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 26 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,070,246 | 1 | . | G | 63.6% | 40.5 / 25.1 | 22 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947 | 1,070,246 | 2 | . | A | 63.6% | 42.3 / 26.3 | 22 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947 | 699,722 | 0 | A | G | 53.3% | ‑4.9 / 54.8 | 45 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 524,180 | 0 | T | G | 51.8% | 13.6 / 28.1 | 29 | intergenic (+47/‑769) | tyrS/PP_16SC | tyrosine‑‑tRNA ligase/16S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 45.7% | 14.4 / 40.0 | 35 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 195,559 | 0 | C | A | 44.8% | 19.7 / 27.7 | 29 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,348,705 | 0 | A | G | 44.7% | 12.4 / 45.4 | 38 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,327,121 | 0 | C | T | 42.2% | 47.0 / 70.5 | 64 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,402,733 | 0 | G | T | 38.1% | 6.9 / 14.4 | 21 | R141S (CGC→AGC) | PP_3881 | terminase large subunit |
| * | NC_002947 | 5,740,471 | 0 | A | T | 35.3% | 8.7 / 10.5 | 17 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 196,351 | 0 | C | G | 34.8% | 12.0 / 20.6 | 23 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,740,467 | 0 | T | G | 29.4% | 5.5 / 11.0 | 17 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947 | 197,590 | 0 | T | C | 28.6% | 37.3 / 14.4 | 32 | D1032D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,403,591 | 0 | T | C | 28.6% | 22.8 / 10.9 | 23 | intergenic (‑57/+24) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947 | 1,403,590 | 0 | G | A | 27.3% | 28.4 / 10.8 | 22 | intergenic (‑56/+25) | PP_1227/PP_1228 | membrane protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947 | 1,670,628 | 0 | C | A | 26.1% | 33.2 / 12.4 | 23 | intergenic (+51/‑44) | rplS/PP_1466 | 50S ribosomal protein L19/acyl‑CoA thioesterase |
| * | NC_002947 | 1,670,626 | 0 | T | C | 25.0% | 35.7 / 10.3 | 24 | intergenic (+49/‑46) | rplS/PP_1466 | 50S ribosomal protein L19/acyl‑CoA thioesterase |
| * | NC_002947 | 1,670,627 | 0 | T | G | 25.0% | 38.6 / 12.7 | 24 | intergenic (+50/‑45) | rplS/PP_1466 | 50S ribosomal protein L19/acyl‑CoA thioesterase |
| * | NC_002947 | 5,194,887 | 0 | T | G | 24.0% | 26.7 / 13.4 | 25 | intergenic (+29/+24) | PP_4574/PP_4575 | hypothetical protein/urea amidolyase‑like protein |
| * | NC_002947 | 197,572 | 0 | G | A | 23.3% | 45.7 / 13.0 | 34 | K1026K (AAG→AAA) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 46 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 6077844 | 18 (0.690) | 3 (0.140) | 3/242 | 3.0 | 17.1% | intergenic (‑146/+92) | PP_5329/PP_5330 | phosphate ABC transporter substrate‑binding protein/MFS transporter |
| ? | NC_002947 | = 6077896 | 14 (0.650) | intergenic (‑198/+40) | PP_5329/PP_5330 | phosphate ABC transporter substrate‑binding protein/MFS transporter | |||||
| * | ? | NC_002947 | 3604024 = | 12 (0.460) | 4 (0.160) | 4/280 | 3.0 | 23.8% | coding (630/900 nt) | PP_3179 | LysR family transcriptional regulator |
| ? | NC_002947 | 3604065 = | 14 (0.560) | coding (589/900 nt) | PP_3179 | LysR family transcriptional regulator | |||||
| * | ? | NC_002947 | 4586034 = | 7 (0.270) | 3 (0.140) | 3/246 | 3.1 | 37.7% | intergenic (+117/+98) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | 4586105 = | 4 (0.180) | intergenic (+188/+27) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | 1425674 = | NA (NA) | 4 (0.160) | 4/286 | 3.1 | 11.9% | intergenic (+76/‑429) | PP_1249/PP_1250 | DUF4223 domain‑containing protein/group II intron‑encoding maturase |
| ? | NC_002947 | 1429500 = | 30 (1.160) | intergenic (+17/‑463) | mqo‑II/PP_1252 | malate:quinone oxidoreductase/group II intron‑encoding maturase | |||||
| * | ? | NC_002947 | 4159083 = | 12 (0.460) | 3 (0.130) | 3/258 | 3.2 | 18.9% | intergenic (+31/‑178) | PP_3661/PP_3662 | membrane protein/hypothetical protein |
| ? | NC_002947 | 4159143 = | 15 (0.650) | intergenic (+91/‑118) | PP_3661/PP_3662 | membrane protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 1792736 | 20 (0.770) | 3 (0.120) | 3/270 | 3.3 | 13.8% | intergenic (+27/‑47) | rseP/bamA‑I | regulatory intramembrane protein RIP/outer membrane protein assembly factor |
| ? | NC_002947 | = 1792742 | 19 (0.790) | intergenic (+33/‑41) | rseP/bamA‑I | regulatory intramembrane protein RIP/outer membrane protein assembly factor | |||||
| * | ? | NC_002947 | 6085712 = | 22 (0.850) | 3 (0.120) | 3/280 | 3.4 | 11.7% | coding (822/1437 nt) | aspA | aspartate ammonia‑lyase |
| ? | NC_002947 | 6085741 = | 24 (0.960) | coding (851/1437 nt) | aspA | aspartate ammonia‑lyase | |||||
| * | ? | NC_002947 | = 5983868 | 33 (1.270) | 4 (0.160) | 3/272 | 3.4 | 12.1% | coding (4513/5049 nt) | PP_5242 | GAF domain‑containing sensor histidine kinase |
| ? | NC_002947 | = 5983896 | 27 (1.110) | coding (4541/5049 nt) | PP_5242 | GAF domain‑containing sensor histidine kinase | |||||
| * | ? | NC_002947 | 5953178 = | 25 (0.960) | 3 (0.120) | 3/274 | 3.4 | 10.6% | intergenic (‑222/‑52) | ppk/PP_5218 | polyphosphate kinase/DedA family protein |
| ? | NC_002947 | 5953209 = | 27 (1.100) | intergenic (‑253/‑21) | ppk/PP_5218 | polyphosphate kinase/DedA family protein | |||||
| * | ? | NC_002947 | 5910975 = | 32 (1.230) | 3 (0.120) | 3/280 | 3.4 | 8.3% | coding (1183/1359 nt) | spuB | glutamylpolyamine synthetase |
| ? | NC_002947 | 5911007 = | 35 (1.400) | coding (1151/1359 nt) | spuB | glutamylpolyamine synthetase | |||||