mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 1,013,252 | T→G | intergenic (+77/+54) | prfC → / ← potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| RA | 1,385,507 | T→C | D319G (GAC→GGC) | oprD ← | basic amino acid specific porin OprD |
| RA | 1,680,017 | T→G | T276P (ACC→CCC) | PP_1475 ← | CAIB/BAIF family protein |
| RA | 3,824,314 | C→G | A279P (GCG→CCG) | kguT ← | 2‑ketogluconate transporter, putative |
| RA | 3,827,925 | G→A | S29F (TCC→TTC) | ptxS ← | 2‑ketogluconate utilization repressor |
| RA | 4,160,432 | T→G | L159R (CTG→CGG) | PP_3661 → | membrane protein |
| RA | 4,160,437 | A→C | S161R (AGC→CGC) | PP_3661 → | membrane protein |
| RA | 4,637,297 | A→G | S143P (TCT→CCT) | uvrY ← | BarA/UvrY two‑componenent system response regulator |
| RA | 4,743,195 | +C | intergenic (+464/+288) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,743,197 | A→G | intergenic (+466/+286) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,743,199 | C→T | intergenic (+468/+284) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,743,202 | C→T | intergenic (+471/+281) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,743,205 | C→G | intergenic (+474/+278) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,743,207 | 2 bp→CT | intergenic (+476/+275) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,743,221 | C→T | intergenic (+490/+262) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,743,223 | A→C | intergenic (+492/+260) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 4,743,226 | 2 bp→GC | intergenic (+495/+256) | gltA → / ← yeiW | citrate synthase/putative oxidoreductase |
| RA | 5,367,766 | A→G | F254L (TTC→CTC) | ftsH ← | integral membrane ATP‑dependent zinc metallopeptidase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_002947 | 97572 | 97603 | 32 | 3 [2] | [2] 4 | PP_0090/PP_0091 | hypothetical protein/putative lipoprotein |
| * | * | ÷ | NC_002947 | 170808 | 170858 | 51 | 4 [2] | [2] 3 | [PP_0159] | [PP_0159] |
| * | * | ÷ | NC_002947 | 171395–172965 | 176282–172972 | 8–4888 | 3 [1] | [2] 3 | [PP_16SA]–[PP_5SA] | [PP_16SA],PP_23SA,[PP_5SA] |
| * | * | ÷ | NC_002947 | 176665–178395 | 181682–178402 | 8–5018 | 3 [1] | [2] 3 | PP_16SB–[PP_r01] | PP_16SB,PP_23SB,[PP_r01] |
| * | * | ÷ | NC_002947 | 353056 | 353112 | 57 | 3 [2] | [2] 3 | hisF/cbcV | imidazole glycerol phosphate synthase subunit HisF/choline/betaine/carnitine ABC transporter ATP binding protein |
| * | * | ÷ | NC_002947 | 1383246 | 1383269 | 24 | 7 [2] | [1] 5 | PP_1204 | lipoprotein |
| * | * | ÷ | NC_002947 | 1499470 | 1499493 | 24 | 3 [2] | [1] 3 | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| * | * | ÷ | NC_002947 | 1592639 | 1592672 | 34 | 3 [2] | [2] 3 | PP_1397 | hypothetical protein |
| * | * | ÷ | NC_002947 | 1712092 | 1712159 | 68 | 3 [1] | [2] 3 | ppc/adk | phosphoenolpyruvate carboxylase/adenylate kinase |
| * | * | ÷ | NC_002947 | 2040193 | 2040244 | 52 | 6 [2] | [2] 3 | PP_mr27/rffE | C4 ncRNA/UDP‑N‑acetylglucosamine‑2‑epimerase |
| * | * | ÷ | NC_002947 | 2243263 | 2243309 | 47 | 3 [2] | [2] 3 | gltX/PP_t25 | glutamate‑‑tRNA ligase/tRNA‑Ala |
| * | * | ÷ | NC_002947 | 2297796 | 2297830 | 35 | 3 [0] | [2] 9 | PP_5496/PP_2023 | hypothetical protein/glutathione S‑transferase family protein |
| * | * | ÷ | NC_002947 | 2839043 | 2839102 | 60 | 3 [2] | [2] 6 | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase |
| * | * | ÷ | NC_002947 | 3055165 | 3055211 | 47 | 3 [2] | [2] 3 | [agmR] | [agmR] |
| * | * | ÷ | NC_002947 | 3778322 | 3778360 | 39 | 3 [2] | [1] 3 | PP_3338/PP_3339 | cytochrome bd‑type quinol oxidase/hypothetical protein |
| * | * | ÷ | NC_002947 | 3847685 | 3847722 | 38 | 4 [2] | [1] 3 | [PP_3395] | [PP_3395] |
| * | * | ÷ | NC_002947 | 4152015 | 4152054 | 40 | 4 [2] | [1] 3 | PP_3654/PP_3655 | leucine‑responsive regulatory protein/cytosine/purine/uracil/thiamine/allantoin permease family protein |
| * | * | ÷ | NC_002947 | 4172138 | 4172182 | 45 | 3 [2] | [1] 6 | katG/PP_3669 | catalase‑peroxidase/LysR family transcriptional regulator |
| * | * | ÷ | NC_002947 | 4531983 | 4532005 | 23 | 3 [2] | [2] 3 | PP_4018/topB | acetyltransferase/DNA topoisomerase III |
| * | * | ÷ | NC_002947 | 4677310 | 4677349 | 40 | 4 [2] | [1] 4 | PP_4137/chrR | outer membrane siderophore receptor/chromate reductase |
| * | * | ÷ | NC_002947 | 4844862 | 4844870 | 9 | 3 [1] | [0] 3 | ccoP‑II/PP_4259 | cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein |
| * | * | ÷ | NC_002947 | 4854421 | 4854444 | 24 | 19 [0] | [2] 4 | recR/ybaB | recombination protein RecR/nucleoid‑associated broad specificity regulator |
| * | * | ÷ | NC_002947 | 5201624 | 5201648 | 25 | 5 [1] | [1] 3 | PP_4579/PP_4580 | LysR family transcriptional regulator/hypothetical protein |
| * | * | ÷ | NC_002947 | 5258807 | 5258866 | 60 | 5 [2] | [2] 3 | [PP_5703]–[PP_4634] | [PP_5703],[PP_4634] |
| * | * | ÷ | NC_002947 | 5487097 | 5487129 | 33 | 3 [2] | [2] 3 | purH/purD | bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase |
| * | * | ÷ | NC_002947 | 5818877 | 5818885 | 9 | 3 [0] | [2] 3 | PP_5092/pilT | NLP/P60 protein/twitching motility protein |
| * | * | ÷ | NC_002947 | 5899728 | 5899768 | 41 | 3 [2] | [1] 5 | PP_5172/PP_5173 | hypothetical protein/RND family transporter |
| * | * | ÷ | NC_002947 | 5905113 | 5905163 | 51 | 3 [2] | [2] 3 | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| * | * | ÷ | NC_002947 | 6011123 | 6011131 | 9 | 5 [2] | [1] 6 | norM/PP_5263 | multidrug resistance protein NorM/GGDEF domain‑containing protein |
| * | * | ÷ | NC_002947 | 6015820 | 6015843 | 24 | 11 [0] | [2] 3 | xpt/PP_5266 | xanthine phosphoribosyltransferase/acetyl‑CoA hydrolase family protein |
| * | * | ÷ | NC_002947 | 6100348 | 6100378 | 31 | 3 [2] | [2] 3 | PP_5350 | RpiR family transcriptional regulator |
| * | * | ÷ | NC_002947 | 6183852 | 6183858 | 7 | 33 [0] | [0] NA | atpI/– | ATP synthase protein I/– |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 1 = | 0 (0.000) | 33 (0.740) | 21/264 | 0.5 | 100% | intergenic (–/+146) | –/parB | –/chromosome‑partitioning protein |
| ? | NC_002947 | = 6183851 | 0 (0.000) | intergenic (‑3/–) | atpI/– | ATP synthase protein I/– | |||||
| * | ? | NC_002947 | 1617825 = | 19 (0.420) | 5 (0.130) | 3/234 | 2.5 | 25.1% | intergenic (‑38/+135) | PP_1417/PP_1418 | tricarboxylate transport protein TctB/tricarboxylate transport protein TctC |
| ? | NC_002947 | 1617914 = | 13 (0.330) | intergenic (‑127/+46) | PP_1417/PP_1418 | tricarboxylate transport protein TctB/tricarboxylate transport protein TctC | |||||
| * | ? | NC_002947 | 2474067 = | 10 (0.220) | 8 (0.250) | 5/186 | 1.6 | 51.6% | intergenic (+6/+143) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947 | 2474191 = | 8 (0.250) | intergenic (+130/+19) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase | |||||
| * | ? | NC_002947 | 4810141 = | 0 (0.000) | 13 (0.400) | 5/194 | 1.7 | 33.8% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5990913 | 51 (1.550) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4810146 | 0 (0.000) | 29 (0.760) | 11/224 | 1.0 | 49.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5990927 | 59 (1.550) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||