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 | seq id | position | mutation | freq | annotation | gene | description |
| RA | NZ_CP022686 | 162,411 | G→T | 9.3% | A48S (GCT→TCT) | ydgH → | DUF1471 family protein YdgH |
| RA | NZ_CP022686 | 235,455 | G→C | 13.6% | G157R (GGT→CGT) | pykF → | pyruvate kinase PykF |
| RA | NZ_CP022686 | 235,673:1 | +T | 11.5% | coding (687/1413 nt) | pykF → | pyruvate kinase PykF |
| RA | NZ_CP022686 | 340,516 | A→C | 15.3% | F31V (TTT→GTT) | ydjK ← | MFS transporter |
| RA | NZ_CP022686 | 372,574 | A→C | 15.3% | N275T (AAC→ACC) | sdaA → | L‑serine ammonia‑lyase |
| RA | NZ_CP022686 | 457,894 | Δ1 bp | 100% | pseudogene (288/997 nt) | CIW80_RS02445 ← | DUF968 domain‑containing protein |
| RA | NZ_CP022686 | 556,948 | A→T | 16.4% | intergenic (+132/‑716) | zinT → / → CIW80_RS03080 | metal‑binding protein ZinT/site‑specific integrase |
| 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 | 28.4% | V1607G (GTC→GGC) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 601,302 | T→G | 19.0% | R1609R (CGT→CGG) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 606,995 | A→C | 7.3% | R344S (AGA→AGC) | ybtU → | yersiniabactin biosynthesis oxidoreductase YbtU |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| RA | NZ_CP022686 | 651,848 | A→C | 9.4% | 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 | 794,460 | C→T | 100% | A568V (GCG→GTG) | dgcE → | diguanylate cyclase |
| RA | NZ_CP022686 | 807,696 | T→G | 7.8% | V187G (GTC→GGC) | mdtC → | multidrug efflux RND transporter permease subunit MdtC |
| RA | NZ_CP022686 | 829,448 | T→A | 17.0% | intergenic (‑37/+190) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,452 | G→T | 24.9% | intergenic (‑41/+186) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,467 | C→A | 20.3% | 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 | 957,112 | T→G | 16.9% | T89P (ACC→CCC) | ccmA ← | cytochrome c biogenesis heme‑transporting ATPase CcmA |
| RA | NZ_CP022686 | 972,697 | A→C | 6.2% | T7P (ACG→CCG) | rcsD → | phosphotransferase RcsD |
| RA | NZ_CP022686 | 1,005,085 | C→A | 12.4% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,040,909 | A→C | 10.6% | E232D (GAA→GAC) | rbn → | ribonuclease BN |
| RA | NZ_CP022686 | 1,249,393 | C→A | 9.3% | intergenic (‑40/+46) | uraA ← / ← upp | uracil permease/uracil phosphoribosyltransferase |
| RA | NZ_CP022686 | 1,360,709 | T→G | 12.6% | intergenic (‑44/+280) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,360,750 | G→T | 14.3% | intergenic (‑85/+239) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,392,487 | A→C | 12.0% | T43P (ACG→CCG) | lhgO → | L‑2‑hydroxyglutarate oxidase |
| RA | NZ_CP022686 | 1,479,607 | A→C | 11.2% | intergenic (‑16/+177) | ftsB ← / ← ygbE | cell division protein FtsB/DUF3561 family protein |
| RA | NZ_CP022686 | 1,479,633 | A→C | 13.7% | intergenic (‑42/+151) | ftsB ← / ← ygbE | cell division protein FtsB/DUF3561 family protein |
| RA | NZ_CP022686 | 1,547,110 | G→C | 22.9% | intergenic (+22/‑12) | CIW80_RS07710 → / → CIW80_RS07715 | tRNA‑Met/tRNA‑Met |
| RA | NZ_CP022686 | 1,558,395 | A→C | 15.0% | K464N (AAA→AAC) | vgrG → | type VI secretion system Vgr family protein |
| RA | NZ_CP022686 | 1,564,296 | A→C | 9.9% | L99F (TTA→TTC) | CIW80_RS07780 → | ImcF‑related family protein |
| RA | NZ_CP022686 | 1,674,244 | T→G | 18.0% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,248 | T→G | 13.5% | Q180H (CAA→CAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,911,602 | T→G | 9.5% | N224T (AAC→ACC) | CIW80_RS09520 ← | MurR/RpiR family transcriptional regulator |
| RA | NZ_CP022686 | 1,954,923 | T→G | 19.7% | T92P (ACG→CCG) | ttdR ← | DNA‑binding transcriptional activator TtdR |
| RA | NZ_CP022686 | 1,971,467 | C→A | 10.9% | intergenic (+58/‑126) | ebgR → / → ebgA | transcriptional regulator EbgR/beta‑galactosidase subunit alpha |
| RA | NZ_CP022686 | 2,049,089 | T→G | 18.0% | N256T (AAC→ACC) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,049,094 | G→T | 11.9% | T254T (ACC→ACA) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,049,097 | A→T | 12.5% | R253R (CGT→CGA) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,056,168 | A→C | 13.7% | G614G (GGT→GGG) | infB ← | translation initiation factor IF‑2 |
| RA | NZ_CP022686 | 2,110,465 | T→G | 11.2% | T10P (ACC→CCC) | rplM ← | 50S ribosomal protein L13 |
| RA | NZ_CP022686 | 2,123,241 | A→C | 7.9% | F208V (TTT→GTT) | tldD ← | metalloprotease TldD |
| RA | NZ_CP022686 | 2,148,136 | T→G | 9.4% | V133G (GTT→GGT) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,172,177 | A→C | 8.4% | G87G (GGT→GGG) | smg ← | DUF494 family protein Smg |
| RA | NZ_CP022686 | 2,184,330 | G→T | 15.2% | F64L (TTC→TTA) | rplO ← | 50S ribosomal protein L15 |
| RA | NZ_CP022686 | 2,185,075 | A→C | 9.7% | 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 | 2,353,173 | T→G | 8.2% | L108V (TTG→GTG) | yhhN → | lysoplasmalogenase |
| RA | NZ_CP022686 | 2,357,324 | A→C | 17.5% | N37T (AAC→ACC) | dcrB → | phage sensitivity protein DcrB |
| RA | NZ_CP022686 | 2,386,496 | T→G | 11.2% | K417N (AAA→AAC) | prlC ← | oligopeptidase A |
| RA | NZ_CP022686 | 2,394,287 | T→G | 14.5% | N115T (AAC→ACC) | chuS ← | hematinate‑forming heme oxygenase ChuS |
| RA | NZ_CP022686 | 2,408,861 | Δ1 bp | 100% | pseudogene (1097/3115 nt) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | NZ_CP022686 | 2,513,068 | A→C | 8.4% | K42N (AAA→AAC) | yibL → | YibL family ribosome‑associated protein |
| RA | NZ_CP022686 | 2,516,577 | A→G | 7.3% | T663A (ACA→GCA) | upaG → | trimeric autotransporter adhesin UpaG |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,703,299 | A→C | 7.3% | intergenic (‑203/‑277) | yieP ← / → CIW80_RS13540 | FadR/GntR family transcriptional regulator/16S ribosomal RNA |
| RA | NZ_CP022686 | 2,760,143 | G→T | 7.0% | D124Y (GAT→TAT) | xerC → | tyrosine recombinase XerC |
| RA | NZ_CP022686 | 2,801,827 | C→A | 10.9% | E29* (GAA→TAA) | CIW80_RS14030 ← | 2‑dehydro‑3‑deoxy‑6‑phosphogalactonate aldolase |
| RA | NZ_CP022686 | 2,821,644 | A→C | 7.1% | intergenic (+100/‑278) | hemG → / → CIW80_RS14130 | menaquinone‑dependent protoporphyrinogen IX dehydrogenase/16S ribosomal RNA |
| RA | NZ_CP022686 | 2,868,740 | T→G | 24.9% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,868,753 | T→G | 12.7% | T18P (ACC→CCC) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,904,915 | T→G | 8.1% | T218P (ACC→CCC) | ftsN ← | cell division protein FtsN |
| RA | NZ_CP022686 | 3,020,229 | T→G | 12.5% | V133G (GTC→GGC) | yjbB → | Na/Pi cotransporter family protein |
| RA | NZ_CP022686 | 3,136,940 | T→G | 9.7% | D161A (GAC→GCC) | phnN ← | ribose 1,5‑bisphosphokinase |
| RA | NZ_CP022686 | 3,150,888 | A→C | 5.0% | T232P (ACG→CCG) | rdcB → | YjcZ‑like family protein |
| RA | NZ_CP022686 | 3,184,651 | A→C | 9.4% | 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 | 3,281,068 | T→G | 8.3% | V96G (GTG→GGG) | yjfF → | sugar ABC transporter permease YjfF |
| RA | NZ_CP022686 | 3,348,371 | T→G | 9.2% | intergenic (‑187/‑13) | 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 | 3,461,229 | T→G | 18.8% | 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 | 3,628,488 | G→C | 8.1% | E193Q (GAA→CAA) | aceF → | pyruvate dehydrogenase complex dihydrolipoyllysine‑residue acetyltransferase |
| RA | NZ_CP022686 | 3,638,666 | T→G | 6.9% | intergenic (‑4/+102) | speE ← / ← yacC | polyamine aminopropyltransferase/YacC family pilotin‑like protein |
| RA | NZ_CP022686 | 3,656,188 | A→G | 100% | S549P (TCC→CCC) | htrE ← | outer membrane usher protein |
| RA | NZ_CP022686 | 3,665,907 | A→C | 9.2% | Q462H (CAA→CAC) | hrpB → | ATP‑dependent helicase HrpB |
| RA | NZ_CP022686 | 3,734,367 | T→G | 16.6% | 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 | 3,797,493 | G→T | 16.6% | 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 | 3,868,846 | T→G | 11.6% | T383P (ACG→CCG) | ecpC ← | fimbrial usher EcpC |
| RA | NZ_CP022686 | 3,935,324 | T→G | 17.1% | N705T (AAC→ACC) | lacZ ← | beta‑galactosidase |
| RA | NZ_CP022686 | 3,949,969 | T→G | 12.4% | D141A (GAC→GCC) | hemB ← | porphobilinogen synthase |
| RA | NZ_CP022686 | 4,214,448 | T→G | 12.8% | intergenic (‑21/+14) | CIW80_RS21095 ← / ← CIW80_RS21100 | tRNA‑Gln/tRNA‑Gln |
| RA | NZ_CP022686 | 4,287,491 | T→G | 6.2% | noncoding (4/76 nt) | CIW80_RS21480 → | tRNA‑Lys |
| RA | NZ_CP022686 | 4,368,341 | T→G | 12.8% | D47A (GAC→GCC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,368,372 | T→G | 12.0% | S37R (AGC→CGC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,368,380 | T→G | 8.7% | N34T (AAC→ACC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,440,297 | T→A | 9.3% | V785D (GTT→GAT) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,440,324 | C→A | 14.0% | P794Q (CCG→CAG) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,440,334 | A→C | 20.1% | Q797H (CAA→CAC) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,485,614 | T→G | 8.0% | F139V (TTT→GTT) | gloC → | hydroxyacylglutathione hydrolase GloC |
| RA | NZ_CP022686 | 4,587,091 | T→G | 10.9% | N609T (AAC→ACC) | CIW80_RS22915 ← | enterotoxin |
| RA | NZ_CP022686 | 4,632,182 | T→G | 9.1% | R276R (CGT→CGG) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| RA | NZ_CP022686 | 4,638,444 | A→C | 5.5% | intergenic (+17/‑355) | CIW80_RS23235 → / → focA | S/F1C fimbrial major subunit operon transcriptional regulator/F1C fimbrial major subunit FocA |
| RA | NZ_CP022686 | 4,764,877 | T→G | 16.7% | intergenic (‑57/‑204) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,780,176 | A→C | 13.9% | intergenic (‑75/+95) | phoP ← / ← purB | two‑component system response regulator PhoP/adenylosuccinate lyase |
| RA | NZ_CP022686 | 4,809,437 | T→G | 7.6% | L49R (CTG→CGG) | CIW80_RS24260 → | head‑tail joining 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 | 5,001,164 | A→C | 14.5% | N163T (AAC→ACC) | ompG → | monomeric porin OmpG |
| RA | NZ_CP022686 | 5,042,289 | T→C | 9.9% | N640N (AAT→AAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,648 | G→C | 5.3% | V1093V (GTG→GTC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,831 | C→T | 8.0% | D1154D (GAC→GAT) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | pMUT1‑hok‑empty | 4,123:1 | +T | 100% | intergenic (‑341/–) | putative rom (RNA I inhibition modulator protein) ← / – | –/– |
| RA | pMUT1‑hok‑empty | 4,127 | C→A | 100% | intergenic (‑345/–) | putative rom (RNA I inhibition modulator protein) ← / – | –/– |
| RA | pMUT1‑hok‑empty | 4,132 | 4 bp→TA | 100% | intergenic (‑350/–) | putative rom (RNA I inhibition modulator protein) ← / – | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 404–2618 | 3047–2957 | 340–2644 | 5882 [5497] | [5727] 5908 | [JNG15_RS00005]–mobA | [JNG15_RS00005],JNG15_RS00010,JNG15_RS00015,mobA |
| * | * | ÷ | pMUT1‑hok‑empty | 1261–1318 | 3987–1722 | 405–2727 | 4769 [4697] | [4737] 5568 | putative HTH domain protein–putative rom (RNA I inhibition modulator protein) | putative HTH domain protein,uncharacterized protein,hypothetical protein,putative rom (RNA I inhibition modulator protein) |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP022686 | 262466 = | 2 (0.010) | 174 (1.130) | 65/250 | NT | 98.9% | 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 | 2 (0.010) | 155 (1.010) | 55/250 | NT | 98.7% | 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 = | 100 (0.650) | 49 (0.370) | 32/218 | NT | 35.9% | intergenic (‑40/+290) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA |
| ? | NZ_CP022686 | 3899944 = | 88 (0.660) | intergenic (‑318/+12) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA | |||||
| * | ? | NZ_CP022686 | = 3899681 | 100 (0.650) | 53 (0.400) | 33/218 | NT | 37.7% | intergenic (‑55/+275) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA |
| ? | NZ_CP022686 | = 3899927 | 88 (0.660) | intergenic (‑301/+29) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA | |||||
| * | ? | pMUT1‑hok‑empty | 456 = | 3599 (0.450) | 5061 (0.640) | 223/250 | NT | 67.1% | intergenic (–/+1261) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | 4136 = | 1373 (0.170) | intergenic (‑354/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||
| * | ? | pMUT1‑hok‑empty | = 491 | 5270 (0.660) | 4026 (0.640) | 175/200 | NT | 59.1% | intergenic (–/+1226) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | = 4098 | 1366 (0.220) | intergenic (‑316/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||