mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 283,582 | C→T | S344S (TCC→TCT) | betT‑II → | choline/carnitine/betaine transporter |
| RA | 787,253 | C→T | A123V (GCC→GTC) | ettA → | ADP/ATP ratio sensor/translation inhibitor |
| RA | 963,645 | C→T | A84V (GCG→GTG) | phnC → | phosphonate ABC transporter ATP‑binding protein |
| RA | 1,173,697 | A→G | L112P (CTG→CCG) | PP_1028 ← | LysR family transcriptional regulator |
| RA | 1,201,211 | C→T | S134S (AGC→AGT) P5S (CCG→TCG) |
xcpU → xcpV → |
type II secretion pathway protein XcpU type II secretion pathway protein XcpV |
| RA | 1,261,817 | (G)6→7 | coding (824/1116 nt) | PP_1104 ← | AotO‑related protein |
| RA | 1,348,789 | A→G | intergenic (‑249/+505) | galP‑I ← / ← PP_1174 | porin‑like protein/hypothetical protein |
| RA | 1,485,547 | (G)6→7 | coding (429/1098 nt) | yhdY → | amino acid ABC transporter permease |
| RA | 1,680,017 | T→G | T276P (ACC→CCC) | PP_1475 ← | CAIB/BAIF family protein |
| RA | 1,825,254 | G→T | Y14* (TAC→TAA) | mutS ← | DNA mismatch repair protein MutS |
| RA | 2,123,260 | T→C | R41R (CGT→CGC) | PP_1886 → | hypothetical protein |
| RA | 2,533,751 | C→T | S14L (TCG→TTG) | PP_2222 → | hypothetical protein |
| RA | 2,601,596 | A→G | T324A (ACC→GCC) | PP_2277 → | hypothetical protein |
| RA | 2,613,426 | A→G | T134A (ACC→GCC) | PP_2287 → | internal core protein |
| RA | 2,758,975 | T→C | A394A (GCA→GCG) | PP_2411 ← | MFS transporter |
| RA | 3,009,219 | A→G | M614T (ATG→ACG) | PP_2628 ← | ABC transporter ATP‑binding protein |
| RA | 3,254,711 | C→A | G232G (GGG→GGT) | PP_2851 ← | hypothetical protein |
| RA | 3,260,681 | (C)6→7 | intergenic (‑38/+24) | PP_2855 ← / ← PP_2856 | hypothetical protein/hypothetical protein |
| RA | 3,368,556 | T→C | intergenic (+257/‑104) | PP_2962 → / → PP_2964 | alcohol dehydrogenase/transposase |
| RA | 3,533,129 | T→C | L994P (CTG→CCG) | dnaEB → | error‑prone DNA polymerase |
| RA | 3,824,314 | C→G | A279P (GCG→CCG) | kguT ← | 2‑ketogluconate transporter, putative |
| RA | 3,824,719 | T→C | M144V (ATG→GTG) | kguT ← | 2‑ketogluconate transporter, putative |
| RA | 3,827,925 | G→A | S29F (TCC→TTC) | ptxS ← | 2‑ketogluconate utilization repressor |
| RA | 3,942,797 | G→A | S123S (AGC→AGT) | PP_3475 ← | type II secretion system pseudopilin PulG‑like signal peptide protein |
| RA | 4,056,572 | (G)6→7 | coding (1180/1320 nt) | PP_3573 → | monooxygenase |
| RA | 4,143,477 | T→C | R158R (CGT→CGC) | PP_3645 → | L‑proline amide hydrolase |
| RA | 4,169,591 | (C)8→9 | intergenic (‑150/+12) | creA ← / ← katG | creatinase/catalase‑peroxidase |
| RA | 4,341,656 | A→G | E266G (GAG→GGG) | ribAB‑II → | 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| RA | 4,618,760 | G→A | G1055S (GGC→AGC) | PP_4085 → | rhs family 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 | 4,958,434 | (C)5→6 | coding (288/1374 nt) | fliI ← | flagellum‑specific ATP synthase |
| RA | 5,060,944 | (C)6→7 | coding (279/1128 nt) | ooxB ← | opine oxidase subunit B |
| RA | 5,367,931 | G→A | P199S (CCC→TCC) | ftsH ← | integral membrane ATP‑dependent zinc metallopeptidase |
| RA | 5,489,180 | G→A | G180D (GGC→GAC) | PP_4824 → | two‑component system sensor histidine kinase/response regulator |
| RA | 5,585,751 | C→T | A652T (GCG→ACG) | parC ← | DNA topoisomerase IV subunit A |
| RA | 5,607,194 | C→T | A242A (GCG→GCA) | PP_4926 ← | HlyD family secretion protein |
| RA | 5,641,230 | (C)7→8 | coding (349/1320 nt) | PP_4950 → | hypothetical protein |
| RA | 5,679,880 | (C)10→11 | coding (99/1860 nt) | PP_4983 ← | amine oxidase |
| RA | 5,749,795 | T→C | T53A (ACA→GCA) | PP_5043 ← | PhoPQ‑activated pathogenicity‑like protein |
| RA | 5,773,577 | G→A | A455V (GCC→GTC) | betT‑I ← | choline transporter |
| RA | 5,895,281 | A→G | intergenic (‑34/+177) | PP_5167 ← / ← cysA | hypothetical protein/sulfate/thiosulfate ABC transporter ATP‑binding protein |
| RA | 6,032,315 | (A)9→8 | intergenic (+22/+45) | PP_5729 → / ← rpmG | hypothetical protein/50S ribosomal protein L33 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_002947 | 27220 | 27542 | 323 | 8 [6] | [7] 8 | PP_0022/PP_0023 | hypothetical protein/hypothetical protein |
| * | * | ÷ | NC_002947 | 97558 | 97611 | 54 | 8 [7] | [5] 9 | [PP_0090]–[PP_0091] | [PP_0090],[PP_0091] |
| * | * | ÷ | NC_002947 | 170777 | 170867 | 91 | 8 [7] | [6] 9 | [PP_0159] | [PP_0159] |
| * | * | ÷ | NC_002947 | 171364–172964 | 176300–172968 | 5–4937 | 8 [5] | [6] 9 | PP_16SA–[PP_5SA] | PP_16SA,PP_23SA,[PP_5SA] |
| * | * | ÷ | NC_002947 | 176641–178394 | 181784–178398 | 5–5144 | 8 [6] | [7] 8 | PP_16SB–[PP_r01] | PP_16SB,PP_23SB,[PP_r01] |
| * | * | ÷ | NC_002947 | 681258 | 681328 | 71 | 8 [7] | [7] 9 | [PP_0583] | [PP_0583] |
| * | * | ÷ | NC_002947 | 1704658 | 1704712 | 55 | 8 [6] | [7] 8 | [PP_1499] | [PP_1499] |
| * | * | ÷ | NC_002947 | 1947824 | 1947877 | 54 | 17 [6] | [7] 8 | PP_1748/PP_1749 | hypothetical protein/acetyltransferase |
| * | * | ÷ | NC_002947 | 2004043 | 2004349 | 307 | 8 [7] | [7] 8 | PP_1787 | hypothetical protein |
| * | * | ÷ | NC_002947 | 2007431 | 2008372 | 942 | 8 [7] | [7] 8 | PP_1791 | aldolase/synthase |
| * | * | ÷ | NC_002947 | 2297794 | 2297842 | 49 | 9 [7] | [4] 8 | PP_5496/PP_2023 | hypothetical protein/glutathione S‑transferase family protein |
| * | * | ÷ | NC_002947 | 2476115 | 2476118 | 4 | 20 [0] | [0] 8 | PP_2167/tal | PhoD‑like phosphatase/transaldolase |
| * | * | ÷ | NC_002947 | 3055136 | 3055221 | 86 | 8 [7] | [7] 9 | [PP_2664]–[agmR] | [PP_2664],[agmR] |
| * | * | ÷ | NC_002947 | 4172118 | 4172190 | 73 | 9 [5] | [7] 8 | katG/PP_3669 | catalase‑peroxidase/LysR family transcriptional regulator |
| * | * | ÷ | NC_002947 | 4325104 | 4325208 | 105 | 8 [7] | [7] 8 | PP_3792/PP_5631 | hypothetical protein/hypothetical protein |
| * | * | ÷ | NC_002947 | 4531961 | 4532022 | 62 | 11 [7] | [6] 8 | PP_4018/topB | acetyltransferase/DNA topoisomerase III |
| * | * | ÷ | NC_002947 | 4742766 | 4742844 | 79 | 8 [7] | [4] 8 | gltA/yeiW | citrate synthase/putative oxidoreductase |
| * | * | ÷ | NC_002947 | 4810127 | 4810140 | 14 | 27 [0] | [0] 12 | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | * | ÷ | NC_002947 | 5023270 | 5023637 | 368 | 8 [5] | [7] 8 | [PP_4425] | [PP_4425] |
| * | * | ÷ | NC_002947 | 5099184 | 5099254 | 71 | 9 [7] | [7] 8 | PP_mr66/acsA‑I | P6/acetyl‑CoA synthetase |
| * | * | ÷ | NC_002947 | 5164459 | 5164592 | 134 | 9 [7] | [6] 9 | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| * | * | ÷ | NC_002947 | 5508444 | 5508582–5508575 | 132–139 | 9 [6] | [7] 9 | [PP_4839] | [PP_4839] |
| * | * | ÷ | NC_002947 | 6100261 | 6100460 | 200 | 9 [7] | [5] 8 | PP_5350 | RpiR family transcriptional regulator |
| * | * | ÷ | NC_002947 | 6162521 | 6162756 | 236 | 8 [6] | [6] 8 | PP_5740 | hypothetical protein |
| * | * | ÷ | NC_002947 | 6183852 | 6183858 | 7 | 36 [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) | 36 (0.680) | 19/264 | 0.9 | 100% | intergenic (–/+146) | –/parB | –/chromosome‑partitioning protein |
| ? | NC_002947 | = 6183851 | 0 (0.000) | intergenic (‑3/–) | atpI/– | ATP synthase protein I/– | |||||
| * | ? | NC_002947 | = 652785 | 46 (0.870) | 17 (0.380) | 7/224 | 2.1 | 46.6% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4810126 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 652786 | 46 (0.870) | 11 (0.210) | 7/264 | 2.5 | 31.4% | coding (1960/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4810125 | 2 (0.040) | intergenic (‑267/‑288) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | 1617825 = | 19 (0.360) | 8 (0.170) | 6/234 | 2.5 | 30.9% | intergenic (‑38/+135) | PP_1417/PP_1418 | tricarboxylate transport protein TctB/tricarboxylate transport protein TctC |
| ? | NC_002947 | 1617914 = | 19 (0.410) | intergenic (‑127/+46) | PP_1417/PP_1418 | tricarboxylate transport protein TctB/tricarboxylate transport protein TctC | |||||
| * | ? | NC_002947 | 2474067 = | 22 (0.420) | 10 (0.270) | 5/186 | 2.3 | 49.4% | intergenic (+6/+143) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947 | 2474191 = | 5 (0.140) | intergenic (+130/+19) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase | |||||
| * | ? | NC_002947 | = 4854420 | 1 (0.020) | 10 (0.280) | 4/182 | 2.5 | 53.1% | intergenic (‑124/+173) | recR/ybaB | recombination protein RecR/nucleoid‑associated broad specificity regulator |
| ? | NC_002947 | = 4854479 | 17 (0.470) | intergenic (‑183/+114) | recR/ybaB | recombination protein RecR/nucleoid‑associated broad specificity regulator | |||||