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 | 70,434 | C→T | 42.9% | N16N (AAC→AAT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,581 | C→T | 41.0% | V65V (GTC→GTT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,740 | T→G | 41.2% | G118G (GGT→GGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,079 | C→T | 38.5% | R231R (CGC→CGT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,082 | T→C | 35.7% | I232I (ATT→ATC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,085 | T→C | 35.9% | S233S (AGT→AGC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,109 | T→C | 26.9% | 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 | 40.0% | 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 | 55.2% | D12A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 236,107 | A→C | 54.3% | 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 | 1,916,448 | C→T | 11.1% | R28H (CGT→CAT) | prc ← | carboxy‑terminal protease for penicillin‑binding protein 3 |
| 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 | 50.4% | 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] | |
| 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 | 4,189,762 | G→A | 6.3% | G237S (GGT→AGT) | rplB → | 50S ribosomal subunit protein L2 |
| 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 | 283071 | 283245 | 175 | 12 [10] | [7] 12 | yagF | predicted dehydratase |
| * | * | ÷ | W3110S.gb | 573870–575008 | 575999 | 992–2130 | 13 [11] | [0] 153 | insH–[nmpC] | insH,[nmpC] |
| * | * | ÷ | W3110S.gb | 721521 | 721542 | 22 | 13 [9] | [11] 12 | kdpE | DNA‑binding response regulator in two‑component regulatory system with KdpD |
| * | * | ÷ | W3110S.gb | 907977 | 908022 | 46 | 12 [11] | [11] 13 | ybjT | conserved hypothetical protein with NAD(P)‑binding Rossmann‑fold domain |
| * | * | ÷ | W3110S.gb | 1328316 | 1328355 | 40 | 12 [9] | [11] 12 | yciQ | predicted inner membrane protein |
| * | * | ÷ | W3110S.gb | 1421298 | 1421338 | 41 | 12 [10] | [10] 12 | ydaG/racR | hypothetical protein/predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 2041776 | 2041817 | 42 | 12 [8] | [10] 12 | yedY | predicted reductase |
| * | * | ÷ | W3110S.gb | 2827378 | 2827421 | 44 | 14 [11] | [11] 13 | gutM | DNA‑binding transcriptional activator |
| * | * | ÷ | W3110S.gb | 4213622–4215889 | 4216714–4215891 | 3–3093 | 13 [11] | [11] 12 | rrlE–[rrfE] | rrlE,[rrfE] |
| * | * | ÷ | W3110S.gb | 4401128 | 4401177 | 50 | 12 [8] | [11] 12 | amiB | N‑acetylmuramoyl‑l‑alanine amidase II |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | W3110S.gb | 16579 = | NA (NA) | 6 (0.130) | 3/92 | NT | NA | intergenic (+22/+172) | insL/hokC | IS186/IS421 transposase/toxic membrane protein, small |
| ? | W3110S.gb | 16610 = | NA (NA) | intergenic (+53/+141) | insL/hokC | IS186/IS421 transposase/toxic membrane protein, small | |||||
| * | ? | W3110S.gb | 70061 = | 63 (1.240) | 31 (0.780) +CGCGTACAACT |
23/80 | NT | 35.7% | intergenic (‑13/‑326) | araB/araC | L‑ribulokinase/DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 236044 = | 80 (1.570) | intergenic (‑42/‑23) | rnhA/dnaQ | ribonuclease HI, degrades RNA of DNA‑RNA hybrids/DNA polymerase III epsilon subunit | |||||
| * | ? | W3110S.gb | = 71265 | 47 (0.920) | 12 (0.330) +AGGGTCCCTAAGTC |
9/74 | NT | 33.6% | coding (879/879 nt) | araC | DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 3464879 = | 19 (0.370) | intergenic (‑255/+46) | murB/rrfB | UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding/5S ribosomal RNA | |||||
| * | ? | W3110S.gb | 227072 = | NA (NA) | 3 (0.060) | 3/94 | NT | NA | noncoding (1314/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | W3110S.gb | 227097 = | NA (NA) | noncoding (1339/2904 nt) | rrlH | 23S ribosomal RNA | |||||
| * | ? | W3110S.gb | 227317 = | NA (NA) | 3 (0.070) | 3/92 | NT | NA | noncoding (1559/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | W3110S.gb | 227342 = | NA (NA) | noncoding (1584/2904 nt) | rrlH | 23S ribosomal RNA | |||||
| * | ? | W3110S.gb | = 236798 | 38 (0.750) | 13 (0.560) +27 bp |
11/48 | NT | 39.1% | coding (732/732 nt) | dnaQ | DNA polymerase III epsilon subunit |
| ? | W3110S.gb | 4124504 = | 50 (0.980) | intergenic (+106/‑1) | damX/dam | hypothetical protein/DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 256044 | 87 (1.710) | 5 (0.100) | 3/100 | NT | 5.8% | coding (68/459 nt) | gpt | guanine‑hypoxanthine phosphoribosyltransferase |
| ? | W3110S.gb | = 256072 | 77 (1.550) | coding (96/459 nt) | gpt | guanine‑hypoxanthine phosphoribosyltransferase | |||||
| * | ? | W3110S.gb | = 274373 | NA (NA) | 80 (1.570) | 41/102 | 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 = | 53 (1.040) | 53 (1.110) +TCA |
31/96 | NT | 68.0% | coding (873/888 nt) | eaeH | attaching and effacing protein, pathogenesis factor |
| ? | W3110S.gb | = 3920281 | 0 (0.000) | coding (88/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | = 315707 | NA (NA) | 63 (1.240) | 35/102 | 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) | 69 (1.360) | 39/102 | 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 = | 44 (0.870) | 42 (0.900) | 29/94 | NT | 55.5% | intergenic (‑156/‑29) | ybfF/seqA | conserved hypothetical protein/regulatory protein for replication initiation |
| ? | W3110S.gb | = 4125340 | 27 (0.580) | coding (836/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 713954 | 50 (0.980) | 62 (1.220) | 38/102 | NT | 50.4% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | W3110S.gb | 2809398 = | 72 (1.420) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | W3110S.gb | = 1088636 | 46 (0.900) | 3 (0.070) | 3/92 | NT | 7.3% | coding (1644/2019 nt) | ycdR | predicted enzyme associated with biofilm formation |
| ? | W3110S.gb | = 1088653 | 35 (0.760) | coding (1627/2019 nt) | ycdR | predicted enzyme associated with biofilm formation | |||||
| * | ? | W3110S.gb | 1099139 = | 62 (1.220) | 3 (0.070) | 3/86 | NT | 6.2% | coding (20/738 nt) | ycdX | predicted zinc‑binding hydrolase |
| ? | W3110S.gb | 1099171 = | 38 (0.890) | coding (52/738 nt) | ycdX | predicted zinc‑binding hydrolase | |||||
| * | ? | W3110S.gb | 1209367 = | 20 (0.390) | 22 (0.640) | 12/70 | NT | 64.1% | coding (290/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | 1211196 = | 11 (0.320) | pseudogene (37/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | = 1209382 | 17 (0.330) | 16 (0.460) | 13/70 | NT | 58.7% | coding (305/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | = 1211179 | 11 (0.320) | pseudogene (54/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | 2018571 = | 3 (0.060) | 39 (0.820) | 28/96 | NT | 93.3% | 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 | 0 (0.000) | 30 (0.610) | 24/98 | NT | 100% | 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 | 2172309 = | NA (NA) | 54 (1.110) | 35/98 | 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) | 81 (1.630) | 42/100 | 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 (0.890) | 28/102 | 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) | 82 (1.610) | 53/102 | NT | 86.3% | intergenic (‑55/‑782) | insA/yfbQ | IS1 element protein/predicted aminotransferase |
| ? | W3110S.gb | = 3748807 | 13 (0.260) | coding (176/984 nt) | tnaB | tryptophan transporter of low affinity | |||||
| * | ? | W3110S.gb | 2764844 = | 65 (1.280) | 4 (0.090) | 3/92 | NT | 7.4% | coding (271/1074 nt) | yfjN | hypothetical protein |
| ? | W3110S.gb | 2764882 = | 41 (0.900) | coding (309/1074 nt) | yfjN | hypothetical protein | |||||
| * | ? | W3110S.gb | = 2979625 | 68 (1.340) | 6 (0.120) | 3/98 | NT | 8.7% | coding (1214/1419 nt) | araE | arabinose transporter |
| ? | W3110S.gb | = 2979644 | 61 (1.250) | coding (1195/1419 nt) | araE | arabinose transporter | |||||
| * | ? | W3110S.gb | = 3210949 | 43 (0.850) | 4 (0.090) | 3/90 | NT | 8.9% | coding (1187/1746 nt) | dnaG | DNA primase |
| ? | W3110S.gb | = 3210964 | 44 (0.980) | coding (1202/1746 nt) | dnaG | DNA primase | |||||
| * | ? | W3110S.gb | 3453209 = | 77 (1.510) | 5 (0.110) | 4/94 | NT | 5.4% | coding (2228/4029 nt) | rpoB | RNA polymerase, beta subunit |
| ? | W3110S.gb | 3453257 = | 104 (2.220) | coding (2180/4029 nt) | rpoB | RNA polymerase, beta subunit | |||||
| * | ? | W3110S.gb | 3748799 = | 7 (0.140) | 61 (1.200) | 39/102 | NT | 89.7% | 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 | = 4178621 | 43 (0.850) | 5 (0.110) | 3/90 | NT | 11.9% | coding (330/510 nt) | gspH | predicted general secretory pathway component, cryptic |
| ? | W3110S.gb | = 4178633 | 36 (0.800) | coding (318/510 nt) | gspH | predicted general secretory pathway component, cryptic | |||||
| * | ? | W3110S.gb | 4369695 = | 83 (1.630) | 4 (0.080) | 3/98 | NT | 5.3% | coding (28/1698 nt) | dipZ | fused thiol:disulfide interchange protein |
| ? | W3110S.gb | 4369721 = | 63 (1.290) | coding (2/1698 nt) coding (316/339 nt) |
dipZ cutA |
fused thiol:disulfide interchange protein copper binding protein, copper sensitivity |
|||||
| * | ? | W3110S.gb | 4547364 = | 29 (0.570) | 5 (0.120) | 5/84 | NT | 15.0% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | 4547678 = | 33 (0.790) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||
| * | ? | W3110S.gb | = 4547372 | 31 (0.610) | 5 (0.120) | 5/84 | NT | 14.6% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | = 4547668 | 33 (0.790) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||