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 | 241,519 | A→G | 6.6% | S94S (AGT→AGC) | sufC ← | Fe‑S cluster assembly ATPase SufC |
| 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 | 601,302 | T→G | 29.3% | R1609R (CGT→CGG) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| RA | NZ_CP022686 | 662,574 | G→A | 6.0% | A118V (GCG→GTG) | clbF ← | colibactin biosynthesis dehydrogenase ClbF |
| RA | NZ_CP022686 | 756,115 | A→G | 100% | G181G (GGT→GGC) | galE ← | UDP‑glucose 4‑epimerase GalE |
| RA | NZ_CP022686 | 764,997 | T→G | 13.2% | N41T (AAC→ACC) | wcaM ← | colanic acid biosynthesis protein WcaM |
| RA | NZ_CP022686 | 765,008 | A→T | 16.2% | I37I (ATT→ATA) | wcaM ← | colanic acid biosynthesis protein WcaM |
| RA | NZ_CP022686 | 794,460 | C→T | 100% | A568V (GCG→GTG) | dgcE → | diguanylate cyclase |
| RA | NZ_CP022686 | 829,441 | C→A | 26.9% | intergenic (‑30/+197) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,452 | G→T | 21.7% | intergenic (‑41/+186) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,467 | C→A | 17.8% | intergenic (‑56/+171) | 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 | 1,000,401 | A→C | 13.1% | V955G (GTG→GGG) | yfaL ← | AIDA‑I family autotransporter adhesin YfaL/EhaC |
| RA | NZ_CP022686 | 1,000,431 | T→G | 29.2% | D945A (GAC→GCC) | yfaL ← | AIDA‑I family autotransporter adhesin YfaL/EhaC |
| RA | NZ_CP022686 | 1,172,467 | C→A | 15.3% | A130E (GCA→GAA) | yfeD → | putative DNA‑binding transcriptional regulator |
| RA | NZ_CP022686 | 1,174,272 | A→C | 18.3% | intergenic (+1/‑43) | CIW80_RS05855 → / → CIW80_RS05860 | tRNA‑Val/tRNA‑Val |
| RA | NZ_CP022686 | 1,209,908 | T→G | 17.5% | D396A (GAC→GCC) | eutH ← | ethanolamine utilization protein EutH |
| RA | NZ_CP022686 | 1,360,727 | A→T | 11.2% | intergenic (‑62/+262) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,371,066 | T→A | 20.0% | V27E (GTA→GAA) | bamD → | outer membrane protein assembly factor BamD |
| RA | NZ_CP022686 | 1,371,092 | T→A | 22.3% | Y36N (TAC→AAC) | bamD → | outer membrane protein assembly factor BamD |
| RA | NZ_CP022686 | 1,479,607 | A→C | 10.5% | intergenic (‑16/+177) | ftsB ← / ← ygbE | cell division protein FtsB/DUF3561 family protein |
| RA | NZ_CP022686 | 1,479,633 | A→C | 14.8% | intergenic (‑42/+151) | ftsB ← / ← ygbE | cell division protein FtsB/DUF3561 family protein |
| RA | NZ_CP022686 | 1,633,846 | T→G | 32.3% | N253T (AAC→ACC) | yqeB ← | selenium‑dependent molybdenum cofactor biosynthesis protein YqeB |
| RA | NZ_CP022686 | 1,674,224 | T→G | 14.3% | K188N (AAA→AAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,244 | T→G | 12.0% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,248 | T→G | 9.1% | Q180H (CAA→CAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,785,695 | T→G | 5.9% | pseudogene (16/186 nt) | CIW80_RS08875 ← | zinc‑ribbon domain‑containing protein |
| RA | NZ_CP022686 | 2,049,089 | T→G | 21.5% | N256T (AAC→ACC) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,049,094 | G→T | 20.0% | T254T (ACC→ACA) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,184,330 | G→T | 14.0% | F64L (TTC→TTA) | rplO ← | 50S ribosomal protein L15 |
| 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 | 2,408,861 | Δ1 bp | 100% | pseudogene (1097/3115 nt) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | NZ_CP022686 | 2,470,422 | T→G | 9.5% | 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 | 2,736,578 | C→A | 7.8% | T180T (ACC→ACA) | rffA → | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| RA | NZ_CP022686 | 2,743,563 | T→G | 13.3% | noncoding (65/87 nt) | CIW80_RS13750 → | tRNA‑Leu |
| RA | NZ_CP022686 | 2,868,740 | T→G | 21.8% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,904,856 | T→G | 12.3% | K237N (AAA→AAC) | ftsN ← | cell division protein FtsN |
| JC | NZ_CP022686 | 3,196,873 | +GCGTAATCGGTT | 100% | coding (944/1122 nt) | ampC ← | BlaEC family class C beta‑lactamase |
| RA | NZ_CP022686 | 3,424,795 | A→C | 100% | intergenic (‑41/+27) | yjiJ ← / ← yjiK | MFS transporter/YjiK family protein |
| 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 | 3,722,443 | T→G | 8.3% | K42N (AAA→AAC) | rcsF ← | Rcs stress response system protein RcsF |
| RA | NZ_CP022686 | 3,734,367 | T→G | 21.7% | F225V (TTT→GTT) | yafD → | endonuclease/exonuclease/phosphatase family protein |
| RA | NZ_CP022686 | 3,792,805 | A→G | 100% | Y421C (TAC→TGC) | fucP → | L‑fucose:H+ symporter permease |
| RA | NZ_CP022686 | 3,800,981 | A→C | 14.0% | pseudogene (1257/1773 nt) | CIW80_RS19080 → | ShlB/FhaC/HecB family hemolysin secretion/activation protein |
| MC JC | NZ_CP022686 | 3,844,426 | Δ1,036 bp | 100% | coding (2‑1037/1056 nt) | dinB → | DNA polymerase IV |
| RA | NZ_CP022686 | 3,868,846 | T→G | 15.2% | T383P (ACG→CCG) | ecpC ← | fimbrial usher EcpC |
| RA | NZ_CP022686 | 3,868,864 | A→C | 14.9% | S377A (TCG→GCG) | ecpC ← | fimbrial usher EcpC |
| RA | NZ_CP022686 | 3,940,707 | A→C | 15.3% | F314V (TTT→GTT) | frmA ← | S‑(hydroxymethyl)glutathione dehydrogenase |
| RA | NZ_CP022686 | 3,949,969 | T→G | 15.5% | D141A (GAC→GCC) | hemB ← | porphobilinogen synthase |
| RA | NZ_CP022686 | 4,056,987 | G→C | 10.7% | D146H (GAC→CAC) | adk → | adenylate kinase |
| RA | NZ_CP022686 | 4,439,653 | A→C | 12.3% | K570N (AAA→AAC) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,445,534 | T→G | 9.8% | intergenic (+40/‑199) | serS → / → dmsA | serine‑‑tRNA ligase/dimethylsulfoxide reductase subunit A |
| RA | NZ_CP022686 | 4,535,349 | A→C | 14.7% | T118T (ACA→ACC) | appA → | bifunctional acid phosphatase/4‑phytase |
| RA | NZ_CP022686 | 4,587,091 | T→G | 13.8% | N609T (AAC→ACC) | CIW80_RS22915 ← | enterotoxin |
| RA | NZ_CP022686 | 4,764,877 | T→G | 15.1% | intergenic (‑57/‑204) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,787,799 | C→A | 9.5% | intergenic (‑52/‑44) | CIW80_RS24075 ← / → CIW80_RS24080 | IS3‑like element ISEc52 family transposase/super‑infection exclusion protein B |
| RA | NZ_CP022686 | 4,839,668 | T→G | 22.3% | V150V (GTA→GTC) | minD ← | septum site‑determining protein MinD |
| 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 | 5,043,648 | G→C | 6.2% | V1093V (GTG→GTC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 188–2618 | 3084–2957 | 340–2897 | 7940 [7711] | [7355] 7946 | JNG15_RS00005–mobA | JNG15_RS00005,JNG15_RS00010,JNG15_RS00015,mobA |
| * | * | ÷ | pHH‑29_RBS | 2777–2841 | 5510–3245 | 405–2734 | 3693 [3578] | [3220] 3746 | 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) | 134 (1.110) | 62/250 | NT | 99.3% | 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) | 112 (0.930) | 50/250 | NT | 99.1% | 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 | |||||