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 43 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,348,749 | 0 | A | G | 62.9% | 15.7 / 32.5 | 36 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 699,725 | 0 | A | G | 57.9% | 6.9 / 11.9 | 19 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,327,127 | 0 | C | T | 54.2% | ‑2.9 / 25.0 | 24 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 195,634 | 0 | C | T | 50.0% | ‑0.9 / 31.8 | 27 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,655,687 | 0 | C | A | 42.1% | 3.9 / 15.2 | 19 | intergenic (‑91/+61) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 5,458,940 | 1 | . | A | 41.7% | 0.1 / 19.3 | 12 | intergenic (+17/‑45) | leuS/PP_4795 | leucine‑‑tRNA ligase/lipoprotein |
| * | NC_002947 | 5,458,946 | 0 | T | . | 38.5% | 21.4 / 14.7 | 13 | intergenic (+23/‑39) | leuS/PP_4795 | leucine‑‑tRNA ligase/lipoprotein |
| * | NC_002947 | 58,747 | 0 | T | A | 35.3% | 14.2 / 11.0 | 17 | intergenic (‑658/+30) | PP_5424/PP_0050 | hypothetical protein/hypothetical protein |
| * | NC_002947 | 58,750 | 0 | T | A | 35.3% | 13.2 / 11.6 | 17 | intergenic (‑661/+27) | PP_5424/PP_0050 | hypothetical protein/hypothetical protein |
| * | NC_002947 | 5,655,682 | 0 | T | G | 33.3% | 13.4 / 11.1 | 18 | intergenic (‑86/+66) | epd/tktA | D‑erythrose 4‑phosphate dehydrogenase/transketolase A |
| * | NC_002947 | 5,566,464 | 0 | T | A | 30.0% | 24.1 / 13.2 | 20 | Q358L (CAG→CTG) | mutL | DNA mismatch repair protein MutL |
| * | NC_002947 | 5,566,467 | 0 | T | A | 30.0% | 22.3 / 13.6 | 20 | Q357L (CAG→CTG) | mutL | DNA mismatch repair protein MutL |
| * | NC_002947 | 5,988,865 | 0 | G | A | 27.6% | 50.3 / 15.2 | 30 | intergenic (+103/‑443) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 195,559 | 0 | C | A | 27.3% | 41.1 / 11.4 | 22 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 196,351 | 0 | C | G | 27.3% | 41.4 / 11.6 | 22 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 322,142 | 0 | T | C | 27.3% | 28.1 / 10.2 | 22 | intergenic (+427/+31) | aguA/PP_0267 | agmatine deiminase/ferric siderophore receptor |
| * | NC_002947 | 3,590,368 | 0 | G | C | 27.3% | 35.2 / 13.7 | 22 | R282R (CGG→CGC) | nicP‑I | porin‑like protein |
| * | NC_002947 | 3,590,373 | 0 | G | C | 27.3% | 32.6 / 14.3 | 22 | G284A (GGC→GCC) | nicP‑I | porin‑like protein |
| * | NC_002947 | 5,988,882 | 0 | C | T | 26.5% | 68.5 / 13.0 | 35 | intergenic (+120/‑426) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,893 | 0 | C | G | 26.5% | 78.2 / 12.4 | 34 | intergenic (+131/‑415) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| Marginal new junction evidence (lowest skew 10 of 29 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 6030386 = | 15 (0.870) | 2 (0.120) | 6/264 | 1.2 | 14.2% | intergenic (+15/+52) | PP_5729/rpmG | hypothetical protein/50S ribosomal protein L33 |
| ? | NC_002947 | 6030423 = | 10 (0.610) | intergenic (+52/+15) | PP_5729/rpmG | hypothetical protein/50S ribosomal protein L33 | |||||
| * | ? | NC_002947 | 4969573 = | 26 (1.510) | 4 (0.260) | 4/252 | 1.5 | 14.1% | coding (715/2064 nt) | fliC | flagellin |
| ? | NC_002947 | = 4969569 | 25 (1.610) | coding (719/2064 nt) | fliC | flagellin | |||||
| * | ? | NC_002947 | = 4864454 | 18 (1.050) | 4 (0.260) | 4/254 | 1.5 | 18.0% | coding (1464/3489 nt) | smc | chromosome partition protein Smc |
| ? | NC_002947 | = 4864479 | 20 (1.280) | coding (1439/3489 nt) | smc | chromosome partition protein Smc | |||||
| * | ? | NC_002947 | = 743469 | 25 (1.460) | 5 (0.330) +AGGCAGGTCTGATTTCGC |
4/242 | 1.5 | 18.7% | intergenic (+145/+129) | PP_0635/PP_0636 | group II intron‑encoding maturase/cold shock DNA‑binding domain‑containing protein |
| ? | NC_002947 | = 1431465 | NA (NA) | intergenic (+74/+78) | PP_1252/PP_1253 | group II intron‑encoding maturase/ArsR family transcriptional regulator | |||||
| * | ? | NC_002947 | = 5560460 | 23 (1.340) | 4 (0.240) | 4/266 | 1.6 | 15.7% | coding (88/1188 nt) | hisZ | ATP phosphoribosyltransferase regulatory subunit |
| ? | NC_002947 | = 5560489 | 21 (1.280) | coding (59/1188 nt) | hisZ | ATP phosphoribosyltransferase regulatory subunit | |||||
| * | ? | NC_002947 | = 5164490 | 24 (1.400) | 5 (0.300) | 4/268 | 1.6 | 19.6% | coding (3438/3906 nt) | hrpA | ATP‑dependent helicase HrpA |
| ? | NC_002947 | = 5164525 | 18 (1.090) | coding (3403/3906 nt) | hrpA | ATP‑dependent helicase HrpA | |||||
| * | ? | NC_002947 | 5162612 = | 18 (1.050) | 4 (0.240) | 4/268 | 1.6 | 16.6% | intergenic (+87/+114) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| ? | NC_002947 | 5162708 = | 23 (1.390) | intergenic (+183/+18) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase | |||||
| * | ? | NC_002947 | 4788744 = | 25 (1.460) | 4 (0.240) | 4/268 | 1.6 | 15.7% | coding (5141/6525 nt) | pvdI | non‑ribosomal peptide synthetase |
| ? | NC_002947 | 4788778 = | 19 (1.150) | coding (5107/6525 nt) | pvdI | non‑ribosomal peptide synthetase | |||||
| * | ? | NC_002947 | 2989224 = | 23 (1.340) | 4 (0.250) | 4/264 | 1.6 | 15.1% | coding (161/951 nt) | PP_2613 | hypothetical protein |
| ? | NC_002947 | 2989248 = | 23 (1.410) | coding (137/951 nt) | PP_2613 | hypothetical protein | |||||
| * | ? | NC_002947 | = 1592189 | 19 (1.110) | 4 (0.240) | 4/266 | 1.6 | 19.0% | coding (52/294 nt) | PP_1396 | hypothetical protein |
| ? | NC_002947 | = 1592237 | 16 (0.970) | coding (100/294 nt) | PP_1396 | hypothetical protein | |||||