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 | 70,434 | C→T | 71.9% | N16N (AAC→AAT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,581 | C→T | 62.2% | V65V (GTC→GTT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,740 | T→G | 36.9% | G118G (GGT→GGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,079 | C→T | 39.0% | R231R (CGC→CGT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,082 | T→C | 37.5% | I232I (ATT→ATC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,085 | T→C | 37.5% | S233S (AGT→AGC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,109 | T→C | 36.8% | T241T (ACT→ACC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,175 | A→G | 52.4% | R263R (CGA→CGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,214 | T→C | 52.3% | 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 | 56.9% | D12A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 236,107 | A→C | 56.1% | 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 | 1,093,686 | T→C | 100% | V130A (GTA→GCA) | ycdT → | predicted diguanylate cyclase |
| 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 | 1,638,314 | G→C | 12.8% | intergenic (‑233/‑156) | nohA ← / → ynfO | predicted packaging protein/hypothetical protein |
| MC JC | 2,176,983 | Δ1,199 bp | 100% | [gatA]–[gatA] | [gatA], insH, [gatA] | |
| MC JC | 2,320,795 | Δ1,336 bp | 100% | insD–[rcsC] | insD, insC, [rcsC] | |
| RA | 2,809,581 | G→A | 59.0% | 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 |
| MC JC | 3,261,134 | Δ1,199 bp | 100% | insH–[tdcD] | insH, [tdcD] | |
| 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] | |
| 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 |
| MC JC | 4,310,365 | Δ1,199 bp | 100% | insH–[alsK] | insH, [alsK] | |
| RA | 4,371,273 | Δ2 bp | 100% | intergenic (‑6/+299) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| 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 | 276165 | 276185 | 21 | 3 [2] | [2] 4 | mmuM | S‑methylmethionine:homocysteine methyltransferase |
| * | * | ÷ | W3110S.gb | 283086 | 283175 | 90 | 3 [2] | [2] 3 | yagF | predicted dehydratase |
| * | * | ÷ | W3110S.gb | 287637 | 287719 | 83 | 3 [2] | [2] 4 | yagI | predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 422752 | 422783 | 32 | 3 [2] | [2] 3 | malZ | maltodextrin glucosidase |
| * | * | ÷ | W3110S.gb | 509119 | 509141 | 23 | 3 [2] | [2] 3 | copA | copper transporter |
| * | * | ÷ | W3110S.gb | 573873–575008 | 575999 | 992–2127 | 4 [2] | [0] 88 | insH–[nmpC] | insH,[nmpC] |
| * | * | ÷ | W3110S.gb | 721524 | 721539 | 16 | 3 [2] | [1] 3 | kdpE | DNA‑binding response regulator in two‑component regulatory system with KdpD |
| * | * | ÷ | W3110S.gb | 832618 | 832677 | 60 | 5 [2] | [1] 4 | [rhlE] | [rhlE] |
| * | * | ÷ | W3110S.gb | 907980 | 908002 | 23 | 4 [2] | [2] 3 | ybjT | conserved hypothetical protein with NAD(P)‑binding Rossmann‑fold domain |
| * | * | ÷ | W3110S.gb | 915600–915637 | 915648 | 12–49 | 3 [2] | [2] 3 | ybjE/aqpZ | predicted transporter/aquaporin |
| * | * | ÷ | W3110S.gb | 1070633 | 1070645 | 13 | 3 [1] | [2] 3 | ycdH | predicted oxidoreductase, flavin:NADH component |
| * | * | ÷ | W3110S.gb | 1173187 | 1173220 | 34 | 3 [2] | [2] 4 | mfd | transcription‑repair coupling factor |
| * | * | ÷ | W3110S.gb | 1296599 | 1296665 | 67 | 3 [2] | [2] 4 | ychG ychG |
ECK1234:JW5883+JW1227:b4573; hypothetical protein ECK1234:JW5883:b1240; hypothetical protein, N‑ter fragment |
| * | * | ÷ | W3110S.gb | 1328319 | 1328346 | 28 | 5 [2] | [2] 3 | yciQ | predicted inner membrane protein |
| * | * | ÷ | W3110S.gb | 1371208 | 1371243 | 36 | 4 [1] | [2] 4 | pspD | peripheral inner membrane phage‑shock protein |
| * | * | ÷ | W3110S.gb | 1928946 | 1928961 | 16 | 3 [1] | [0] 3 | ptrB | protease II |
| * | * | ÷ | W3110S.gb | 2041779 | 2041815 | 37 | 3 [2] | [2] 3 | yedY | predicted reductase |
| * | * | ÷ | W3110S.gb | 2569111 | 2569135 | 25 | 3 [2] | [2] 4 | eutE | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| * | * | ÷ | W3110S.gb | 2777819 | 2777833 | 15 | 3 [1] | [2] 3 | ypjA | adhesin‑like autotransporter |
| * | * | ÷ | W3110S.gb | 3799041 | 3799070 | 30 | 3 [2] | [2] 3 | yicM | predicted transporter |
| * | * | ÷ | W3110S.gb | 4213633–4216709 | 4216709 | 1–3077 | 3 [2] | [2] 3 | rrlE–[rrfE] | rrlE,[rrfE] |
| * | * | ÷ | W3110S.gb | 4601154 | 4601191 | 38 | 3 [2] | [2] 3 | yjjN | predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | W3110S.gb | 70061 = | 22 (0.970) | 24 (1.370) +CGCGTACAACT |
14/76 | NT | 53.1% | intergenic (‑13/‑326) | araB/araC | L‑ribulokinase/DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 236044 = | 33 (1.450) | intergenic (‑42/‑23) | rnhA/dnaQ | ribonuclease HI, degrades RNA of DNA‑RNA hybrids/DNA polymerase III epsilon subunit | |||||
| * | ? | W3110S.gb | = 71265 | 33 (1.450) | 9 (0.560) +AGGGTCCCTAAGTC |
8/70 | NT | 39.5% | coding (879/879 nt) | araC | DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 3464879 = | 6 (0.260) | intergenic (‑255/+46) | murB/rrfB | UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding/5S ribosomal RNA | |||||
| * | ? | W3110S.gb | 205097 = | 22 (0.970) | 8 (0.420) +TTATAACA |
7/82 | NT | 37.5% | intergenic (+8/‑29) | rnhB/dnaE | ribonuclease HII, degrades RNA of DNA‑RNA hybrids/DNA polymerase III alpha subunit |
| ? | W3110S.gb | = 467579 | 10 (0.440) | intergenic (+125/‑28) | cof/ybaO | thiamin pyrimidine pyrophosphate hydrolase/predicted DNA‑binding transcriptional regulator | |||||
| * | ? | W3110S.gb | = 236798 | 17 (0.750) | 5 (0.500) +27 bp |
4/44 | NT | 34.7% | coding (732/732 nt) | dnaQ | DNA polymerase III epsilon subunit |
| ? | W3110S.gb | 4124504 = | 26 (1.150) | intergenic (+106/‑1) | damX/dam | hypothetical protein/DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 274373 | NA (NA) | 38 (1.670) | 24/98 | 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 | = 315707 | NA (NA) | 21 (0.920) | 14/98 | 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) | 29 (1.280) | 20/98 | 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 = | 17 (0.750) | 25 (1.200) | 17/90 | NT | 62.8% | intergenic (‑156/‑29) | ybfF/seqA | conserved hypothetical protein/regulatory protein for replication initiation |
| ? | W3110S.gb | = 4125340 | 14 (0.670) | coding (836/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 713954 | 36 (1.590) | 26 (1.150) | 17/98 | NT | 39.4% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | W3110S.gb | 2809398 = | 44 (1.940) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | W3110S.gb | 2018571 = | 3 (0.130) | 23 (1.080) | 19/92 | NT | 89.1% | 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 | 1 (0.040) | 13 (0.600) | 12/94 | NT | 93.1% | 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) | 42 (1.890) | 30/96 | 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 | 2172309 = | NA (NA) | 35 (1.610) | 28/94 | 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) | 32 (1.440) | 18/96 | 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) | 14 (0.620) | 10/98 | 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) | 35 (1.540) | 23/98 | NT | 83.3% | intergenic (‑55/‑782) | insA/yfbQ | IS1 element protein/predicted aminotransferase |
| ? | W3110S.gb | = 3748807 | 7 (0.310) | coding (176/984 nt) | tnaB | tryptophan transporter of low affinity | |||||
| * | ? | W3110S.gb | 3748799 = | 6 (0.260) | 33 (1.450) | 27/98 | NT | 84.6% | 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 | = 3750592 | 1 (0.040) | 34 (1.630) | 23/90 | NT | 98.7% | intergenic (‑104/‑69) | tnaA/insH | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent/IS5 element protein |
| ? | W3110S.gb | 3751792 = | 0 (0.000) | intergenic (+151/+116) | insH/tnaC | IS5 element protein/tryptophanase leader peptide | |||||
| * | ? | W3110S.gb | = 4547372 | 21 (0.920) | 7 (0.380) | 5/80 | NT | 31.8% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | = 4547668 | 13 (0.700) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||