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 | 93.3% | N16N (AAC→AAT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,581 | C→T | 93.9% | V65V (GTC→GTT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,740 | T→G | 90.9% | G118G (GGT→GGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,079 | C→T | 93.4% | R231R (CGC→CGT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,082 | T→C | 93.2% | I232I (ATT→ATC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,085 | T→C | 92.3% | S233S (AGT→AGC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,109 | T→C | 90.5% | T241T (ACT→ACC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,175 | A→G | 93.9% | R263R (CGA→CGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,214 | T→C | 93.3% | 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 | 92.0% | D12A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 236,107 | A→C | 92.0% | E14A (GAA→GCA) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 454,926 | C→T | 9.7% | G190G (GGC→GGT) | tig → | peptidyl‑prolyl cis/trans isomerase |
| 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 |
| 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 | 94.7% | 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 |
| MC JC | 3,261,134 | Δ1,199 bp | 100% | insH–[tdcD] | insH, [tdcD] | |
| RA | 3,265,554 | T→C | 7.4% | P110P (CCA→CCG) | tdcB ← | catabolic threonine dehydratase, PLP‑dependent |
| RA | 3,388,193 | A→T | 5.7% | V263V (GTT→GTA) | aaeA ← | p‑hydroxybenzoic acid efflux system component |
| RA | 3,414,454 | G→C | 16.4% | V246L (GTC→CTC) | acrE → | cytoplasmic membrane lipoprotein |
| RA | 3,721,254 | A→C | 23.4% | intergenic (+124/‑229) | atpC → / → glmU | F1 sector of membrane‑bound ATP synthase, epsilon subunit/fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase and glucosamine‑1‑phosphate acetyl transferase |
| 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 |
| 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 | 164563 | 164602 | 40 | 7 [4] | [4] 5 | hrpB/mrcB | predicted ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| * | * | ÷ | W3110S.gb | 422763 | 422795 | 33 | 5 [4] | [4] 5 | malZ | maltodextrin glucosidase |
| * | * | ÷ | W3110S.gb | 573865–575008 | 575999 | 992–2135 | 5 [4] | [0] 113 | insH–[nmpC] | insH,[nmpC] |
| * | * | ÷ | W3110S.gb | 915575 | 915642 | 68 | 6 [4] | [3] 5 | ybjE/aqpZ | predicted transporter/aquaporin |
| * | * | ÷ | W3110S.gb | 1173186 | 1173220 | 35 | 7 [3] | [3] 6 | mfd | transcription‑repair coupling factor |
| * | * | ÷ | W3110S.gb | 1328306 | 1328351 | 46 | 5 [4] | [2] 5 | yciQ | predicted inner membrane protein |
| * | * | ÷ | W3110S.gb | 1421315 | 1421331 | 17 | 6 [1] | [3] 6 | ydaG/racR | hypothetical protein/predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 2041778 | 2041808 | 31 | 5 [3] | [4] 5 | yedY | predicted reductase |
| * | * | ÷ | W3110S.gb | 2232512 | 2232559 | 48 | 6 [4] | [4] 5 | yohH/dusC | conserved hypothetical protein/tRNA‑dihydrouridine synthase C |
| * | * | ÷ | W3110S.gb | 2296384 | 2296408 | 25 | 5 [4] | [4] 5 | ccmF | heme lyase, CcmF subunit |
| * | * | ÷ | W3110S.gb | 2569108 | 2569131 | 24 | 5 [4] | [4] 6 | eutE | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| * | * | ÷ | W3110S.gb | 3944463 | 3944475 | 13 | 8 [0] | [4] 5 | yhjQ | ECK3519:JW5941:b3534; cell division protein; chromosome partitioning ATPase |
| * | * | ÷ | W3110S.gb | 4213624–4216703 | 4216703 | 1–3080 | 5 [4] | [4] 5 | rrlE–[rrfE] | rrlE,[rrfE] |
| * | * | ÷ | W3110S.gb | 4329957 | 4329971 | 15 | 8 [4] | [4] 5 | phnC/phnB | phosphonate/organophosphate ester transporter subunit/conserved hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | W3110S.gb | = 7063 | 38 (0.990) | 19 (0.540) +GATT |
6/90 | NT | 50.2% | coding (897/1431 nt) | yaaJ | predicted transporter |
| ? | W3110S.gb | = 2564144 | 3 (0.080) | coding (1397/1404 nt) | eutA | reactivating factor for ethanolamine ammonia lyase | |||||
| * | ? | W3110S.gb | 37631 = | 25 (0.650) | 4 (0.130) +GCTGATGCCG |
3/78 | NT | 9.8% | coding (209/1569 nt) | caiC | predicted crotonobetaine CoA ligase:carnitine CoA ligase |
| ? | W3110S.gb | = 3401750 | 68 (1.770) | coding (1438/1941 nt) | yhdA | conserved inner membrane protein | |||||
| * | ? | W3110S.gb | 70061 = | 50 (1.300) | 563 (18.940) +CGCGTACAACT |
85/76 | NT | 93.1% | intergenic (‑13/‑326) | araB/araC | L‑ribulokinase/DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 236044 = | 58 (1.510) | intergenic (‑42/‑23) | rnhA/dnaQ | ribonuclease HI, degrades RNA of DNA‑RNA hybrids/DNA polymerase III epsilon subunit | |||||
| * | ? | W3110S.gb | = 71265 | 47 (1.230) | 253 (9.240) +AGGGTCCCTAAGTC |
67/70 | NT | 92.6% | coding (879/879 nt) | araC | DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 3464879 = | 10 (0.260) | intergenic (‑255/+46) | murB/rrfB | UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding/5S ribosomal RNA | |||||
| * | ? | W3110S.gb | 205097 = | 26 (0.680) | 54 (1.920) +TTATAACATTTTA |
21/72 | NT | 71.4% | intergenic (+8/‑29) | rnhB/dnaE | ribonuclease HII, degrades RNA of DNA‑RNA hybrids/DNA polymerase III alpha subunit |
| ? | W3110S.gb | 4139149 = | 33 (0.860) | coding (2/1023 nt) | frlB | fructoselysine‑6‑P‑deglycase | |||||
| * | ? | W3110S.gb | = 225915 | NA (NA) | 3 (0.090) | 3/82 | NT | NA | noncoding (157/2904 nt) | rrlH | 23S ribosomal RNA |
| ? | W3110S.gb | = 225926 | NA (NA) | noncoding (168/2904 nt) | rrlH | 23S ribosomal RNA | |||||
| * | ? | W3110S.gb | = 236798 | 24 (0.630) | 248 (14.410) +27 bp |
48/44 | NT | 94.8% | coding (732/732 nt) | dnaQ | DNA polymerase III epsilon subunit |
| ? | W3110S.gb | 4124504 = | 37 (0.970) | intergenic (+106/‑1) | damX/dam | hypothetical protein/DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 274373 | NA (NA) | 55 (1.430) | 29/98 | 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 = | 32 (0.830) | 61 (1.660) +TC |
36/94 | NT | 79.9% | 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 (1.430) | 35/98 | 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 | 470633 = | 34 (0.890) | 12 (0.370) +GTTTCAGT |
8/82 | NT | 25.0% | coding (774/1782 nt) | mdlB | fused predicted multidrug transporter subunits and ATP binding components of ABC superfamily |
| ? | W3110S.gb | 3414451 = | 52 (1.360) | coding (733/1158 nt) | acrE | cytoplasmic membrane lipoprotein | |||||
| * | ? | W3110S.gb | 566000 = | NA (NA) | 45 (1.170) | 24/98 | 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 = | 40 (1.040) | 478 (13.580) | 94/90 | NT | 94.1% | intergenic (‑156/‑29) | ybfF/seqA | conserved hypothetical protein/regulatory protein for replication initiation |
| ? | W3110S.gb | = 4125340 | 23 (0.650) | coding (836/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 713954 | 41 (1.070) | 713 (18.600) | 97/98 | NT | 93.8% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | W3110S.gb | 2809398 = | 53 (1.380) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | W3110S.gb | = 1131120 | 40 (1.040) | 15 (0.520) +GTAGCCGGACTT |
4/74 | NT | 40.7% | coding (288/417 nt) | flgN | export chaperone for FlgK and FlgL |
| ? | W3110S.gb | = 4641028 | 18 (0.470) | coding (340/690 nt) | creB | DNA‑binding response regulator in two‑component regulatory system with CreC | |||||
| * | ? | W3110S.gb | 1209367 = | 11 (0.290) | 17 (0.660) | 14/66 | NT | 68.8% | coding (290/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | 1211196 = | 8 (0.310) | pseudogene (37/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | = 1209382 | 11 (0.290) | 13 (0.500) | 11/66 | NT | 62.8% | coding (305/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | = 1211179 | 8 (0.310) | pseudogene (54/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | = 1499913 | 17 (0.440) | 12 (0.390) +ATATCACCAG |
5/78 | NT | 32.7% | coding (1314/1626 nt) | mdoD | glucan biosynthesis protein, periplasmic |
| ? | W3110S.gb | 1787483 = | 45 (1.170) | coding (1344/2379 nt) | pps | phosphoenolpyruvate synthase | |||||
| * | ? | W3110S.gb | 2018571 = | 2 (0.050) | 33 (0.920) | 21/92 | NT | 94.6% | 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 (0.820) | 21/94 | 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 | = 2107291 | 41 (1.070) | 138 (3.670) +A |
25/96 | NT | 76.4% | coding (904/993 nt) | wbbI | conserved hypothetical protein |
| ? | W3110S.gb | = 2809956 | 46 (1.200) | coding (531/531 nt) | mprA | DNA‑binding transcriptional regulator | |||||
| * | ? | W3110S.gb | 2172308 = | NA (NA) | 53 (1.410) | 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) | 66 (1.760) | 33/96 | 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) | 22 (0.570) | 19/98 | 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 | = 2401919 | 28 (0.730) | 19 (0.610) +GGCATTTCA |
6/80 | NT | 41.0% | coding (194/978 nt) | nuoH | NADH:ubiquinone oxidoreductase, membrane subunit H |
| ? | W3110S.gb | = 2562879 | 39 (1.020) | coding (1247/1362 nt) | eutB | ethanolamine ammonia‑lyase, large subunit, heavy chain | |||||
| * | ? | W3110S.gb | = 2412225 | NA (NA) | 58 (1.510) | 36/98 | NT | 96.7% | intergenic (‑55/‑782) | insA/yfbQ | IS1 element protein/predicted aminotransferase |
| ? | W3110S.gb | = 3748807 | 2 (0.050) | coding (176/984 nt) | tnaB | tryptophan transporter of low affinity | |||||
| * | ? | W3110S.gb | 2691202 = | 32 (0.830) | 7 (0.220) +GTCAGTTC |
4/82 | NT | 16.9% | coding (2998/3888 nt) | purL | phosphoribosylformyl‑glycineamide synthetase |
| ? | W3110S.gb | 2980369 = | 50 (1.300) | coding (470/1419 nt) | araE | arabinose transporter | |||||
| * | ? | W3110S.gb | 2772255 = | 67 (1.750) | 3 (0.090) | 3/90 | NT | 5.4% | coding (282/1704 nt) | yfjW | predicted inner membrane protein |
| ? | W3110S.gb | 2772277 = | 43 (1.220) | coding (304/1704 nt) | yfjW | predicted inner membrane protein | |||||
| * | ? | W3110S.gb | 2858376 = | 43 (1.120) | 4 (0.120) | 4/82 | NT | 10.4% | intergenic (+66/‑40) | mutS/pphB | methyl‑directed mismatch repair protein/serine/threonine‑specific protein phosphatase 2 |
| ? | W3110S.gb | 2858410 = | 33 (1.030) | intergenic (+100/‑6) | mutS/pphB | methyl‑directed mismatch repair protein/serine/threonine‑specific protein phosphatase 2 | |||||
| * | ? | W3110S.gb | 3698252 = | 65 (1.700) | 3 (0.090) | 3/88 | NT | 5.1% | coding (205/993 nt) | rbsR | DNA‑binding transcriptional repressor |
| ? | W3110S.gb | 3698272 = | 54 (1.570) | coding (185/993 nt) | rbsR | DNA‑binding transcriptional repressor | |||||
| * | ? | W3110S.gb | = 3721256 | 46 (1.200) | 16 (0.490) +TTTCAAT |
3/84 | NT | 32.1% | intergenic (+126/‑227) | atpC/glmU | F1 sector of membrane‑bound ATP synthase, epsilon subunit/fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase and glucosamine‑1‑phosphate acetyl transferase |
| ? | W3110S.gb | 3931426 = | 33 (0.860) | coding (1485/1692 nt) | eptB | predicted metal dependent hydrolase | |||||
| * | ? | W3110S.gb | 3748799 = | 5 (0.130) | 51 (1.330) | 30/98 | NT | 91.1% | 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 | 4100855 = | 25 (0.650) | 4 (0.110) | 3/90 | NT | 13.1% | coding (2179/2322 nt) | yhgF | predicted transcriptional accessory protein |
| ? | W3110S.gb | 4100877 = | 30 (0.850) | coding (2157/2322 nt) | yhgF | predicted transcriptional accessory protein | |||||
| * | ? | W3110S.gb | 4547364 = | 37 (0.970) | 8 (0.260) | 8/80 | NT | 23.1% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | 4547678 = | 23 (0.730) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||