mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 2,154 | C→T | 89.8% | D606D (GAC→GAT) | thrA → | fused aspartokinase I and homoserine dehydrogenase I |
| RA | 70,434 | C→T | 35.9% | N16N (AAC→AAT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,581 | C→T | 57.4% | V65V (GTC→GTT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,740 | T→G | 65.6% | G118G (GGT→GGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,079 | C→T | 26.3% | R231R (CGC→CGT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,082 | T→C | 26.5% | I232I (ATT→ATC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,085 | T→C | 25.7% | S233S (AGT→AGC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,109 | T→C | 45.5% | T241T (ACT→ACC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,175 | A→G | 43.6% | R263R (CGA→CGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,214 | T→C | 45.4% | F276F (TTT→TTC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 155,463 | A→T | 100% | *247K (TAA→AAA) | ecpD ← | predicted periplasmic pilin chaperone |
| RA | 236,101 | A→C | 54.4% | D12A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 236,107 | A→C | 56.2% | E14A (GAA→GCA) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 547,694 | A→G | 100% | pseudogene (114/261 nt) pseudogene (114/1259 nt) |
ylbE → ylbE → |
ECK0512:JW0507:b4507; hypothetical protein, N‑ter fragment ECK0512:JW0508+JW0507:b4572; hypothetical protein |
| RA | 547,831:1 | +G | 100% | pseudogene (251/261 nt) pseudogene (251/1259 nt) |
ylbE → ylbE → |
ECK0512:JW0507:b4507; hypothetical protein, N‑ter fragment ECK0512:JW0508+JW0507:b4572; hypothetical protein |
| RA | 556,858 | A→T | 100% | L36Q (CTG→CAG) | folD ← | bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase and 5,10‑methylene‑tetrahydrofolate cyclohydrolase |
| RA | 561,882 | T→C | 10.2% | D106D (GAT→GAC) | sfmH → | predicted fimbrial‑like adhesin protein |
| MC JC | 654,214 | Δ1,199 bp | 100% | [dcuC]–[dcuC] | [dcuC], insH, [dcuC] | |
| RA | 907,713 | G→A | 100% | T331I (ACC→ATC) | ybjT ← | conserved hypothetical protein with NAD(P)‑binding Rossmann‑fold domain |
| RA | 1,093,686 | T→C | 100% | V130A (GTA→GCA) | ycdT → | predicted diguanylate cyclase |
| RA | 1,151,925 | A→C | 100% | P207P (CCA→CCC) | fabD → | malonyl‑CoA‑[acyl‑carrier‑protein] transacylase |
| MC JC | 1,301,041 | Δ1,336 bp | 100% | insC–insD | insC, insD | |
| RA | 1,303,631 | C→T | 100% | Q246Y (CAG→TAT) | oppA → | oligopeptide transporter subunit |
| RA | 1,303,633 | G→T | 100% | Q246Y (CAG→TAT) | oppA → | oligopeptide transporter subunit |
| RA | 1,413,585 | C→T | 8.3% | V26V (GTG→GTA) | ydaO ← | predicted C32 tRNA thiolase |
| RA | 2,058,034 | C→T | 70.7% | G279G (GGC→GGT) | amn → | AMP nucleosidase |
| MC JC | 2,176,983 | Δ1,199 bp | 100% | [gatA]–[gatA] | [gatA], insH, [gatA] | |
| RA | 2,286,501 | C→A | 100% | A261S (GCG→TCG) | yejK ← | nucleotide associated protein |
| MC JC | 2,320,795 | Δ1,336 bp | 100% | insD–[rcsC] | insD, insC, [rcsC] | |
| RA | 2,691,177 | G→A | 14.3% | A1008V (GCG→GTG) | purL ← | phosphoribosylformyl‑glycineamide synthetase |
| RA | 2,809,581 | G→A | 45.7% | G52G (GGG→GGA) | mprA → | DNA‑binding transcriptional regulator |
| RA | 2,866,110 | T→A | 100% | intergenic (‑20/+160) | rpoS ← / ← nlpD | RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein |
| RA | 2,909,884 | C→T | 14.0% | V38M (GTG→ATG) | chpR ← | antitoxin of the ChpA‑ChpR toxin‑antitoxin system |
| RA | 3,053,471 | A→G | 100% | F9S (TTT→TCT) | pepP ← | proline aminopeptidase P II |
| RA | 3,152,234 | G→A | 73.9% | D6N (GAT→AAT) | yghB → | conserved inner membrane protein |
| MC JC | 3,261,134 | Δ1,199 bp | 100% | insH–[tdcD] | insH, [tdcD] | |
| RA | 3,315,139 | T→A | 100% | D244V (GAT→GTT) | infB ← | fused protein chain initiation factor 2, IF2 |
| RA | 3,688,001 | A→G | 100% | S440G (AGT→GGT) | yifB → | predicted bifunctional protein, enzyme and transcriptional regulator |
| MC JC | 3,742,938 | Δ1,336 bp | 100% | insD–insC | insD, insC | |
| MC JC | 3,746,913 | Δ1,199 bp | 100% | [tnaB]–[tnaB] | [tnaB], insH, [tnaB] | |
| MC JC | 3,750,593 | Δ1,199 bp | 100% | insH | insH | |
| RA | 3,816,294 | C→T | 25.0% | R575H (CGC→CAC) | spoT ← | bifunctional (p)ppGpp synthetase II and guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,824,280 | T→C | 100% | pseudogene (413/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,326 | T→C | 100% | pseudogene (459/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,362 | A→T | 100% | pseudogene (495/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,368 | G→A | 100% | pseudogene (501/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,374 | C→T | 100% | pseudogene (507/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,380 | 2 bp→AA | 100% | pseudogene (513‑514/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,410 | T→A | 100% | pseudogene (543/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,514 | T→C | 100% | pseudogene (647/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,524 | T→G | 100% | pseudogene (657/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,533:1 | +G | 100% | pseudogene (666/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 4,090,233 | G→A | 25.0% | E763E (GAG→GAA) | malP → | maltodextrin phosphorylase |
| RA | 4,195,173 | A→G | 77.8% | *118* (TAA→TGA) | rplR → | 50S ribosomal subunit protein L18 |
| RA | 4,246,990 | C→T | 77.3% | R40H (CGT→CAT) | malG ← | maltose transporter subunit |
| MC JC | 4,310,365 | Δ1,199 bp | 100% | insH–[alsK] | insH, [alsK] | |
| RA | 4,340,671 | G→A | 65.9% | T347T (ACC→ACT) | adiC ← | arginine:agmatin |
| RA | 4,371,273 | Δ2 bp | 100% | intergenic (‑6/+299) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,416,062 | A→G | 100% | N27D (AAT→GAT) | yjfK → | conserved hypothetical protein |
| RA | 4,434,349 | T→A | 100% | intergenic (+112/‑197) | fklB → / → cycA | FKBP‑type peptidyl‑prolyl cis‑trans isomerase/D‑alanine/D‑serine/glycine transporter |
| RA | 4,563,589 | T→A | 100% | K207M (AAG→ATG) | iadA ← | isoaspartyl dipeptidase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | W3110S.gb | 3991 | 3996 | 6 | 2 [1] | [0] 2 | thrC | threonine synthase |
| * | * | ÷ | W3110S.gb | 126566 | 126567 | 2 | 2 [0] | [1] 2 | aceF | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| * | * | ÷ | W3110S.gb | 283084 | 283138 | 55 | 4 [1] | [1] 2 | yagF | predicted dehydratase |
| * | * | ÷ | W3110S.gb | 283200 | 283245 | 46 | 2 [1] | [1] 2 | yagF | predicted dehydratase |
| * | * | ÷ | W3110S.gb | 573866–575007 | 575999 | 993–2134 | 3 [0] | [0] 117 | insH–[nmpC] | insH,[nmpC] |
| * | * | ÷ | W3110S.gb | 598785 | 598805 | 21 | 3 [0] | [1] 4 | cusA | copper/silver efflux system, membrane component |
| * | * | ÷ | W3110S.gb | 777496 | 777503 | 8 | 5 [0] | [1] 2 | tolA | membrane anchored protein in TolA‑TolQ‑TolR complex |
| * | * | ÷ | W3110S.gb | 907995 | 908036 | 42 | 3 [0] | [1] 4 | ybjT | conserved hypothetical protein with NAD(P)‑binding Rossmann‑fold domain |
| * | * | ÷ | W3110S.gb | 1070497 | 1070520 | 24 | 3 [0] | [1] 2 | ycdH | predicted oxidoreductase, flavin:NADH component |
| * | * | ÷ | W3110S.gb | 1207222 | 1207235 | 14 | 2 [1] | [1] 2 | ymfR | hypothetical protein |
| * | * | ÷ | W3110S.gb | 1274324 | 1274350 | 27 | 2 [1] | [1] 2 | chaC | regulatory protein for cation transport |
| * | * | ÷ | W3110S.gb | 1328310 | 1328347 | 38 | 6 [1] | [1] 2 | yciQ | predicted inner membrane protein |
| * | * | ÷ | W3110S.gb | 1338213 | 1338228 | 16 | 5 [1] | [1] 3 | acnA | aconitate hydratase 1 |
| * | * | ÷ | W3110S.gb | 1352890 | 1352923–1352916 | 27–34 | 3 [1] | [0] 3 | fabI/ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/conserved hypothetical protein |
| * | * | ÷ | W3110S.gb | 1382885 | 1382889 | 5 | 3 [0] | [1] 2 | ycjV | predicted sugar transporter subunit |
| * | * | ÷ | W3110S.gb | 1421319 | 1421330 | 12 | 2 [1] | [0] 4 | ydaG/racR | hypothetical protein/predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 1928954 | 1928958 | 5 | 2 [0] | [0] 2 | ptrB | protease II |
| * | * | ÷ | W3110S.gb | 2041783 | 2041791 | 9 | 2 [1] | [0] 3 | yedY | predicted reductase |
| * | * | ÷ | W3110S.gb | 2296367 | 2296394 | 28 | 2 [1] | [0] 2 | ccmF | heme lyase, CcmF subunit |
| * | * | ÷ | W3110S.gb | 2551389 | 2551396 | 8 | 2 [0] | [1] 2 | yfeU | predicted PTS component |
| * | * | ÷ | W3110S.gb | 2569104 | 2569133 | 30 | 2 [1] | [0] 2 | eutE | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| * | * | ÷ | W3110S.gb | 2692142 | 2692180 | 39 | 3 [1] | [1] 2 | purL | phosphoribosylformyl‑glycineamide synthetase |
| * | * | ÷ | W3110S.gb | 2777818 | 2777819 | 2 | 4 [0] | [0] 3 | ypjA | adhesin‑like autotransporter |
| * | * | ÷ | W3110S.gb | 2827395 | 2827409 | 15 | 2 [0] | [1] 2 | gutM | DNA‑binding transcriptional activator |
| * | * | ÷ | W3110S.gb | 2893906 | 2893930 | 25 | 6 [1] | [0] 2 | ygcQ | predicted flavoprotein |
| * | * | ÷ | W3110S.gb | 3044675 | 3044704 | 30 | 3 [1] | [1] 2 | ygfF/gcvP | predicted NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex |
| * | * | ÷ | W3110S.gb | 3799044 | 3799051 | 8 | 4 [1] | [0] 4 | yicM | predicted transporter |
| * | * | ÷ | W3110S.gb | 3859248 | 3859277 | 30 | 2 [1] | [1] 2 | yibK/lldD | predicted rRNA methylase/L‑lactate dehydrogenase, FMN‑linked |
| * | * | ÷ | W3110S.gb | 4163816 | 4163829 | 14 | 2 [1] | [1] 2 | fkpA/yheO | FKBP‑type peptidyl‑prolyl cis‑trans isomerase/predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 4401138 | 4401165 | 28 | 4 [0] | [1] 5 | amiB | N‑acetylmuramoyl‑l‑alanine amidase II |
| * | * | ÷ | W3110S.gb | 4619270 | 4619274 | 5 | 3 [0] | [1] 3 | yjjV/yjjW | predicted DNase/predicted pyruvate formate lyase activating enzyme |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | W3110S.gb | 70061 = | 33 (1.180) | 30 (1.370) +CGCGTACAACT |
15/78 | NT | 47.5% | intergenic (‑13/‑326) | araB/araC | L‑ribulokinase/DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 236044 = | 52 (1.860) | intergenic (‑42/‑23) | rnhA/dnaQ | ribonuclease HI, degrades RNA of DNA‑RNA hybrids/DNA polymerase III epsilon subunit | |||||
| * | ? | W3110S.gb | = 71265 | 34 (1.210) | 19 (0.940) +AGGGTCCCTAAGTC |
7/72 | NT | 51.9% | coding (879/879 nt) | araC | DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 3464879 = | 15 (0.540) | intergenic (‑255/+46) | murB/rrfB | UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding/5S ribosomal RNA | |||||
| * | ? | W3110S.gb | = 274373 | NA (NA) | 53 (1.890) | 21/100 | NT | 100% | intergenic (‑32/‑176) | insH/mmuP | IS5 transposase and trans‑activator/predicted S‑methylmethionine transporter |
| ? | W3110S.gb | 576000 = | 0 (0.000) | pseudogene (109/1128 nt) | nmpC | DLP12 prophage region; ECK0544:JW5078:b0553; truncated outer membrane porin | |||||
| * | ? | W3110S.gb | = 315707 | NA (NA) | 49 (1.750) | 21/100 | NT | 100% | coding (654/687 nt) | ykgA | predicted DNA‑binding transcriptional regulator |
| ? | W3110S.gb | 576911 = | 0 (0.000) | coding (76/498 nt) | ybcS | predicted lysozyme | |||||
| * | ? | W3110S.gb | 566000 = | NA (NA) | 27 (0.960) | 14/100 | NT | 100% | intergenic (+90/‑56) | ybcD/insE | DLP12 prophage region; ECK0532:JW0527:b4508; predicted replication protein fragment/IS3 element protein InsE |
| ? | W3110S.gb | = 576913 | 0 (0.000) | coding (78/498 nt) | ybcS | predicted lysozyme | |||||
| * | ? | W3110S.gb | 713380 = | 29 (1.040) | 25 (0.970) | 13/92 | NT | 45.2% | intergenic (‑156/‑29) | ybfF/seqA | conserved hypothetical protein/regulatory protein for replication initiation |
| ? | W3110S.gb | = 4125340 | 34 (1.320) | coding (836/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 713954 | 33 (1.180) | 60 (2.140) | 28/100 | NT | 56.1% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | W3110S.gb | 2809398 = | 61 (2.180) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | W3110S.gb | 1209367 = | 15 (0.540) | 14 (0.740) | 11/68 | NT | 64.8% | coding (290/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | 1211196 = | 5 (0.260) | pseudogene (37/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | 2018571 = | 0 (0.000) | 21 (0.800) | 11/94 | NT | 100% | coding (567/687 nt) | fliH | flagellar biosynthesis protein |
| ? | W3110S.gb | 2519723 = | NA (NA) | intergenic (+33/‑54) | nupC/insL | nucleoside (except guanosine) transporter/predicted transposase | |||||
| * | ? | W3110S.gb | = 2018583 | 3 (0.110) | 34 (1.270) | 14/96 | NT | 92.2% | coding (579/687 nt) | fliH | flagellar biosynthesis protein |
| ? | W3110S.gb | = 2521059 | NA (NA) | intergenic (+170/+30) | insL/yfeA | predicted transposase/predicted diguanylate cyclase | |||||
| * | ? | W3110S.gb | 2172308 = | NA (NA) | 45 (1.640) | 19/98 | NT | 100% | pseudogene (1563/2041 nt) | gatR | DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 |
| ? | W3110S.gb | = 3920281 | 0 (0.000) | coding (88/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | 2172309 = | NA (NA) | 40 (1.490) | 18/96 | NT | 100% | pseudogene (1562/2041 nt) | gatR | DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 |
| ? | W3110S.gb | 3932930 = | 0 (0.000) | coding (219/1608 nt) | dppA | dipeptide transporter | |||||
| * | ? | W3110S.gb | = 2173564 | NA (NA) | 38 (1.390) | 17/98 | NT | 100% | pseudogene (307/2041 nt) pseudogene (307/339 nt) |
gatR gatR |
DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 DNA‑binding transcriptional regulator, C‑ter fragment; ECK2083:JW2074:b2090 |
| ? | W3110S.gb | 3920278 = | 0 (0.000) | coding (91/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | = 2173565 | NA (NA) | 32 (1.140) | 12/100 | NT | 100% | pseudogene (306/2041 nt) pseudogene (306/339 nt) |
gatR gatR |
DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 DNA‑binding transcriptional regulator, C‑ter fragment; ECK2083:JW2074:b2090 |
| ? | W3110S.gb | = 3932933 | 0 (0.000) | coding (222/1608 nt) | dppA | dipeptide transporter | |||||
| * | ? | W3110S.gb | = 2412225 | NA (NA) | 39 (1.390) | 15/100 | NT | 95.1% | intergenic (‑55/‑782) | insA/yfbQ | IS1 element protein/predicted aminotransferase |
| ? | W3110S.gb | = 3748807 | 2 (0.070) | coding (176/984 nt) | tnaB | tryptophan transporter of low affinity | |||||
| * | ? | W3110S.gb | 3748799 = | 2 (0.070) | 45 (1.610) | 20/100 | NT | 95.7% | coding (184/984 nt) | tnaB | tryptophan transporter of low affinity |
| ? | W3110S.gb | 4056222 = | NA (NA) | intergenic (‑564/+15) | yrhB/insB | hypothetical protein/IS1 transposase InsAB' | |||||
| * | ? | W3110S.gb | 4547364 = | 23 (0.820) | 12 (0.520) | 5/82 | NT | 45.4% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | 4547678 = | 10 (0.440) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||
| * | ? | W3110S.gb | = 4547372 | 20 (0.710) | 7 (0.300) | 4/82 | NT | 34.7% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | = 4547668 | 10 (0.440) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||