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 | 90.5% | N16N (AAC→AAT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,581 | C→T | 87.9% | V65V (GTC→GTT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 70,740 | T→G | 85.2% | G118G (GGT→GGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,079 | C→T | 90.8% | R231R (CGC→CGT) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,082 | T→C | 90.8% | I232I (ATT→ATC) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,085 | T→C | 90.2% | 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 | 86.2% | R263R (CGA→CGG) | araC → | DNA‑binding transcriptional dual regulator |
| RA | 71,214 | T→C | 88.4% | 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 | 89.2% | D12A (GAT→GCT) | dnaQ → | DNA polymerase III epsilon subunit |
| RA | 236,107 | A→C | 88.8% | 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 | 641,942 | C→A | 15.9% | A211E (GCG→GAG) | ybdR → | predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding |
| RA | 641,944 | G→A | 16.1% | E212K (GAA→AAA) | ybdR → | predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding |
| MC JC | 654,214 | Δ1,199 bp | 100% | [dcuC]–[dcuC] | [dcuC], insH, [dcuC] | |
| RA | 798,218 | A→G | 5.9% | G212G (GGT→GGC) | ybhA ← | predicted hydrolase |
| RA | 798,224 | C→T | 6.1% | A210A (GCG→GCA) | ybhA ← | predicted hydrolase |
| 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 | 1,342,709 | G→A | 7.4% | Q146Q (CAG→CAA) | yciM → | conserved hypothetical protein |
| RA | 1,342,710 | T→C | 7.5% | L147L (TTG→CTG) | yciM → | conserved 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 | 89.4% | 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 |
| RA | 3,249,944 | C→A | 11.8% | P89T (CCG→ACG) | yqjG → | predicted S‑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 | 422758 | 422787 | 30 | 12 [10] | [5] 11 | malZ | maltodextrin glucosidase |
| * | * | ÷ | W3110S.gb | 573865–575008 | 575999 | 992–2135 | 11 [10] | [2] 118 | insH–[nmpC] | insH,[nmpC] |
| * | * | ÷ | W3110S.gb | 721514 | 721545 | 32 | 12 [10] | [10] 11 | kdpE | DNA‑binding response regulator in two‑component regulatory system with KdpD |
| * | * | ÷ | W3110S.gb | 2041771 | 2041810 | 40 | 11 [10] | [9] 12 | yedY | predicted reductase |
| * | * | ÷ | W3110S.gb | 2569104 | 2569138 | 35 | 11 [9] | [10] 11 | eutE | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| * | * | ÷ | W3110S.gb | 3799035 | 3799079 | 45 | 13 [10] | [10] 11 | yicM | predicted transporter |
| * | * | ÷ | W3110S.gb | 4213628–4215889 | 4216712–4215891 | 3–3085 | 11 [10] | [8] 11 | rrlE–[rrfE] | rrlE,[rrfE] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | W3110S.gb | = 49701 | 24 (0.490) | 3 (0.080) | 3/80 | NT | 12.0% | intergenic (+70/‑122) | kefC/folA | potassium:proton antiporter/dihydrofolate reductase |
| ? | W3110S.gb | = 49712 | 25 (0.640) | intergenic (+81/‑111) | kefC/folA | potassium:proton antiporter/dihydrofolate reductase | |||||
| * | ? | W3110S.gb | 70061 = | 42 (0.860) | 338 (8.900) +CGCGTACAACT |
81/78 | NT | 89.4% | intergenic (‑13/‑326) | araB/araC | L‑ribulokinase/DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 236044 = | 61 (1.250) | intergenic (‑42/‑23) | rnhA/dnaQ | ribonuclease HI, degrades RNA of DNA‑RNA hybrids/DNA polymerase III epsilon subunit | |||||
| * | ? | W3110S.gb | = 71265 | 55 (1.130) | 139 (3.960) +AGGGTCCCTAAGTC |
58/72 | NT | 84.1% | coding (879/879 nt) | araC | DNA‑binding transcriptional dual regulator |
| ? | W3110S.gb | 3464879 = | 18 (0.370) | intergenic (‑255/+46) | murB/rrfB | UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding/5S ribosomal RNA | |||||
| * | ? | W3110S.gb | 205097 = | 55 (1.130) | 48 (1.260) +TTATAACATTT |
21/78 | NT | 58.6% | intergenic (+8/‑29) | rnhB/dnaE | ribonuclease HII, degrades RNA of DNA‑RNA hybrids/DNA polymerase III alpha subunit |
| ? | W3110S.gb | 1624400 = | 32 (0.660) | intergenic (+167/+274) | ydeE/ydeH | predicted transporter/conserved hypothetical protein | |||||
| * | ? | W3110S.gb | = 225915 | NA (NA) | 5 (0.120) | 4/84 | 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 | 33 (0.680) | 203 (9.060) +27 bp |
51/46 | NT | 91.8% | coding (732/732 nt) | dnaQ | DNA polymerase III epsilon subunit |
| ? | W3110S.gb | 4124504 = | 46 (0.940) | intergenic (+106/‑1) | damX/dam | hypothetical protein/DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 274373 | NA (NA) | 57 (1.170) | 37/100 | NT | 96.6% | intergenic (‑32/‑176) | insH/mmuP | IS5 transposase and trans‑activator/predicted S‑methylmethionine transporter |
| ? | W3110S.gb | 576000 = | 2 (0.040) | pseudogene (109/1128 nt) | nmpC | DLP12 prophage region; ECK0544:JW5078:b0553; truncated outer membrane porin | |||||
| * | ? | W3110S.gb | 314453 = | 39 (0.800) | 43 (0.920) +TC |
33/96 | NT | 69.7% | 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) | 66 (1.350) | 42/100 | 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 | 381043 = | NA (NA) | 3 (0.070) | 3/86 | NT | NA | coding (146/906 nt) | insD | IS2 insertion element transposase InsAB' |
| ? | W3110S.gb | 381065 = | NA (NA) | coding (168/906 nt) | insD | IS2 insertion element transposase InsAB' | |||||
| * | ? | W3110S.gb | 566000 = | NA (NA) | 51 (1.050) | 39/100 | 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 | = 641963 | 40 (0.820) | 50 (1.250) +AGAACTGTT |
5/82 | NT | 56.0% | coding (653/1239 nt) | ybdR | predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding |
| ? | W3110S.gb | 1868457 = | 56 (1.150) | intergenic (‑271/‑165) | mipA/yeaG | scaffolding protein for murein synthesizing machinery/conserved hypothetical protein with nucleoside triphosphate hydrolase domain | |||||
| * | ? | W3110S.gb | 713380 = | 37 (0.760) | 342 (7.630) | 93/92 | NT | 90.4% | intergenic (‑156/‑29) | ybfF/seqA | conserved hypothetical protein/regulatory protein for replication initiation |
| ? | W3110S.gb | = 4125340 | 39 (0.870) | coding (836/837 nt) | dam | DNA adenine methylase | |||||
| * | ? | W3110S.gb | = 713954 | 59 (1.210) | 508 (10.430) | 95/100 | NT | 90.0% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | W3110S.gb | 2809398 = | 54 (1.110) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | W3110S.gb | = 738472 | 38 (0.780) | 4 (0.090) | 3/92 | NT | 11.8% | intergenic (+89/‑42) | ybfL/ybfD | ECK0694:JW0695:b0705; predicted transposase/conserved hypothetical protein |
| ? | W3110S.gb | 4016100 = | 25 (0.560) | intergenic (‑61/+185) | yhhI/yrhC | predicted transposase/ECK3468:JW5678:b4552; hypothetical protein fragment | |||||
| * | ? | W3110S.gb | 1209367 = | 13 (0.270) | 29 (0.880) | 22/68 | NT | 78.5% | coding (290/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | 1211196 = | 7 (0.210) | pseudogene (37/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | = 1209382 | 14 (0.290) | 35 (1.060) | 25/68 | NT | 80.9% | coding (305/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | = 1211179 | 7 (0.210) | pseudogene (54/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | = 1225529 | 28 (0.570) | 11 (0.300) +GCAAAAGATTAC |
6/76 | NT | 36.7% | intergenic (+45/+327) | ycgI/minE | hypothetical protein/cell division topological specificity factor |
| ? | W3110S.gb | = 3595831 | 22 (0.450) | intergenic (+56/+214) | mobB/rrfA | molybdopterin‑guanine dinucleotide biosynthesis protein B/5S ribosomal RNA | |||||
| * | ? | W3110S.gb | = 1871062 | 42 (0.860) | 3 (0.070) | 3/90 | NT | 7.7% | coding (394/1284 nt) | yeaH | conserved hypothetical protein |
| ? | W3110S.gb | = 1871073 | 34 (0.780) | coding (405/1284 nt) | yeaH | conserved hypothetical protein | |||||
| * | ? | W3110S.gb | = 1963538 | 28 (0.570) | 3 (0.080) | 3/80 | NT | 10.8% | intergenic (+29/‑148) | argS/yecT | arginyl‑tRNA synthetase/hypothetical protein |
| ? | W3110S.gb | = 1963548 | 27 (0.690) | intergenic (+39/‑138) | argS/yecT | arginyl‑tRNA synthetase/hypothetical protein | |||||
| * | ? | W3110S.gb | 2018571 = | 4 (0.080) | 35 (0.760) | 26/94 | NT | 90.3% | 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 | 2 (0.040) | 44 (0.940) | 28/96 | NT | 95.8% | 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 | 2091895 = | 68 (1.400) | 4 (0.100) | 3/86 | NT | 6.9% | intergenic (‑45/‑238) | yefM/hisL | antitoxin of the YoeB‑YefM toxin‑antitoxin system/his operon leader peptide |
| ? | W3110S.gb | 2091916 = | 49 (1.170) | intergenic (‑66/‑217) | yefM/hisL | antitoxin of the YoeB‑YefM toxin‑antitoxin system/his operon leader peptide | |||||
| * | ? | W3110S.gb | 2172308 = | NA (NA) | 58 (1.220) | 43/98 | NT | 98.3% | pseudogene (1563/2041 nt) | gatR | DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 |
| ? | W3110S.gb | = 3920281 | 1 (0.020) | coding (88/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | = 2173564 | NA (NA) | 46 (0.960) | 30/98 | 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) | 65 (1.330) | 35/100 | 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 | = 2257626 | 51 (1.050) | 3 (0.070) | 3/94 | NT | 5.0% | coding (895/942 nt) | rihB | ribonucleoside hydrolase 2 |
| ? | W3110S.gb | = 2257664 | 65 (1.420) | coding (857/942 nt) | rihB | ribonucleoside hydrolase 2 | |||||
| * | ? | W3110S.gb | = 2401919 | 50 (1.030) | 8 (0.200) +GGCATTTCA |
3/82 | NT | 14.5% | coding (194/978 nt) | nuoH | NADH:ubiquinone oxidoreductase, membrane subunit H |
| ? | W3110S.gb | = 2562879 | 65 (1.330) | coding (1247/1362 nt) | eutB | ethanolamine ammonia‑lyase, large subunit, heavy chain | |||||
| * | ? | W3110S.gb | = 2412225 | NA (NA) | 58 (1.190) | 36/100 | NT | 92.1% | intergenic (‑55/‑782) | insA/yfbQ | IS1 element protein/predicted aminotransferase |
| ? | W3110S.gb | = 3748807 | 5 (0.100) | coding (176/984 nt) | tnaB | tryptophan transporter of low affinity | |||||
| * | ? | W3110S.gb | 2564137 = | 5 (0.100) | 23 (0.550) +ATGCGGT |
13/86 | NT | 55.4% | coding (1404/1404 nt) | eutA | reactivating factor for ethanolamine ammonia lyase |
| ? | W3110S.gb | = 3997968 | 38 (0.780) | coding (684/753 nt) | yhiQ | predicted SAM‑dependent methyltransferase | |||||
| * | ? | W3110S.gb | 3078146 = | 75 (1.540) | 5 (0.110) | 5/92 | NT | 6.9% | intergenic (‑160/+154) | cmtB/tktA | predicted mannitol‑specific enzyme IIA component of PTS/transketolase 1, thiamin‑binding |
| ? | W3110S.gb | 3078170 = | 65 (1.450) | intergenic (‑184/+130) | cmtB/tktA | predicted mannitol‑specific enzyme IIA component of PTS/transketolase 1, thiamin‑binding | |||||
| * | ? | W3110S.gb | = 3261133 | 0 (0.000) | 25 (0.560) | 21/92 | 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 | 3309695 = | 45 (0.920) | 4 (0.090) | 3/94 | NT | 9.1% | coding (1398/2205 nt) | pnp | polynucleotide phosphorylase/polyadenylase |
| ? | W3110S.gb | 3309732 = | 38 (0.830) | coding (1361/2205 nt) | pnp | polynucleotide phosphorylase/polyadenylase | |||||
| * | ? | W3110S.gb | 3569741 = | 77 (1.580) | 4 (0.090) | 3/88 | NT | 6.2% | coding (276/1407 nt) | yihP | predicted transporter |
| ? | W3110S.gb | 3569763 = | 53 (1.240) | coding (298/1407 nt) | yihP | predicted transporter | |||||
| * | ? | W3110S.gb | 3748799 = | 6 (0.120) | 65 (1.330) | 38/100 | NT | 91.5% | 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 = | 41 (0.840) | 7 (0.180) | 7/82 | NT | 17.8% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | 4547678 = | 31 (0.780) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||