (0.000) | 20 (0.300) | 16/270 | 4.4 | 88.9% | coding (879/1533 nt) | PP_4025 | transposase |
| ? | NC_002947 | = 4626651 | 5 (0.080) | coding (853/1533 nt) | PP_4091 | transposase | |||||
| * | ? | NC_002947 | 4537518 = | NA (NA) | 20 (0.300) | 16/270 | 4.4 | 100% | coding (853/1533 nt) | PP_4025 | transposase |
| ? | NC_002947 | 4537544 = | 0 (0.000) | coding (879/1533 nt) | PP_4025 | transposase | |||||
| * | ? | NC_002947 | = 4808179 | 4 (0.060) | 18 (0.310) | 13/240 | 4.6 | 49.7% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5988949 | 33 (0.570) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 5914184 | 51 (0.750) | 11 (0.200) | 10/224 | 5.2 | 24.2% | intergenic (+76/+77) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase |
| ? | NC_002947 | = 5914224 | 28 (0.510) | intergenic (+116/+37) | spuI/argA | glutamylpolyamine synthetase/amino acid N‑acetyltransferase | |||||
| * | ? | NC_002947 | 4647557 = | 28 (0.410) | 9 (0.180) | 8/202 | 5.4 | 29.4% | intergenic (+10/+121) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | 4647665 = | 23 (0.470) | intergenic (+118/+13) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||