mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 165,749 | Δ1 bp | intergenic (+42/‑5) | rrnI‑5S → / → trnI‑Asn | ribosomal RNA‑5S/tRNA‑Asn |
| RA | 165,751 | Δ1 bp | intergenic (+44/‑3) | rrnI‑5S → / → trnI‑Asn | ribosomal RNA‑5S/tRNA‑Asn |
| RA | 165,826 | +C | intergenic (+1/‑4) | trnI‑Asn → / → trnI‑Thr | tRNA‑Asn/tRNA‑Thr |
| RA | 166,037 | +T | intergenic (+4/‑27) | trnI‑Gly → / → trnI‑Arg | tRNA‑Gly/tRNA‑Arg |
| RA | 166,345 | Δ1 bp | intergenic (+17/‑155) | trnI‑Ala → / → rrnH‑16S | tRNA‑Ala/ribosomal RNA‑16S |
| MC JC | 202,128 | 17908 bp→AAA | [ybbU]–skfH | 19 genes [ybbU], alkA, adaA, adaB, ndhF, ybcC, ybcF, ybcH, ybcI, ybzH, ybcL, ybcM, skfA, skfB, skfC, skfE, skfF, skfG, skfH |
|
| JC | 268,678 | (CCGGT)1→2 | coding (789/927 nt) | kdgD → | 5‑dehydro‑4‑deoxyglucarate dehydratase |
| MC JC | 529,504 | Δ104,880 bp | ydcL–gmuG | 117 genes ydcL, immA, immR, xis, ydzL, ydcO, BSU_04849, helP, conQ, nicK, ydcS, ydcT, yddA, conB, conC, conD, conE, yddF, conG, cwlT, yddI, yddJ, yddK, rapI, phrI, yddM, yddN, lrpA, lrpB, yddQ, yddR, yddS, ydzM, yddT, ydzN, sufLC, cspC, cdnL, ydzE, ydeC, ydeD, ydeE, ydeF, ydeG, ydeH, ydeI, ydeJ, ydeK, ydeL, ydeM, ydeN, ydzF, ydeO, ydeP, ydeQ, ydeR, ydeS, ydzO, aseR, arsF, ydfB, ydfC, ydfD, ydfE, ydfF, ydfG, ydzP, ydzQ, ydfH, ydfI, ydfJ, cesA, ydfK, ydfL, mneP, ydfN, ydfO, ydfP, ydfQ, ydzH, ydzR, ydfR, ydfS, cotP, ydgA, ydgB, ydgC, ydgD, ydgE, vmlR, ydgF, dinB, ydgG, ydgH, ydgI, ydgJ, ydgK, ydhB, ydhC, spoL, ydhE, ydhF, phoB, fra, ydhH, ydhI, ydhJ, ydhK, pbuE, gmuB, gmuA, gmuC, gmuD, gmuR, gmuE, gmuF, gmuG |
|
| RA | 652,828 | A→G | intergenic (+960/‑604) | groEL → / → ydiM | chaperonin large subunit/hypothetical protein; prophage 3 region |
| MC JC | 653,283 | Δ11,391 bp | ydiM–ydjC | ydiM, ydzU, bsuMA, bsuMB, bsuRA, bsuRB, bsuRC, ydjB, ydjC | |
| RA | 785,980 | G→A | intergenic (‑75/‑1735) | yetH ← / → yezD | putative lyase/dioxygenase/hypothetical protein |
| RA | 1,147,714 | T→C | V989A (GTT→GCT) | sbcC → | DNA ATP‑dependent repair enzyme |
| MC JC | 1,148,155 | Δ25,941 bp | [hlpB]–slpS | 30 genes [hlpB], gerPF, gerPE, gerPD, gerPC, gerPB, gerPA, pchI, yisJ, mblK, yisL, wprA, yisN, asnO, yizA, farP, yisQ, yisR, iolQ, iolX, yisT, yisU, yisV, yisX, yisY, yisZ, yitA, yitB, slpH, slpS |
|
| RA | 1,174,107 | +G | intergenic (+16/+29) | slpS → / ← yitE | 2‑phospho‑3‑sulfolactate synthase/putative integral inner membrane protein |
| RA | 1,174,312 | T→C | I152V (ATC→GTC) | yitE ← | putative integral inner membrane protein |
| RA | 1,263,383 | A→G | intergenic (+522/+319) | trnSL‑Val2 → / ← yjcM | tRNA‑Val/conserved hypothetical protein; phage island |
| RA | 1,263,447 | A→G | intergenic (+586/+255) | trnSL‑Val2 → / ← yjcM | tRNA‑Val/conserved hypothetical protein; phage island |
| RA | 1,263,647 | T→C | intergenic (+786/+55) | trnSL‑Val2 → / ← yjcM | tRNA‑Val/conserved hypothetical protein; phage island |
| MC JC | 1,263,668 | Δ15,828 bp | yjcM–yjdJ | 20 genes yjcM, yjcN, yjzF, yjzG, yjcO, yjcP, yjcQ, yjcR, yjcS, yjdA, yjdB, manR, manP, manA, yjdF, yjdG, yjdH, trnE, yjzH, yjdJ |
|
| RA | 1,279,570 | A→G | C312R (TGC→CGC) | ctaO ← | minor protoheme IX farnesyltransferase 1 (heme O synthase) |
| RA | 1,279,662 | C→T | G281D (GGC→GAC) | ctaO ← | minor protoheme IX farnesyltransferase 1 (heme O synthase) |
| RA | 1,279,841 | T→C | K221K (AAA→AAG) | ctaO ← | minor protoheme IX farnesyltransferase 1 (heme O synthase) |
| RA | 1,280,111 | T→C | G131G (GGA→GGG) | ctaO ← | minor protoheme IX farnesyltransferase 1 (heme O synthase) |
| RA | 1,317,152 | +GT | intergenic (+23/+5) | phrA → / ← yjpA | secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
| RA | 1,317,158 | (T)5→6 | coding (257/258 nt) | yjpA ← | putative enzyme |
| MC JC | 1,320,630 | Δ27,517 bp | [xkdA]–[xlyA] | 38 genes [xkdA], xre, yjzJ, xkdB, xkdC, ykzK, xkdD, xtrA, xpf, xtmA, xtmB, xkdE, xkdF, xkdG, ykzL, xkdH, xkdI, xkdJ, ykzM, xkdK, xkdM, xkdN, xkzB, xkdO, xkdP, xkdQ, xkdR, xkdS, xkdT, xkdU, xkzA, xkdV, xkdW, xkdX, xepA, xhlA, xhlB, [xlyA] |
|
| RA | 1,708,027 | G→T | G105V (GGA→GTA) | flhA → | component of the flagellar export machinery |
| RA | 1,781,832 | T→C | intergenic (‑47/‑74) | ymcC ← / → pksA | putative integral inner membrane protein/transcriptional regulator of bacillaene synthesis operon |
| MC JC | 1,782,126 | Δ81,684 bp | [pksA]–[pghC] | 21 genes [pksA], pksB, BSU_17099, pksC, pksD, pksE, acpK, pksF, pksG, pksH, pksI, pksJ, pksL, pksM, pksN, pksR, pksS, ymzB, ymaE, aprX, [pghC] |
|
| RA | 1,879,987 | A→G | intergenic (+228/‑100) | glnA → / → ynxB | glutamine synthetase/putative phage protein; defective, phage region |
| MC JC | 1,880,060 | 20479 bp→TCTC | ynxB–dutA | 21 genes ynxB, ynzF, ynzG, ynaB, ynaC, ynaD, ynaE, ynaF, ynaG, ynzI, ynaI, xynP, xynB, xylR, xylA, xylB, yncB, yncC, alrB, yncE, dutA |
|
| MC JC | 1,960,197 | Δ37,772 bp | ppsE–ppsA | ppsE, ppsD, ppsC, ppsB, ppsA | |
| RA | 2,045,799 | T→A | I10I (ATA→ATT) | yoaU ← | putative transcriptional regulator (LysR family) |
| RA | 2,046,458 | T→C | I177T (ATT→ACT) | yoaV → | putative modified amino acid or TCA compound efflux permease |
| MC JC | 2,046,840 | Δ32,219 bp | yoaW–yobO | 29 genes yoaW, yoaZ, penP, yobA, yobB, yppS, xynA, yozV, yobD, yozH, yozI, yobE, yobF, yozW, yozX, yozJ, yozY, rapK, phrK, yozL, yozM, yobI, bsrE, yobJ, rttM, rttL, yobM, yobN, yobO |
|
| RA | 2,097,087 | (A)7→8 | intergenic (‑111/+39) | azoJ ← / ← yocK | FMN‑dependent NADH‑azoreductase/putative general stress protein |
| MC JC | 2,152,032 | Δ134,410 bp | sprB–sprA | 198 genes sprB, yotM, yotL, yotK, yotJ, yotI, yotH, yotG, yotF, yotE, BSU_19915, yotD, yotC, yotB, sspC, yosX, yosW, yosV, yojW, yosU, yosT, dutB, nrdFB, yosQ, nrdFB, nrdEB, nrdEB, nrdIB, yosL, yosK, yosJ, yosI, yosH, yosG, yosF, yosE, yosD, yosC, yosB, yosA, yorZ, yorY, yorX, yorW, yorV, mtbP, yorT, yorS, yorR, yorQ, yorP, yorO, yorN, yorM, dpoL, yorK, yorJ, yorI, yorH, yorG, yorF, yorE, yorD, yorC, yorB, yorA, pghZ, yoqY, yoqX, yoqW, yoqV, yoqU, yoqT, yoqS, yoqR, yoqP, yoqO, yoqN, yoqM, yoqL, yoqK, yoqJ, yoqI, yoqH, yoqG, yoqF, yoqE, yoqD, yoqC, yoqB, yoqA, yopZ, yopY, yopX, yopW, yopV, yopU, yopT, yopS, yopR, yopQ, yopP, yopO, yopN, yopM, aimX, aimP, aimR, yopJ, yopI, sieB, yopG, yopF, yopE, yoyH, yoyI, yopD, yopC, yopB, yopA, yonX, yonV, yonU, yoyJ, spbT, yonS, yonR, yonP, yonO, hupN, BSU_21058, yonK, yonJ, yonI, yonH, yonG, yonF, yonE, yonD, yonC, yonB, yonA, yomZ, yomY, yomX, yomW, yomV, yomU, youA, yomT, yomS, yomR, yomQ, yomP, yomO, yomN, yomM, yozP, yomL, youB, yomK, yomJ, cwlP, yomH, yomG, yomF, yomE, yomD, BSU_21409, blyA, bhlA, bhlB, bdbB, sunS, bdbA, sunT, sunA, sunI, uvrX, yolD, yolC, yolB, yolA, bsrG, yokL, yokK, yokJ, yokI, yokH, yokG, nukF, yokE, aacD, BSU_21638, BSU_21639, yokC, yokB, sprA |
|
| RA | 2,480,646 | 2 bp→AT | intergenic (+21/+103) | zwf → / ← gndA | glucose‑6‑phosphate 1‑dehydrogenase (NADP‑dependent)/NADP+‑dependent 6‑P‑gluconate dehydrogenase |
| RA | 2,480,654 | Δ1 bp | intergenic (+29/+96) | zwf → / ← gndA | glucose‑6‑phosphate 1‑dehydrogenase (NADP‑dependent)/NADP+‑dependent 6‑P‑gluconate dehydrogenase |
| RA | 2,480,667 | Δ1 bp | intergenic (+42/+83) | zwf → / ← gndA | glucose‑6‑phosphate 1‑dehydrogenase (NADP‑dependent)/NADP+‑dependent 6‑P‑gluconate dehydrogenase |
| RA | 2,527,177 | G→C | Q364E (CAG→GAG) | xseA ← | exodeoxyribonuclease VII (large subunit) |
| RA | 2,532,497 | A→G | L171L (CTT→CTC) | spoIIIAH ← | stage III sporulation ratchet engulfment protein |
| RA | 2,536,709 | G→A | T302M (ACG→ATG) | spoIIIAA ← | ATP‑binding stage III sporulation protein |
| RA | 2,581,732 | (T)6→7 | intergenic (‑115/+39) | pstS ← / ← pbpA | phosphate ABC transporter (phosphate binding lipoprotein)/transpeptidase (penicillin‑binding protein 2A) |
| RA | 2,626,956 | G→A | A331V (GCG→GTG) | dnaK ← | molecular chaperone, ATP‑dependent |
| MC JC | 2,652,993 | Δ48,762 bp | spoIVCA–[BSU_26399] | 66 genes spoIVCA, arsC, arsB, yqcK, arsR, yqcI, rapE, phrE, yqzI, rttG, rttF, BSU_25875, yqxJ, yqxI, cwlA, yqxH, yqxG, yqcE, yqcD, yqcC, yqcB, yqcA, yqbT, yqbS, yqbR, yqbQ, yqbP, yqbO, txpA, bsrH, yqbM, yqbK, yqzN, yqbJ, yqbI, yqbH, yqbG, yqbF, yqbE, yqbD, yqbC, yqbB, yqbA, yqaT, yqaS, yqaR, yqaQ, yqaP, yqaO, yqaN, yqzO, sknM, yqaL, yqaK, yqaJ, yqaI, BSU_26305, sknH, yqaG, yqdA, yqaF, sknR, yqaD, yqaC, yqaB, [BSU_26399] |
|
| RA | 3,355,078 | C→T | P82P (CCG→CCA) | yuzN ← | putative transcriptional regulator |
| RA | 3,400,383 | A→T | intergenic (‑23/+154) | yvqJ ← / ← yvqK | putative efflux protein/putative ATP:cob(I)alamin adenosyltransferase |
| RA | 3,770,066 | (A)8→9 | intergenic (‑613/+38) | ywzE ← / ← csbD | conserved protein of unknown function (putative phage interference protein)/stress response protein |
| RA | 3,935,825 | Δ1 bp | coding (1190/1191 nt) | rlmI ← | large subunit ribosomal RNA m5C1962 methyltransferase |
| RA | 4,036,008 | T→A | L97F (TTA→TTT) | yxxE ← | hypothetical protein |
| RA | 4,155,395 | (A)5→6 | intergenic (‑186/+38) | trnY‑Lys ← / ← purA | tRNA‑Lys/adenylosuccinate synthetase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000964 | 161170–161240 | 165482–164903 | 3664–4313 | 16 [15] | [15] 16 | [rrnI‑16S]–[rrnI‑23S] | [rrnI‑16S],[rrnI‑23S] |
| * | * | ÷ | NC_000964 | 166548–166761 | 176111–172533 | 5773–9564 | 16 [15] | [14] 16 | [rrnH‑16S]–[rrnG‑23S] | [rrnH‑16S],rrnH‑23S,rrnH‑5S,rrnG‑16S,[rrnG‑23S] |
| * | * | ÷ | NC_000964 | 3321308 | 3354969 | 33662 | 18 [15] | [15] 16 | lytH–glxB | lytH,fisB,yunC,yunD,yunE,yunF,yunG,pucH,pucR,pucJ,pucK,pucL,pucM,yuzJ,auzJ,pucE,pucD,pucC,pucB,pucA,pucG,pucF,BSU_32539,bsnA,frlP,frlR,frlD,frlM,frlN,frlO,frlB,yurQ,dadA,sspG,yurS,glxB |