mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.7 revision b7a44cd89118
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 2,450 | G→T | L705L (CTG→CTT) | thrA → | bifunctional aspartokinase I/homeserine dehydrogenase I |
| RA | 45,662 | C→T | V155I (GTC→ATC) | caiT ← | L‑carnitine/gamma‑butyrobetaine antiporter |
| RA | 70,867 | T→C | D92G (GAC→GGC) | araA ← | L‑arabinose isomerase |
| JC JC | 183,262 | IS150 (+) +3 bp | coding (1184‑1186/1518 nt) | dgt → | deoxyguanosinetriphosphate triphosphohydrolase |
| RA | 226,159 | C→A | P163T (CCT→ACT) | gmhB → | hypothetical protein |
| RA | 239,002 | A→C | A4A (GCA→GCC) | dnaQ → | DNA polymerase III subunit epsilon |
| JC JC | 336,055 | IS150 (–) +3 bp | coding (2805‑2807/3075 nt) | lacZ ← | beta‑D‑galactosidase |
| RA | 393,720 | G→A | R96H (CGC→CAC) | queA → | S‑adenosylmethionine:tRNA ribosyltransferase‑isomerase |
| RA | 430,835 | C→T | intergenic (‑48/‑108) | insL‑2 ← / → lon | putative transposase insL for insertion sequence IS186/DNA‑binding ATP‑dependent protease La |
| RA | 433,668 | C→T | R55C (CGT→TGT) | hupB → | HU, DNA‑binding transcriptional regulator, beta subunit |
| JC | 474,391 | (GTCGCCAGC)1→2 | coding (915/1677 nt) | ybaL ← | predicted transporter with NAD(P)‑binding Rossmann‑fold domain |
| MC JC JC | 490,484 | IS150 (+) Δ1 bp :: +CATT | intergenic (‑37/+24) | ybbN ← / ← ybbO | predicted thioredoxin domain‑containing protein/short chain dehydrogenase |
| JC JC | 502,543 | IS150 (–) +3 bp | coding (848‑850/1095 nt) | ybbB ← | tRNA 2‑selenouridine synthase, selenophosphate‑dependent |
| MC JC | 547,700 | Δ8,125 bp | IS1‑mediated | [nmpC]–[ECB_00513] | [nmpC], ybcR, ybcS, ybcT, ybcU, ECB_00510, nohB, ECB_00512, [ECB_00513] |
| RA | 588,492 | +AA | intergenic (‑219/‑50) | ybdK ← / → insJ‑1 | gamma‑glutamyl:cysteine ligase/IS150 hypothetical protein |
| JC JC | 651,703 | +GAA :: IS150 (+) +2 bp | intergenic (‑83/+176) | ybeB ← / ← phpB | hypothetical protein/predicted alpha‑ribazole‑5'‑P phosphatase |
| RA | 666,133 | +T | pseudogene (355/387 nt) | gltL ← | ATP‑binding protein of glutamate/aspartate transport system; b0652_1 |
| RA | 735,660 | T→A | intergenic (‑401/‑308) | gltA ← / → sdhC | citrate synthase/succinate dehydrogenase cytochrome b556 large membrane subunit |
| RA | 761,693 | T→G | noncoding (47/76 nt) | valT → | tRNA‑Val |
| RA | 796,336 | (T)8→7 | intergenic (‑7/‑419) | ECB_00737 ← / → ECB_00738 | hypothetical protein/hypothetical protein |
| RA | 875,094 | G→C | H65D (CAT→GAT) | deoR ← | DNA‑binding transcriptional repressor |
| JC JC | 896,463 | IS150 (+) +3 bp | coding (159‑161/432 nt) | ECB_00838 → | putative phage tail protein |
| JC JC | 929,574 | IS150 (+) +3 bp | coding (946‑948/1653 nt) | hcp ← | hydroxylamine reductase |
| RA | 943,554 | A→C | intergenic (‑53/+232) | infA ← / ← aat | translation initiation factor IF‑1/leucyl/phenylalanyl‑tRNA‑protein transferase |
| RA | 962,002 | G→A | intergenic (+13/+22) | dmsC → / ← ycaC | dimethyl sulfoxide reductase, anaerobic, subunit C/predicted hydrolase |
| JC JC | 969,836 | IS150 (+) +3 bp | coding (810‑812/2283 nt) | pflB ← | pyruvate formate lyase I |
| JC JC | 1,102,032 | IS150 (–) +3 bp | coding (756‑758/1065 nt) | phoH → | conserved protein with nucleoside triphosphate hydrolase domain |
| RA | 1,162,594 | A→G | P135P (CCA→CCG) | plsX → | fatty acid/phospholipid synthesis protein |
| RA | 1,166,129 | T→C | intergenic (+156/‑55) | fabG → / → acpP | 3‑oxoacyl‑[acyl‑carrier‑protein] reductase/acyl carrier protein |
| RA | 1,207,861 | T→G | N47T (AAC→ACC) | ycfC ← | hypothetical protein |
| JC JC | 1,218,697 | IS150 (+) +3 bp | coding (1209‑1211/1524 nt) | ycgG → | conserved inner membrane protein |
| JC JC | 1,270,660 | IS150 (–) +4 bp | intergenic (‑167/+235) | ldrC ← / ← chaA | toxic polypeptide, small/calcium/sodium:proton antiporter |
| RA | 1,343,489 | G→A | L542L (CTG→TTG) | yciR ← | modulator of Rnase II stability |
| JC JC | 1,354,425 | IS150 (–) +3 bp | coding (1053‑1055/1644 nt) | sapA ← | predicted antimicrobial peptide transporter subunit |
| JC JC | 1,448,695 | IS1 (+) +9 bp | coding (224‑232/1758 nt) | ynbC → | predicted hydrolase |
| JC JC | 1,462,266 | IS150 (+) +3 bp | intergenic (‑28/‑311) | mokB ← / → trg | regulatory peptide/methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor |
| MC | 1,609,175 | Δ7,554 bp | between IS3 | ybcW–[ECB_01526] | ybcW, gnsB, ynfN, ECB_01516, cspI, ydfP, ydfQ, ydfR, essQ, ECB_01522, ECB_01523, insE‑4, insF‑4, [ECB_01526] |
| JC JC | 1,619,834 | IS150 (–) +3 bp | intergenic (‑71/+139) | hokD ← / ← ECB_01533 | small toxic polypeptide/conserved hypothetical protein |
| RA | 1,733,865 | G→T | A301S (GCC→TCC) | pykF → | pyruvate kinase |
| RA | 1,746,189 | G→A | intergenic (‑237/‑152) | ydiJ ← / → ydiK | predicted FAD‑linked oxidoreductase/predicted inner membrane protein |
| RA | 1,749,019 | G→A | pseudogene (326/858 nt) | ydiM → | putative transport protein (MFS family); b1690_1 |
| RA | 1,879,026 | T→A | D380V (GAT→GTT) | yoaE ← | fused predicted membrane protein/conserved protein |
| RA | 1,902,276 | (T)7→8 | coding (7/342 nt) | yebY ← | hypothetical protein |
| RA | 1,915,108 | (A)8→7 | intergenic (‑218/‑120) | zwf ← / → yebK | glucose‑6‑phosphate 1‑dehydrogenase/predicted DNA‑binding transcriptional regulator |
| RA | 1,916,109 | A→G | intergenic (+12/‑116) | yebK → / → pykA | predicted DNA‑binding transcriptional regulator/pyruvate kinase |
| JC JC | 1,916,224 | IS1 (–) +9 bp | [pykA] | [pykA] | |
| RA | 1,930,575 | C→A | F137L (TTC→TTA) | yecE → | hypothetical protein |
| RA | 1,948,728 | T→C | M343V (ATG→GTG) | tap ← | methyl‑accepting protein IV |
| MC JC | 1,974,040 | Δ8,273 bp | IS1‑mediated | [yedU]–[yeeI] | [yedU], yedV, yedW, yedX, yedY, yedZ, yodA, yodB, serU, [yeeI] |
| MC JC | 2,034,358 | Δ19,491 bp | [insB‑14]–[wcaJ] | 20 genes [insB‑14], insA‑14, wbbD, wbbC, wzy, wbbB, wbbA, vioB, vioA, wzx, rmlC, rfbA, rfbD, rfbB, galF, wcaM, wcaL, wcaK, wzxC, [wcaJ] |
|
| JC JC | 2,196,656 | IS150 (–) +3 bp | coding (1350‑1352/1992 nt) | cirA ← | ferric iron‑catecholate outer membrane transporter |
| MC JC | 2,263,508 | Δ3,531 bp | IS1‑mediated | rcsC–[atoS] | rcsC, [atoS] |
| RA | 2,268,951 | T→G | I129S (ATC→AGC) | atoC → | fused response regulator of ato operon, in two‑component system with AtoS: response regulator/sigma54 interaction protein |
| JC JC | 2,322,340 | IS186 (+) +6 bp | coding (131‑136/963 nt) | menC ← | O‑succinylbenzoate synthase |
| MC JC JC | 2,397,529 | IS150 (–) Δ14 bp | coding (1124‑1137/2646 nt) | yfcTU ← | predicted outer membrane export usher protein |
| JC JC | 2,405,131 | IS1 (–) +9 bp | coding (168‑176/1347 nt) | fadL → | long‑chain fatty acid outer membrane transporter |
| JC JC | 2,448,493 | IS186 (–) +6 bp | intergenic (+24/+21) | nupC → / ← yfeA | nucleoside (except guanosine) transporter/predicted diguanylate cyclase |
| JC JC | 2,522,900 | IS150 (–) +3 bp | coding (255‑257/2019 nt) | hyfB → | NADH dehydrogenase subunit N |
| RA | 2,702,361 | G→A | G160S (GGC→AGC) | proX → | glycine betaine transporter subunit |
| RA | 2,758,314 | A→C | K374Q (AAA→CAA) | ygbK → | hypothetical protein |
| RA | 2,775,879 | Δ1 bp | intergenic (‑49/+200) | insJ‑3 ← / ← cysH | IS150 hypothetical protein/phosphoadenosine phosphosulfate reductase |
| RA | 2,847,052 | A→G | V10A (GTT→GCT) | recD ← | exonuclease V (RecBCD complex), alpha chain |
| RA | 3,067,926 | G→A | A40V (GCA→GTA) | yghS ← | predicted protein with nucleoside triphosphate hydrolase domain |
| RA | 3,093,020 | T→G | F74L (TTT→TTG) | yqhH → | predicted outer membrane lipoprotein |
| JC JC | 3,270,443 | IS150 (–) +4 bp | intergenic (+21/+24) | nlp → / ← murA | DNA‑binding transcriptional activator of maltose metabolism/UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase |
| RA | 3,271,926 | T→C | D38G (GAC→GGC) | yrbA ← | predicted DNA‑binding transcriptional regulator |
| RA | 3,287,483 | T→C | M260V (ATG→GTG) | arcB ← | hybrid sensory histidine kinase in two‑component regulatory system with ArcA |
| RA | 3,308,106 | G→A | A6A (GCG→GCA) | yhcB → | hypothetical protein |
| RA | 3,312,775 | G→A | R59H (CGC→CAC) | argR → | arginine repressor |
| RA | 3,328,272 | A→G | V236A (GTT→GCT) | mreB ← | cell wall structural complex MreBCD, actin‑like component MreB |
| RA | 3,338,108 | T→G | intergenic (+266/‑63) | prmA → / → yhdG | ribosomal protein L11 methyltransferase/tRNA‑dihydrouridine synthase B |
| RA | 3,396,621 | T→G | N380H (AAC→CAC) | chiA ← | periplasmic endochitinase |
| RA | 3,409,316 | T→G | S41S (TCT→TCG) | yheS → | fused predicted transporter subunits of ABC superfamily: ATP‑binding components |
| JC | 3,482,398 | Δ25 bp | coding (714‑738/2706 nt) | malT → | transcriptional regulator MalT |
| RA | 3,533,061 | T→G | K124N (AAA→AAC) | ftsE ← | predicted transporter subunit: ATP‑binding component of ABC superfamily |
| RA | 3,536,881 | A→G | E148G (GAA→GGA) | yhhN → | conserved inner membrane protein |
| JC JC | 3,537,178 | +GTACTGACCCCAAAA :: IS150 (–) :: +CAA | coding (40/2199 nt) | zntA → | zinc, cobalt and lead efflux system |
| RA | 3,684,366 | C→A | R216S (CGT→AGT) | ECB_03438 → | conserved hypothetical protein |
| JC JC | 3,766,595 | IS150 (+) +3 bp | coding (1111‑1113/1206 nt) | gltS ← | glutamate transporter |
| JC JC | 3,841,192 | IS150 (+) +3 bp | coding (389‑391/1074 nt) | recF ← | recombination protein F |
| MC JC | 3,894,997 | Δ6,138 bp | IS150‑mediated | rbsD–[yieO] | rbsD, rbsA, rbsC, rbsB, rbsK, rbsR, [yieO] |
| JC | 3,947,872 | (TAATTGA)2→3 | intergenic (‑66/+620) | aslA ← / ← hemY | acrylsulfatase‑like enzyme/predicted protoheme IX synthesis protein |
| JC JC | 3,981,782 | IS150 (–) +3 bp | coding (249‑251/1224 nt) | ECB_03710 ← | putative permease |
| JC JC | 3,990,387 | IS150 (+) +3 bp | coding (1250‑1252/1491 nt) | ECB_03719 ← | conserved hypothetical protein |
| JC JC | 4,092,861 | IS150 (+) +3 bp | coding (87‑89/429 nt) | yiiT → | stress‑induced protein |
| RA | 4,096,877 | G→T | Y232* (TAC→TAA) | glpF ← | glycerol facilitator |
| RA | 4,101,091 | T→C | E47G (GAA→GGA) | hslU ← | ATP‑dependent protease ATP‑binding subunit |
| RA | 4,133,104 | G→A | R34R (CGC→CGT) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,201,980 | G→A | P194S (CCT→TCT) | iclR ← | DNA‑binding transcriptional repressor |
| JC | 4,205,069 | Δ5 bp | coding (2311‑2315/3684 nt) | metH → | B12‑dependent methionine synthase |
| MC JC | 4,275,717 | 57510 bp→5 bp | [yjcO]–[lysU] | 52 genes [yjcO], fdhF, yjcP, yjcQ, yjcR, yjcS, alsK, alsE, alsC, alsA, alsB, rpiR, rpiB, yjdP, phnP, phnO, phnN, phnM, phnL, phnK, phnJ, phnI, phnH, phnG, phnF, phnE, phnD, phnC, phnB, phnA, yjdA, yjcZ, proP, basS, basR, yjdB, yjdE, adiY, adiA, melR, melA, melB, yjdF, fumB, dcuB, dcuR, dcuS, dcuS, yjdI, yjdJ, yjdK, [lysU] |
|
| RA | 4,384,430 | C→A | S29Y (TCT→TAT) | yjeB → | predicted DNA‑binding transcriptional regulator |
| JC JC | 4,415,710 | IS150 (–) +3 bp | coding (848‑850/1413 nt) | cycA → | D‑alanine/D‑serine/glycine transporter |
| RA | 4,459,658 | A→G | P315P (CCA→CCG) | yjgL → | hypothetical protein |
| JC JC | 4,462,655 | IS1 (+) +9 bp | intergenic (‑85/‑100) | yjgM ← / → yjgN | predicted acetyltransferase/conserved inner membrane protein |
| RA | 4,558,781 | (T)7→6 | coding (657/1425 nt) | hsdS ← | specificity determinant for hsdM and hsdR |
| JC JC | 4,615,673 | IS150 (+) +4 bp | coding (145‑148/1233 nt) | nadR → | nicotinamide‑nucleotide adenylyltransferase |
| RA | 4,628,460 | T→G | T3P (ACC→CCC) | arcA ← | DNA‑binding response regulator in two‑component regulatory system with ArcB or CpxA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | REL606 | 16975 | 18001 | 1027 | 76 [0] | [1] 64 | [nhaA] | [nhaA] |
| * | * | ÷ | REL606 | 762209 | 762410–762361 | 153–202 | 22 [19] | [21] 22 | [lysZ]–[lysQ] | [lysZ],[lysQ] |
| * | * | ÷ | REL606 | 2086926 | 2093026 | 6101 | 91 [0] | [2] 66 | yegM–[yegO] | yegM,yegN,[yegO] |
| * | * | ÷ | REL606 | 2655705 | 2655780 | 76 | 88 [0] | [1] 79 | [yfiH] | [yfiH] |
| * | * | ÷ | REL606 | 2842061 | 2842259 | 199 | 22 [20] | [21] 25 | [metZ]–[metV] | [metZ],metW,[metV] |
| * | * | ÷ | REL606 | 2999597 | 3048488 | 48892 | 106 [0] | [0] 104 | [flu]–yghK | [flu],yeeR,ECB_02802,yafZ,ECB_02804,yeeS,yeeT,yeeU,yeeV,yeeW,ECB_02810,ECB_02811,ECB_02812,ECB_02813,ECB_02814,ECB_02815,ECB_02816,ECB_02817,ECB_02818,ECB_02819,ECB_02820,ECB_02821,ECB_02822,insB‑22,insA‑22,ECB_02825,ECB_02826,ECB_02827,ECB_02828,yghD,yghE,ECB_02831,ECB_02832,ECB_02833,ECB_02834,ECB_02835,ECB_02836,ECB_02837,ECB_02838,yghF,yghG,pppA,yghJ,yghK |
| * | * | ÷ | REL606 | 4047676 | 4049579 | 1904 | 128 [0] | [1] 103 | [yihR]–[yihS] | [yihR],[yihS] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | REL606 | = 16974 | 0 (0.000) | 73 (1.160) | 54/196 | 0.2 | 100% | intergenic (‑16/‑514) | mokC/nhaA | regulatory protein for HokC, overlaps CDS of hokC/pH‑dependent sodium/proton antiporter |
| ? | REL606 | = 590471 | NA (NA) | noncoding (1977/1977 nt) | IS150 | repeat region | |||||
| * | ? | REL606 | 18002 = | 1 (0.020) | 63 (0.980) | 52/200 | 0.2 | 98.4% | coding (515/1167 nt) | nhaA | pH‑dependent sodium/proton antiporter |
| ? | REL606 | 588495 = | NA (NA) | noncoding (1/1977 nt) | IS150 | repeat region | |||||
| * | ? | REL606 | 588495 = | NA (NA) | 107 (1.700) | 68/196 | 0.0 | NA | noncoding (1/1977 nt) | IS150 | repeat region |
| ? | REL606 | 589936 = | NA (NA) | noncoding (387/768 nt) | IS1 | repeat region | |||||
| * | ? | REL606 | 664688 = | NA (NA) | 91 (1.410) | 70/200 | 0.0 | 100% | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | REL606 | = 2086925 | 0 (0.000) | intergenic (‑1346/‑199) | yegL/yegM | hypothetical protein/multidrug efflux system, subunit A | |||||
| * | ? | REL606 | = 666130 | NA (NA) | 128 (1.990) | 81/200 | 0.0 | NA | noncoding (1443/1443 nt) | IS150 | repeat region |
| ? | REL606 | = 711957 | NA (NA) | coding (102/1665 nt) | rhsC | rhsC element core protein RshC | |||||
| * | ? | REL606 | 2093027 = | 2 (0.030) | 63 (0.980) | 49/200 | 0.3 | 96.9% | coding (1534/3078 nt) | yegO | multidrug efflux system, subunit C |
| ? | REL606 | 2774435 = | NA (NA) | noncoding (1443/1443 nt) | IS150 | repeat region | |||||
| * | ? | REL606 | = 2655704 | 0 (0.000) | 85 (1.330) | 67/198 | 0.0 | 100% | intergenic (‑123/+7) | clpB/yfiH | protein disaggregation chaperone/hypothetical protein |
| ? | REL606 | 3651091 = | NA (NA) | noncoding (1/1443 nt) | IS150 | repeat region | |||||
| * | ? | REL606 | 2655781 = | 1 (0.020) | 75 (1.190) | 56/196 | 0.1 | 98.7% | coding (662/732 nt) | yfiH | hypothetical protein |
| ? | REL606 | 2774435 = | NA (NA) | noncoding (1443/1443 nt) | IS150 | repeat region | |||||
| * | ? | REL606 | 2713428 = | 105 (1.680) | 93 (1.490) | 60/194 | 0.1 | 47.0% | noncoding (77/93 nt) | serV | tRNA‑Ser |
| ? | REL606 | = 2774196 | NA (NA) | noncoding (1343/1343 nt) | IS186 | repeat region | |||||
| * | ? | REL606 | 2774435 = | NA (NA) | 58 (0.930) | 49/194 | 0.3 | NA | noncoding (1443/1443 nt) | IS150 | repeat region |
| ? | REL606 | = 2822512 | NA (NA) | noncoding (443/768 nt) | IS1 | repeat region | |||||
| * | ? | REL606 | 2774435 = | NA (NA) | 106 (1.650) | 72/200 | 0.0 | 100% | noncoding (1443/1443 nt) | IS150 | repeat region |
| ? | REL606 | = 2999596 | 0 (0.000) | coding (33/2847 nt) | flu | antigen 43 (Ag43) phase‑variable biofilm formation autotransporter | |||||
| * | ? | REL606 | = 2775877 | NA (NA) | 104 (1.620) | 75/200 | 0.0 | 100% | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | REL606 | 3048489 = | 0 (0.000) | intergenic (‑318/+37) | yghK/glcB | glycolate transporter/malate synthase | |||||
| * | ? | REL606 | 3651091 = | NA (NA) | 67 (1.040) | 58/200 | 0.1 | NA | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | REL606 | 3697154 = | NA (NA) | coding (278/4134 nt) | rhsA | rhsA element core protein RshA | |||||
| * | ? | REL606 | 3651091 = | NA (NA) | 128 (1.990) | 79/200 | 0.0 | 100% | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | REL606 | = 4047675 | 0 (0.000) | coding (874/927 nt) | yihR | predicted aldose‑1‑epimerase | |||||
| * | ? | REL606 | 3697156 = | NA (NA) | 84 (1.310) | 66/200 | 0.0 | NA | coding (280/4134 nt) | rhsA | rhsA element core protein RshA |
| ? | REL606 | 3893553 = | NA (NA) | intergenic (+8/‑48) | kup/insJ‑5 | potassium transporter/IS150 hypothetical protein | |||||
| * | ? | REL606 | = 3741582 | NA (NA) | 80 (1.260) | 62/198 | 0.1 | NA | noncoding (384/768 nt) | IS1 | repeat region |
| ? | REL606 | = 3894996 | NA (NA) | noncoding (1443/1443 nt) | IS150 | repeat region | |||||
| * | ? | REL606 | = 3894996 | NA (NA) | 102 (1.590) | 66/200 | 0.0 | 99.0% | noncoding (1443/1443 nt) | IS150 | repeat region |
| ? | REL606 | 4049580 = | 1 (0.020) | coding (324/1242 nt) | yihS | predicted glucosamine isomerase | |||||
| * | ? | REL606 | 4034655 = | 92 (1.430) | 81 (1.270) | 60/198 | 0.1 | 51.6% | intergenic (‑58/+228) | glnL/glnA | sensory histidine kinase in two‑component regulatory system with GlnG/glutamine synthetase |
| ? | REL606 | = 4034991 | 61 (0.960) | coding (1302/1410 nt) | glnA | glutamine synthetase | |||||