mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 18.2% | D606D (GAC→GAT) | thrA → | fused aspartokinase I and homoserine dehydrogenase I |
| RA | 70,434 | C→T | 55.4% | N16N (AAC→AAT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,581 | C→T | 48.3% | V65V (GTC→GTT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,740 | T→G | 49.4% | G118G (GGT→GGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,079 | C→T | 37.9% | R231R (CGC→CGT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,082 | T→C | 34.7% | I232I (ATT→ATC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,085 | T→C | 32.3% | S233S (AGT→AGC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,109 | T→C | 35.4% | T241T (ACT→ACC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,175 | A→G | 38.6% | R263R (CGA→CGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,214 | T→C | 38.0% | 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 | 63.1% | D12A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 236,107 | A→C | 63.1% | 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 |
| MC JC | 654,214 | Δ1,199 bp | 100% | [dcuC]–[dcuC] | [dcuC], insH, [dcuC] | |
| RA | 810,113 | G→A | 27.5% | M116I (ATG→ATA) | bioB → | biotin synthase |
| RA | 859,171 | A→G | 7.3% | S105P (TCG→CCG) | ybiU ← | hypothetical protein |
| RA | 907,713 | G→A | 33.3% | 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 | 21.2% | 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 | 2,058,034 | C→T | 25.3% | 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 | 30.3% | A261S (GCG→TCG) | yejK ← | nucleotide associated protein |
| MC JC | 2,320,795 | Δ1,336 bp | 100% | insD–[rcsC] | insD, insC, [rcsC] | |
| RA | 2,809,581 | G→A | 49.3% | 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 | 3,053,471 | A→G | 28.4% | F9S (TTT→TCT) | pepP ← | proline aminopeptidase P II |
| RA | 3,152,234 | G→A | 26.9% | D6N (GAT→AAT) | yghB → | conserved inner membrane protein |
| RA | 3,315,139 | T→A | 27.0% | D244V (GAT→GTT) | infB ← | fused protein chain initiation factor 2, IF2 |
| RA | 3,688,001 | A→G | 40.0% | 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 | 3,824,280 | 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 | 4,195,173 | A→G | 30.2% | *118* (TAA→TGA) | rplR → | 50S ribosomal subunit protein L18 |
| RA | 4,246,990 | C→T | 16.7% | 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 | 21.9% | 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 | 33.3% | N27D (AAT→GAT) | yjfK → | conserved hypothetical protein |
| RA | 4,434,349 | T→A | 40.9% | 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 | 573861–575008 | 575999 | 992–2139 | 9 [6] | [0] 175 | insH–[nmpC] | insH,[nmpC] |
| * | * | ÷ | W3110S.gb | 721519 | 721538 | 20 | 10 [6] | [7] 8 | kdpE | DNA‑binding response regulator in two‑component regulatory system with KdpD |
| * | * | ÷ | W3110S.gb | 915606 | 915652 | 47 | 8 [7] | [7] 9 | ybjE/aqpZ | predicted transporter/aquaporin |
| * | * | ÷ | W3110S.gb | 1041888 | 1041917 | 30 | 8 [6] | [6] 8 | appA | phosphoanhydride phosphorylase |
| * | * | ÷ | W3110S.gb | 1081313 | 1081368 | 56 | 10 [7] | [7] 10 | putP/ycdN | proline:sodium symporter/ECK1007:JW5141:b1016; hypothetical protein, N‑ter fragment |
| * | * | ÷ | W3110S.gb | 1328316 | 1328352 | 37 | 8 [6] | [7] 9 | yciQ | predicted inner membrane protein |
| * | * | ÷ | W3110S.gb | 1421318 | 1421334 | 17 | 8 [7] | [6] 11 | ydaG/racR | hypothetical protein/predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 1828079 | 1828116 | 38 | 8 [7] | [7] 9 | astE | succinylglutamate desuccinylase |
| * | * | ÷ | W3110S.gb | 1928934 | 1928961 | 28 | 10 [7] | [6] 12 | ptrB | protease II |
| * | * | ÷ | W3110S.gb | 2569114 | 2569140 | 27 | 10 [7] | [6] 15 | eutE | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| * | * | ÷ | W3110S.gb | 2827392 | 2827430 | 39 | 8 [7] | [7] 8 | gutM | DNA‑binding transcriptional activator |
| * | * | ÷ | W3110S.gb | 3859257 | 3859276 | 20 | 8 [7] | [4] 8 | yibK/lldD | predicted rRNA methylase/L‑lactate dehydrogenase, FMN‑linked |
| * | * | ÷ | W3110S.gb | 4213636–4215889 | 4216704–4215891 | 3–3069 | 8 [4] | [6] 8 | [rrlE]–[rrfE] | [rrlE],[rrfE] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | W3110S.gb | = 7063 | 66 (1.330) | 16 (0.350) +GATT |
9/90 | NT | 32.6% | coding (897/1431 nt) | yaaJ | predicted transporter |
| ? | W3110S.gb | = 2564144 | 6 (0.120) | coding (1397/1404 nt) | eutA | reactivating factor for ethanolamine ammonia lyase | |||||
| * | ? | W3110S.gb | 70061 = | 62 (1.250) | 46 (1.200) +CGCGTACAACT |
26/76 | NT | 47.3% | intergenic (‑13/‑326) | araB/araC | L‑ribulokinase/DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 236044 = | 70 (1.410) | intergenic (‑42/‑23) | rnhA/dnaQ | ribonuclease HI, degrades RNA of DNA‑RNA hybrids/DNA polymerase III epsilon subunit | |||||
| * | ? | W3110S.gb | = 236798 | 48 (0.970) | 24 (1.080) +27 bp |
16/44 | NT | 51.2% | coding (732/732 nt) | dnaQ | DNA polymerase III epsilon subunit |
| ? | W3110S.gb | 4124504 = | 54 (1.090) | intergenic (+106/‑1) | damX/dam | hypothetical protein/DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 274373 | NA (NA) | 74 (1.490) | 35/98 | 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 | 314453 = | 47 (0.950) | 46 (0.970) +TC |
27/94 | NT | 67.1% | coding (873/888 nt) | eaeH | attaching and effacing protein, pathogenesis factor |
| ? | W3110S.gb | 3932930 = | 0 (0.000) | coding (219/1608 nt) | dppA | dipeptide transporter | |||||
| * | ? | W3110S.gb | = 315707 | NA (NA) | 55 (1.110) | 38/98 | 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) | 68 (1.370) | 32/98 | 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 = | 45 (0.910) | 43 (0.940) | 28/90 | NT | 49.3% | intergenic (‑156/‑29) | ybfF/seqA | conserved hypothetical protein/regulatory protein for replication initiation |
| ? | W3110S.gb | = 4125340 | 47 (1.030) | coding (836/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 713954 | 74 (1.490) | 77 (1.550) | 39/98 | NT | 51.3% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | W3110S.gb | 2809398 = | 72 (1.450) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | W3110S.gb | 1209367 = | 18 (0.360) | 25 (0.750) | 16/66 | NT | 66.6% | coding (290/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | 1211196 = | 13 (0.390) | pseudogene (37/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | = 1209382 | 21 (0.420) | 14 (0.420) | 8/66 | NT | 50.8% | coding (305/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | = 1211179 | 13 (0.390) | pseudogene (54/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | 2018571 = | 6 (0.120) | 45 (0.970) | 26/92 | NT | 88.9% | 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 | 5 (0.100) | 41 (0.860) | 27/94 | NT | 89.5% | 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) | 56 (1.150) | 34/96 | 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 | = 2173564 | NA (NA) | 71 (1.460) | 36/96 | 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) | 45 (0.910) | 27/98 | 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) | 74 (1.490) | 34/98 | NT | 92.5% | intergenic (‑55/‑782) | insA/yfbQ | IS1 element protein/predicted aminotransferase |
| ? | W3110S.gb | = 3748807 | 6 (0.120) | coding (176/984 nt) | tnaB | tryptophan transporter of low affinity | |||||
| * | ? | W3110S.gb | = 3261133 | 0 (0.000) | 35 (0.770) | 25/90 | NT | 100% | intergenic (‑59/‑69) | tdcE/insH | pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase/IS5 element protein |
| ? | W3110S.gb | 3262333 = | 0 (0.000) | coding (1183/1296 nt) | tdcD | propionate kinase/acetate kinase C, anaerobic | |||||
| * | ? | W3110S.gb | 3748799 = | 7 (0.140) | 67 (1.350) | 31/98 | NT | 90.5% | 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 = | 31 (0.620) | 13 (0.320) | 10/80 | NT | 37.0% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | 4547678 = | 19 (0.470) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||
| * | ? | W3110S.gb | = 4547372 | 30 (0.600) | 8 (0.200) | 7/80 | NT | 26.9% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | = 4547668 | 19 (0.470) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||