mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 42 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947_CJ‑RC | 1,070,246 | 1 | . | G | 70.8% | 45.8 / 19.8 | 28 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 70.4% | 51.2 / 24.1 | 28 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 55.8% | ‑4.1 / 139.4 | 113 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 648,237 | 0 | T | G | 55.0% | ‑2.2 / 14.3 | 20 | intergenic (+6/+85) | acoR/accC | acetoin catabolism regulatory protein/acetyl‑CoA carboxylase biotin carboxylase subunit |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 54.6% | 34.4 / 233.4 | 172 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 52.9% | ‑5.7 / 12.9 | 20 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,769,335 | 0 | G | A | 51.7% | ‑3.6 / 79.9 | 58 | A421T (GCA→ACA) | tpaK | probable terephthalate transporter, MFS superfamily protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 43.6% | 52.3 / 124.5 | 102 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 36.5% | 31.3 / 15.0 | 55 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 5,743,286 | 0 | A | T | 31.8% | 14.4 / 16.1 | 23 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 1,440,082 | 0 | G | T | 30.4% | 33.0 / 10.1 | 25 | intergenic (‑413/‑246) | yveA/PP_1260 | aspartate‑proton symporter/transposase |
| * | NC_002947_CJ‑RC | 5,743,285 | 0 | A | T | 30.4% | 19.0 / 14.3 | 23 | intergenic (+35/+36) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 5,987,251 | 0 | T | C | 30.4% | 26.1 / 13.3 | 23 | intergenic (+32/+57) | PP_5242/ycaC‑II | GAF domain‑containing sensor histidine kinase/putative hydrolase |
| * | NC_002947_CJ‑RC | 2,101,751 | 0 | A | C | 29.6% | 55.9 / 10.9 | 58 | L186R (CTG→CGG) | PP_1878 | hypothetical protein |
| * | NC_002947_CJ‑RC | 4,340,196 | 0 | G | C | 29.4% | 31.2 / 12.3 | 17 | intergenic (+74/‑257) | ribAB‑II/PP_3814 | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/polyamine ABC transportersubstrate‑binding protein |
| * | NC_002947_CJ‑RC | 5,743,282 | 0 | T | G | 29.2% | 26.0 / 17.6 | 24 | intergenic (+32/+39) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 5,743,289 | 0 | C | A | 29.2% | 40.2 / 14.3 | 24 | intergenic (+39/+32) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 4,001,773 | 0 | T | G | 27.8% | 78.4 / 11.0 | 54 | intergenic (+90/‑44) | dmoA‑II/allE | dimethyl‑sulfide monooxygenase/S‑ureidoglycine aminohydrolase |
| * | NC_002947_CJ‑RC | 2,737,109 | 0 | T | G | 26.6% | 126.6 / 11.3 | 65 | V1336G (GTG→GGG) | PP_2394 | leucine‑rich repeat‑containing protein |
| * | NC_002947_CJ‑RC | 4,340,183 | 0 | G | C | 26.3% | 41.0 / 12.1 | 19 | intergenic (+61/‑270) | 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 58 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 1844137 | 39 (0.520) | 33 (0.450) | 28/282 | 3.1 | 36.7% | coding (657/2754 nt) | gacS | sensor protein GacS |
| ? | NC_002947_CJ‑RC | 2177702 = | 76 (1.040) | intergenic (+103/‑63) | PP_5485/PP_1931 | GNAT family acetyltransferase/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4274080 | 0 (0.000) | 15 (0.340) +61 bp |
14/168 | 3.2 | 55.8% | intergenic (‑204/‑71) | glcC/glcD | transcriptional regulator GlcC/glycolate oxidase FAD‑linked subunit |
| ? | NC_002947_CJ‑RC | 4768023 = | 41 (0.540) | intergenic (+130/‑52) | fpvA/tpaK | TonB‑dependent outer membrane ferripyoverdine receptor FpvA/probable terephthalate transporter, MFS superfamily protein | |||||
| * | ? | NC_002947_CJ‑RC | 1440000 = | NA (NA) | 26 (0.360) | 23/280 | 4.1 | 35.5% | intergenic (‑331/‑328) | yveA/PP_1260 | aspartate‑proton symporter/transposase |
| ? | NC_002947_CJ‑RC | = 1844451 | 49 (0.650) | coding (343/2754 nt) | gacS | sensor protein GacS | |||||
| * | ? | NC_002947_CJ‑RC | = 1441693 | NA (NA) | 24 (0.330) | 22/284 | 4.4 | 36.3% | intergenic (+37/+395) | PP_1260/ghrB | transposase/2‑ketoaldonate reductase/hydroxypyruvate/glyoxylate reductase |
| ? | NC_002947_CJ‑RC | 1844449 = | 43 (0.570) | coding (345/2754 nt) | gacS | sensor protein GacS | |||||
| * | ? | NC_002947_CJ‑RC | 1844449 = | 43 (0.570) | 21 (0.280) | 20/284 | 4.9 | 33.3% | coding (345/2754 nt) | gacS | sensor protein GacS |
| ? | NC_002947_CJ‑RC | 2937689 = | NA (NA) | intergenic (+46/+37) | PP_2569/PP_2570 | MHS family metabolite MFS transporter/transposase | |||||
| * | ? | NC_002947_CJ‑RC | = 4768004 | 53 (0.700) | 21 (0.280) +AT |
19/286 | 5.3 | 28.7% | intergenic (+111/‑71) | fpvA/tpaK | TonB‑dependent outer membrane ferripyoverdine receptor FpvA/probable terephthalate transporter, MFS superfamily protein |
| ? | NC_002947_CJ‑RC | 4768023 = | 53 (0.700) | intergenic (+130/‑52) | fpvA/tpaK | TonB‑dependent outer membrane ferripyoverdine receptor FpvA/probable terephthalate transporter, MFS superfamily protein | |||||
| * | ? | NC_002947_CJ‑RC | 4768023 = | 52 (0.690) | 19 (0.250) | 18/290 | 5.7 | 22.1% | intergenic (+130/‑52) | fpvA/tpaK | TonB‑dependent outer membrane ferripyoverdine receptor FpvA/probable terephthalate transporter, MFS superfamily protein |
| ? | NC_002947_CJ‑RC | 5398523 = | 82 (1.090) | intergenic (‑69/‑67) | tphA2II/hsdM | terephthalate 1,2‑dioxygenase subunit alpha/type I restriction modification system methylase | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 3 (0.040) | 19 (0.270) | 15/266 | 5.9 | 44.3% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 45 (0.650) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 11 (0.150) | 17 (0.300) | 11/220 | 6.0 | 44.0% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 35 (0.610) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 0 (0.000) | 19 (0.260) +CGGG |
16/282 | 6.1 | 100% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 0 (0.000) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||