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 |
| Predicted mutations | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | NZ_CP022686 | 60,184 | C→A | 6.4% | L109L (CTG→CTT) | narZ ← | nitrate reductase Z subunit alpha |
| RA | NZ_CP022686 | 256,604 | C→T | 5.7% | R98C (CGT→TGT) | ydiO → | acyl‑CoA dehydrogenase |
| RA | NZ_CP022686 | 291,196 | T→A | 5.9% | P45P (CCT→CCA) | katE → | catalase HPII |
| RA | NZ_CP022686 | 457,894 | Δ1 bp | 100% | pseudogene (288/997 nt) | CIW80_RS02445 ← | DUF968 domain‑containing protein |
| RA | NZ_CP022686 | 560,880 | C→T | 100% | intergenic (+62/+53) | CIW80_RS03085 → / ← pilV | hypothetical protein/shufflon system plasmid conjugative transfer pilus tip adhesin PilV |
| RA | NZ_CP022686 | 596,637 | T→G | 14.3% | G54G (GGT→GGG) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| RA | NZ_CP022686 | 694,391 | C→A | 15.9% | intergenic (+151/‑45) | CIW80_RS03555 → / → CIW80_RS03560 | transposase/PfkB family carbohydrate kinase |
| RA | NZ_CP022686 | 756,115 | A→G | 100% | G181G (GGT→GGC) | galE ← | UDP‑glucose 4‑epimerase GalE |
| RA | NZ_CP022686 | 794,460 | C→T | 100% | A568V (GCG→GTG) | dgcE → | diguanylate cyclase |
| RA | NZ_CP022686 | 829,435 | C→A | 29.4% | intergenic (‑24/+203) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 917,427:1 | +TT | 100% | intergenic (+130/‑91) | yeiP → / → yeiQ | elongation factor P‑like protein YeiP/mannitol dehydrogenase family protein |
| RA | NZ_CP022686 | 1,174,306 | T→A | 10.4% | intergenic (+35/‑9) | CIW80_RS05855 → / → CIW80_RS05860 | tRNA‑Val/tRNA‑Val |
| RA | NZ_CP022686 | 1,210,499 | A→T | 5.5% | M199K (ATG→AAG) | eutH ← | ethanolamine utilization protein EutH |
| RA | NZ_CP022686 | 1,239,865 | G→T | 22.2% | intergenic (‑162/+6) | ypfJ ← / ← purC | neutral zinc metallopeptidase/phosphoribosylaminoimidazolesuccinocarboxamide synthase |
| RA | NZ_CP022686 | 1,360,724 | G→T | 17.2% | intergenic (‑59/+265) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,632,480 | T→G | 10.5% | V159G (GTC→GGC) | arcC → | carbamate kinase |
| RA | NZ_CP022686 | 1,632,501 | T→G | 15.6% | V166G (GTT→GGT) | arcC → | carbamate kinase |
| RA | NZ_CP022686 | 1,785,695 | T→G | 9.9% | pseudogene (16/186 nt) | CIW80_RS08875 ← | zinc‑ribbon domain‑containing protein |
| RA | NZ_CP022686 | 2,049,094 | G→T | 12.3% | T254T (ACC→ACA) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,185,075 | A→C | 14.6% | V46G (GTT→GGT) | rpsE ← | 30S ribosomal protein S5 |
| RA | NZ_CP022686 | 2,214,419 | T→C | 100% | K43R (AAA→AGA) | rpsL ← | 30S ribosomal protein S12 |
| RA | NZ_CP022686 | 2,320,775 | C→T | 100% | G274S (GGC→AGC) | CIW80_RS11675 ← | DNA‑processing protein DprA |
| RA | NZ_CP022686 | 2,398,896 | A→C | 12.8% | K206N (AAA→AAC) | hutW → | heme anaerobic degradation radical SAM methyltransferase ChuW/HutW |
| RA | NZ_CP022686 | 2,408,861 | Δ1 bp | 100% | pseudogene (1097/3115 nt) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | NZ_CP022686 | 2,470,422 | T→G | 13.3% | K72N (AAA→AAC) | glyS ← | glycine‑‑tRNA ligase subunit beta |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,703,299 | A→C | 11.9% | intergenic (‑203/‑277) | yieP ← / → CIW80_RS13540 | FadR/GntR family transcriptional regulator/16S ribosomal RNA |
| RA | NZ_CP022686 | 2,758,109 | A→C | 9.1% | N34T (AAC→ACC) | yifL → | lipoprotein |
| RA | NZ_CP022686 | 2,961,325 | A→C | 11.9% | intergenic (+103/‑270) | murI → / → CIW80_RS14765 | glutamate racemase/16S ribosomal RNA |
| RA | NZ_CP022686 | 3,090,101 | A→C | 12.1% | V9G (GTT→GGT) | yjcB ← | YjcB family protein |
| JC | NZ_CP022686 | 3,196,873 | +GCGTAATCGGTT | 100% | coding (944/1122 nt) | ampC ← | BlaEC family class C beta‑lactamase |
| RA | NZ_CP022686 | 3,348,345 | G→T | 11.6% | intergenic (‑161/‑39) | CIW80_RS16685 ← / → CIW80_RS26495 | inovirus Gp2 family protein/hypothetical protein |
| RA | NZ_CP022686 | 3,390,614 | G→T | 13.6% | A143A (GCC→GCA) | sgcX ← | M42 family metallopeptidase |
| RA | NZ_CP022686 | 3,424,795 | A→C | 100% | intergenic (‑41/+27) | yjiJ ← / ← yjiK | MFS transporter/YjiK family protein |
| RA | NZ_CP022686 | 3,461,223 | G→T | 20.5% | intergenic (‑32/+3) | CIW80_RS17335 ← / ← CIW80_RS17340 | tRNA‑Leu/tRNA‑Leu |
| RA | NZ_CP022686 | 3,526,241 | T→G | 7.8% | R212R (CGT→CGG) | dapB → | 4‑hydroxy‑tetrahydrodipicolinate reductase |
| MC JC | NZ_CP022686 | 3,559,837 | Δ2,343 bp | 100% | coding (10‑2352/2352 nt) | polB ← | DNA polymerase II |
| RA | NZ_CP022686 | 3,656,188 | A→G | 100% | S549P (TCC→CCC) | htrE ← | outer membrane usher protein |
| RA | NZ_CP022686 | 3,713,141 | G→T | 14.2% | D26Y (GAT→TAT) | yaeR → | VOC family protein |
| RA | NZ_CP022686 | 3,770,524 | T→G | 9.8% | intergenic (‑260/+203) | CIW80_RS26265 ← / ← CIW80_RS18890 | ATP‑binding protein/hypothetical protein |
| RA | NZ_CP022686 | 3,792,805 | A→G | 100% | Y421C (TAC→TGC) | fucP → | L‑fucose:H+ symporter permease |
| MC JC | NZ_CP022686 | 3,844,426 | Δ1,036 bp | 100% | coding (2‑1037/1056 nt) | dinB → | DNA polymerase IV |
| RA | NZ_CP022686 | 3,940,707 | A→C | 11.3% | F314V (TTT→GTT) | frmA ← | S‑(hydroxymethyl)glutathione dehydrogenase |
| RA | NZ_CP022686 | 3,949,969 | T→G | 13.7% | D141A (GAC→GCC) | hemB ← | porphobilinogen synthase |
| RA | NZ_CP022686 | 4,368,341 | T→G | 17.1% | D47A (GAC→GCC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,440,292 | A→G | 9.2% | Q783Q (CAA→CAG) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,440,324 | C→A | 14.9% | P794Q (CCG→CAG) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,678,041 | A→C | 15.4% | intergenic (+39/‑82) | agn43 → / → CIW80_RS23450 | autotransporter adhesin Ag43/hypothetical protein |
| MC JC | NZ_CP022686 | 4,844,868 | Δ1,662 bp | 100% | [umuD]–[umuC] | [umuD], [umuC] | |
| RA | NZ_CP022686 | 4,870,912 | Δ1 bp | 100% | intergenic (‑108/‑120) | dhaK ← / → dhaR | dihydroxyacetone kinase subunit DhaK/dihydroxyacetone kinase operon transcriptional regulator DhaR |
| RA | NZ_CP022686 | 4,951,521 | A→C | 11.8% | T39P (ACC→CCC) | topA → | type I DNA topoisomerase |
| RA | NZ_CP022686 | 5,042,289 | T→C | 10.2% | N640N (AAT→AAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,648 | G→C | 8.5% | V1093V (GTG→GTC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | pHH‑29_RBS | 1,659 | T→G | 88.3% | L54* (TTA→TGA) | Aldafermin (NGM282) → | |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 316–2617 | 3082–2957 | 341–2767 | 6663 [6498] | [6507] 6679 | [JNG15_RS00005]–mobA | [JNG15_RS00005],JNG15_RS00010,JNG15_RS00015,mobA |
| * | * | ÷ | pHH‑29_RBS | 2777–2892 | 5510–3105 | 214–2734 | 3355 [3262] | [2981] 3482 | putative HTH domain protein (MarR‑like)–hypothetical protein | putative HTH domain protein (MarR‑like),putative HTH domain protein,uncharacterized protein,hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP022686 | 262466 = | 1 (0.010) | 98 (0.980) | 43/250 | NT | 99.0% | coding (320/1647 nt) | fadK | medium‑chain fatty‑acid‑‑CoA ligase |
| ? | NZ_CP022686 | = 1524130 | NA (NA) | intergenic (+8/+232) | CIW80_RS07590/syd | IS3‑like element ISEc52 family transposase/SecY‑interacting protein | |||||
| * | ? | NZ_CP022686 | = 262468 | 1 (0.010) | 85 (0.850) | 47/250 | NT | 98.8% | coding (322/1647 nt) | fadK | medium‑chain fatty‑acid‑‑CoA ligase |
| ? | NZ_CP022686 | = 1761697 | NA (NA) | intergenic (‑72/‑70) | CIW80_RS08710/CIW80_RS08720 | IS3‑like element ISEc52 family transposase/IS3‑like element IS600 family transposase | |||||
| * | ? | NZ_CP022686 | 3899666 = | 116 (1.160) | 8 (0.090) | 8/218 | NT | 7.8% | intergenic (‑40/+290) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA |
| ? | NZ_CP022686 | 3899944 = | 89 (1.020) | intergenic (‑318/+12) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA | |||||
| * | ? | NZ_CP022686 | = 3899681 | 110 (1.100) | 8 (0.090) | 7/218 | NT | 8.0% | intergenic (‑55/+275) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA |
| ? | NZ_CP022686 | = 3899927 | 89 (1.020) | intergenic (‑301/+29) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA | |||||