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 | 457,894 | Δ1 bp | 100% | pseudogene (288/997 nt) | CIW80_RS02445 ← | DUF968 domain‑containing protein |
| RA | NZ_CP022686 | 482,321 | C→A | 14.7% | A181A (GCG→GCT) | flhA ← | flagellar biosynthesis protein FlhA |
| 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 | 601,295 | T→G | 30.1% | V1607G (GTC→GGC) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 601,302 | T→G | 24.2% | R1609R (CGT→CGG) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| RA | NZ_CP022686 | 651,848 | A→C | 18.1% | R238R (CGT→CGG) | clbJ ← | colibactin non‑ribosomal peptide synthetase ClbJ |
| RA | NZ_CP022686 | 756,115 | A→G | 100% | G181G (GGT→GGC) | galE ← | UDP‑glucose 4‑epimerase GalE |
| RA | NZ_CP022686 | 765,008 | A→T | 20.2% | 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 | 837,589 | A→T | 13.3% | intergenic (‑162/+61) | thiM ← / ← rcnR | hydroxyethylthiazole kinase/Ni(II)/Co(II)‑binding transcriptional repressor RcnR |
| 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 | 948,090 | C→A | 19.5% | intergenic (+159/‑98) | CIW80_RS04855 → / → CIW80_RS04860 | terminase small subunit/hypothetical protein |
| RA | NZ_CP022686 | 1,005,085 | C→A | 17.3% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,100,959 | T→G | 12.0% | D182A (GAC→GCC) | aroC ← | chorismate synthase |
| RA | NZ_CP022686 | 1,360,724 | G→T | 12.3% | intergenic (‑59/+265) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,370,556 | T→G | 20.9% | P99P (CCA→CCC) | rluD ← | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD |
| RA | NZ_CP022686 | 1,396,420 | T→G | 14.0% | intergenic (+26/‑211) | gabT → / → gabP | 4‑aminobutyrate‑‑2‑oxoglutarate transaminase/GABA permease |
| RA | NZ_CP022686 | 1,674,244 | T→G | 11.7% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,248 | T→G | 14.7% | Q180H (CAA→CAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,706,023 | T→A | 9.0% | intergenic (‑633/‑22) | yqgB ← / → metK | acid stress response protein YqgB/methionine adenosyltransferase |
| RA | NZ_CP022686 | 1,805,047 | G→T | 18.4% | pseudogene (328/934 nt) | CIW80_RS09020 → | nucleotidyl transferase AbiEii/AbiGii toxin family protein |
| RA | NZ_CP022686 | 1,925,332 | A→C | 9.0% | N151T (AAC→ACC) | ygiB → | DUF1190 family protein |
| RA | NZ_CP022686 | 1,964,332 | A→C | 8.5% | G27G (GGT→GGG) | mug ← | G/U mismatch‑specific DNA glycosylase |
| RA | NZ_CP022686 | 1,965,173 | A→C | 15.6% | R86R (CGT→CGG) | nfeF ← | NADPH‑dependent ferric chelate reductase |
| RA | NZ_CP022686 | 2,016,160 | T→G | 11.3% | noncoding (114/377 nt) | rnpB ← | RNase P RNA component class A |
| RA | NZ_CP022686 | 2,047,987 | A→C | 8.5% | R623R (CGT→CGG) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,148,141 | T→G | 12.1% | F135V (TTC→GTC) | panF → | sodium/pantothenate symporter |
| 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 | 19.0% | K72N (AAA→AAC) | glyS ← | glycine‑‑tRNA ligase subunit beta |
| RA | NZ_CP022686 | 2,572,721 | A→C | 15.1% | F186C (TTT→TGT) | CIW80_RS12885 ← | ROK family protein |
| RA | NZ_CP022686 | 2,574,429 | T→G | 10.7% | N230T (AAC→ACC) | CIW80_RS12895 ← | class II fructose‑bisphosphate aldolase family protein |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,617,885 | T→G | 8.4% | K190N (AAA→AAC) | ilvB ← | acetolactate synthase large subunit |
| RA | NZ_CP022686 | 2,631,870 | A→C | 8.9% | V376G (GTC→GGC) | dgoT ← | MFS transporter |
| RA | NZ_CP022686 | 2,736,586 | A→C | 11.4% | Y183S (TAC→TCC) | rffA → | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| RA | NZ_CP022686 | 2,801,827 | C→A | 8.3% | E29* (GAA→TAA) | CIW80_RS14030 ← | 2‑dehydro‑3‑deoxy‑6‑phosphogalactonate aldolase |
| RA | NZ_CP022686 | 2,829,007 | G→A | 5.7% | E155K (GAG→AAG) | srkA → | stress response kinase SrkA |
| RA | NZ_CP022686 | 2,868,740 | T→G | 33.6% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,868,753 | T→G | 19.0% | T18P (ACC→CCC) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 3,184,651 | A→C | 10.5% | intergenic (‑98/+18) | cutA ← / ← dcuA | divalent cation tolerance protein CutA/anaerobic C4‑dicarboxylate transporter DcuA |
| 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 | 7.5% | intergenic (‑161/‑39) | CIW80_RS16685 ← / → CIW80_RS26495 | inovirus Gp2 family protein/hypothetical protein |
| 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 | 20.6% | intergenic (‑32/+3) | CIW80_RS17335 ← / ← CIW80_RS17340 | tRNA‑Leu/tRNA‑Leu |
| RA | NZ_CP022686 | 3,461,229 | T→G | 18.2% | noncoding (84/87 nt) | CIW80_RS17340 ← | tRNA‑Leu |
| 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 | 3,792,805 | A→G | 100% | Y421C (TAC→TGC) | fucP → | L‑fucose:H+ symporter permease |
| RA | NZ_CP022686 | 3,797,493 | G→T | 17.5% | G134C (GGT→TGT) | CIW80_RS19065 → | LacI family DNA‑binding transcriptional regulator |
| MC JC | NZ_CP022686 | 3,844,426 | Δ1,036 bp | 100% | coding (2‑1037/1056 nt) | dinB → | DNA polymerase IV |
| RA | NZ_CP022686 | 4,108,979 | T→G | 12.1% | S196A (TCT→GCT) | cysS → | cysteine‑‑tRNA ligase |
| RA | NZ_CP022686 | 4,217,332 | A→C | 8.9% | G151G (GGT→GGG) | nagD ← | ribonucleotide monophosphatase NagD |
| RA | NZ_CP022686 | 4,249,121 | A→C | 8.1% | V35G (GTC→GGC) | kdpD ← | two‑component system sensor histidine kinase KdpD |
| RA | NZ_CP022686 | 4,331,940 | A→C | 16.3% | F289V (TTT→GTT) | ybhR ← | ABC transporter permease |
| RA | NZ_CP022686 | 4,570,086 | A→C | 8.8% | L68V (TTA→GTA) | pgaD ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine biosynthesis protein PgaD |
| RA | NZ_CP022686 | 4,632,182 | T→G | 9.3% | R276R (CGT→CGG) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| 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 | 5,042,289 | T→C | 8.8% | N640N (AAT→AAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,042,304 | T→C | 8.2% | N645N (AAT→AAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,044,641 | C→T | 5.1% | N1424N (AAC→AAT) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 338–2618 | 3068–2957 | 340–2731 | 5693 [5666] | [5215] 5783 | [JNG15_RS00005]–mobA | [JNG15_RS00005],JNG15_RS00010,JNG15_RS00015,mobA |
| * | * | ÷ | pHH‑29_RBS | 2771–3097 | 5512–3244 | 148–2742 | 3760 [3606] | [3574] 3867 | 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 = | 0 (0.000) | 111 (0.910) | 55/250 | NT | 100% | 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 | 0 (0.000) | 99 (0.810) | 51/250 | NT | 100% | 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 | |||||