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 99 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 699,725 | 0 | A | G | 65.5% | 57.2 / 42.7 | 56 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,741,298 | 1 | . | T | 59.0% | 79.2 / 54.8 | 39 | intergenic (+489/+263) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,302 | 0 | A | G | 59.0% | 23.2 / 35.2 | 39 | intergenic (+493/+259) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,305 | 0 | A | . | 59.0% | 24.9 / 65.3 | 39 | intergenic (+496/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 1,327,127 | 0 | C | T | 55.2% | 2.2 / 105.4 | 88 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 4,741,299 | 0 | C | T | 41.0% | 25.9 / 34.0 | 39 | intergenic (+490/+262) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,301 | 0 | A | C | 41.0% | 20.8 / 40.3 | 39 | intergenic (+492/+260) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,741,304 | 0 | C | G | 41.0% | 37.9 / 35.3 | 39 | intergenic (+495/+257) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | NC_002947 | 4,348,749 | 0 | A | G | 40.7% | 53.9 / 88.5 | 87 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,544,536 | 0 | C | G | 39.0% | 51.1 / 46.0 | 41 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,541 | 0 | C | G | 39.0% | 48.5 / 46.9 | 41 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,543 | 0 | G | C | 39.0% | 49.8 / 48.5 | 41 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,534 | 0 | G | C | 36.4% | 57.8 / 49.6 | 44 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,546 | 0 | T | G | 36.4% | 39.6 / 42.0 | 44 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,531 | 0 | C | A | 35.6% | 64.7 / 34.5 | 45 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 195,634 | 0 | C | T | 34.9% | 125.2 / 111.1 | 128 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,070,268 | 0 | G | C | 33.3% | 37.8 / 25.7 | 30 | intergenic (+65/+79) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947 | 5,988,882 | 0 | C | T | 32.9% | 162.5 / 69.6 | 85 | intergenic (+120/‑426) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,881 | 0 | G | T | 32.1% | 187.0 / 66.8 | 85 | intergenic (+119/‑427) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 4,796,657 | 0 | C | T | 32.1% | 60.3 / 40.9 | 53 | intergenic (‑170/+48) | pvdH/PP_4224 | diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase |
| Marginal new junction evidence (lowest skew 10 of 599 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 5652989 = | 75 (1.160) | 22 (0.400) | 16/224 | 3.3 | 27.3% | intergenic (‑39/+122) | PP_4961/PP_4962 | lipoprotein/hypothetical protein |
| ? | NC_002947 | 5653045 = | 54 (0.990) | intergenic (‑95/+66) | PP_4961/PP_4962 | lipoprotein/hypothetical protein | |||||
| * | ? | NC_002947 | = 4586100 | 45 (0.690) | 12 (0.260) | 11/190 | 3.8 | 32.4% | intergenic (+139/+78) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947 | = 4586128 | 18 (0.390) | intergenic (+167/+50) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947 | = 6009197 | 22 (0.340) | 14 (0.290) | 11/200 | 4.0 | 52.3% | intergenic (+38/+44) | norM/PP_5263 | multidrug resistance protein NorM/GGDEF domain‑containing protein |
| ? | NC_002947 | = 6009208 | 9 (0.190) | intergenic (+49/+33) | norM/PP_5263 | multidrug resistance protein NorM/GGDEF domain‑containing protein | |||||
| * | ? | NC_002947 | = 4861197 | 77 (1.190) | 22 (0.420) | 12/216 | 4.1 | 27.1% | intergenic (‑103/+134) | ligA/PP_4275 | DNA ligase/cell division protein ZipA |
| ? | NC_002947 | = 4861238 | 56 (1.070) | intergenic (‑144/+93) | ligA/PP_4275 | DNA ligase/cell division protein ZipA | |||||
| * | ? | NC_002947 | = 176399 | NA (NA) | 45 (0.720) +CGAAA |
15/256 | 4.2 | 41.9% | intergenic (+43/‑420) | PP_5SA/PP_16SB | 5S ribosomal RNA/16S ribosomal RNA |
| ? | NC_002947 | = 182013 | 65 (1.000) | intergenic (+2/+63) | PP_5SB/PP_0160 | 5S ribosomal RNA/ferrioxamine receptor | |||||
| * | ? | NC_002947 | 5506609 = | 56 (0.860) | 11 (0.220) | 10/208 | 4.5 | 21.4% | intergenic (+20/‑179) | PP_4839/cycA | iron‑regulated membrane protein/D‑alanine/beta‑alanine/D‑serine/glycine permease |
| ? | NC_002947 | 5506680 = | 37 (0.730) | intergenic (+91/‑108) | PP_4839/cycA | iron‑regulated membrane protein/D‑alanine/beta‑alanine/D‑serine/glycine permease | |||||
| * | ? | NC_002947 | 235331 = | 72 (1.110) | 19 (0.330) | 12/234 | 4.5 | 24.2% | intergenic (+28/+97) | PP_0183/argH | glutathione S‑transferase/argininosuccinate lyase |
| ? | NC_002947 | 235390 = | 56 (0.980) | intergenic (+87/+38) | PP_0183/argH | glutathione S‑transferase/argininosuccinate lyase | |||||
| * | ? | NC_002947 | 6013865 = | 27 (0.420) | 15 (0.290) | 10/212 | 4.6 | 39.8% | intergenic (+14/+96) | xpt/PP_5266 | xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein |
| ? | NC_002947 | 6013947 = | 24 (0.470) | intergenic (+96/+14) | xpt/PP_5266 | xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein | |||||
| * | ? | NC_002947 | = 2429960 | 42 (0.650) | 10 (0.210) | 9/200 | 4.7 | 21.6% | intergenic (+47/+66) | PP_2129/PP_2130 | hypothetical protein/lytic transglycosylase |
| ? | NC_002947 | = 2429975 | 41 (0.840) | intergenic (+62/+51) | PP_2129/PP_2130 | hypothetical protein/lytic transglycosylase | |||||
| * | ? | NC_002947 | = 5201663 | 36 (0.560) | 8 (0.170) | 8/192 | 4.8 | 23.9% | intergenic (‑101/‑79) | PP_4582/PP_4583 | membrane protein/putative Peptidase |
| ? | NC_002947 | = 5201684 | 25 (0.540) | intergenic (‑122/‑58) | PP_4582/PP_4583 | membrane protein/putative Peptidase | |||||