mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 377,028 | Δ1 bp | 2.6% | coding (257/540 nt) | yaiL → | DUF2058 family protein |
| RA | 516,405:1 | +G | 2.6% | coding (487/678 nt) | fetA → | iron export ABC transporter ATPase, peroxide resistance protein |
| RA | 747,673 | G→A | 2.8% | P33S (CCG→TCG) | abrB ← | regulator of aidB expression, inner membrane protein |
| RA | 759,809 | A→T | 2.8% | E368D (GAA→GAT) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 759,810 | A→T | 2.8% | T369S (ACC→TCC) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 915,080 | G→C | 4.5% | intergenic (‑223/+272) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 915,081 | G→C | 4.6% | intergenic (‑224/+271) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 929,582 | Δ1 bp | 2.6% | coding (1381/1767 nt) | cydD ← | glutathione/cysteine ABC transporter export permease/ATPase |
| RA | 1,073,122 | T→A | 2.5% | D297V (GAT→GTT) | rutA ← | pyrimidine oxygenase, FMN‑dependent |
| RA | 1,188,545 | Δ1 bp | 2.8% | coding (1232/1461 nt) | phoQ ← | sensory histidine kinase in two‑component regulatory system with PhoP |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,380,273 | Δ1 bp | 2.8% | coding (126/660 nt) | ycjU → | beta‑phosphoglucomutase |
| RA | 1,466,210 | G→A | 5.7% | pseudogene (819/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,711 | T→C | 3.7% | pseudogene (1320/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,708,751 | A→G | 8.2% | E611E (GAA→GAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,758 | G→C | 8.8% | E614Q (GAA→CAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,930 | C→A | 7.2% | P671Q (CCG→CAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,739,637 | A→C | 5.2% | R54R (CGT→CGG) | ydhB ← | LysR family putative transcriptional regulator |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,304,873 | C→T | 5.2% | intergenic (+482/+233) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,986 | T→C | 4.2% | intergenic (+595/+120) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,316,391 | T→C | 3.7% | Y73H (TAC→CAC) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,569,817 | A→G | 3.8% | S173S (TCT→TCC) | eutJ ← | ethanolamine utilization protein, HSP70/actin superfamily protein |
| RA | 2,649,860 | T→C | 7.3% | D809G (GAT→GGT) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM, anti‑host protease defense factor, periplasmic inner membrane‑anchored lipoprotein |
| JC | 2,836,454:1 | (TACCGCTCAGGTT)1→2 | 5.1% | coding (970/2253 nt) | hypF ← | carbamoyl phosphate phosphatase and [NiFe] hydrogenase maturation protein |
| RA | 2,984,429 | T→C | 4.6% | T388A (ACC→GCC) | yqeF ← | short chain acyltransferase |
| RA | 3,359,720 | C→T | 2.6% | F175F (TTC→TTT) | gltD → | glutamate synthase, 4Fe‑4S protein, small subunit |
| RA | 3,409,381 | C→G | 2.6% | P105R (CCG→CGG) | prmA → | methyltransferase for 50S ribosomal subunit protein L11 |
| JC | 3,527,656 | Δ5 bp | 4.8% | coding (1190‑1194/2136 nt) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,528,106 | T→G | 49.8% | L547R (CTG→CGG) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,591,615 | A→G | 4.7% | L237P (CTC→CCC) | ugpB ← | sn‑glycerol‑3‑phosphate ABC transporter periplasmic binding protein |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,876,894 | T→G | 9.0% | T20P (ACC→CCC) | yidA ← | sugar phosphate phosphatase |
| RA | 3,992,437 | T→G | 9.8% | L429* (TTA→TGA) | cyaA → | adenylate cyclase |
| JC | 3,992,468 | Δ4 bp | 6.8% | coding (1317‑1320/2547 nt) | cyaA → | adenylate cyclase |
| JC | 3,992,523 | (CGGGC)2→1 | 2.5% | coding (1372‑1376/2547 nt) | cyaA → | adenylate cyclase |
| JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,022,662 | T→C | 2.6% | V149A (GTG→GCG) | tatB → | TatABCE protein translocation system subunit |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,200,321 | A→G | 3.2% | A14A (GCA→GCG) | hupA → | HU, DNA‑binding transcriptional regulator, alpha subunit |
| RA | 4,203,677 | C→T | 2.8% | A120V (GCG→GTG) | zraR → | fused DNA‑binding response regulator in two‑component regulatory system with ZraS: response regulator/sigma54 interaction protein |
| RA | 4,296,189 | A→G | 44.7% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 57.4% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,472,237 | T→G | 22.4% | T54P (ACC→CCC) | pyrB ← | aspartate carbamoyltransferase, catalytic subunit |
| RA | 4,587,967 | G→A | 2.9% | I300I (ATC→ATT) | yjiA ← | metal‑binding GTPase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2533680 | 2536431 | 2752 | 80 [78] | [74] 79 | ptsH–[pdxK] | ptsH, ptsI, crr, [pdxK] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 127 (0.780) | 80/506 | NT | 99.2% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 1 (0.010) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 381292 = | NA (NA) | 3 (0.020) | 3/488 | NT | NA | intergenic (‑32/‑59) | yaiX/insC1 | pseudogene, interrupted by IS2A, hexapeptide transferase superfamily, putative transferase/IS2 repressor TnpA |
| ? | NC_000913 | 381312 = | NA (NA) | intergenic (‑52/‑39) | yaiX/insC1 | pseudogene, interrupted by IS2A, hexapeptide transferase superfamily, putative transferase/IS2 repressor TnpA | |||||
| * | ? | NC_000913 | 759801 = | 143 (0.880) | 4 (0.030) | 4/492 | NT | 2.9% | coding (1096/2802 nt) | sucA | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| ? | NC_000913 | 759819 = | 130 (0.820) | coding (1114/2802 nt) | sucA | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding | |||||
| * | ? | NC_000913 | 1207790 = | 82 (0.510) | 102 (0.670) | 69/474 | NT | 59.7% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 61 (0.400) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 80 (0.490) | 81 (0.530) | 57/474 | NT | 54.4% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 61 (0.400) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1242594 | 151 (0.930) | 6 (0.040) | 6/470 | NT | 4.3% | coding (487/915 nt) | ldcA | murein tetrapeptide carboxypeptidase, LD‑carboxypeptidase A |
| ? | NC_000913 | = 1242576 | 127 (0.840) | coding (505/915 nt) | ldcA | murein tetrapeptide carboxypeptidase, LD‑carboxypeptidase A | |||||
| * | ? | NC_000913 | 1265438 = | 129 (0.790) | 4 (0.030) | 4/490 | NT | 3.2% | coding (427/1083 nt) | prfA | peptide chain release factor RF‑1 |
| ? | NC_000913 | 1265469 = | 121 (0.770) | coding (458/1083 nt) | prfA | peptide chain release factor RF‑1 | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 178 (1.100) | 106/506 | NT | 100% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1320390 | 108 (0.670) | 4 (0.020) | 3/502 | NT | 3.8% | coding (995/1596 nt) | trpD | fused glutamine amidotransferase (component II) of anthranilate synthase/anthranilate phosphoribosyl transferase |
| ? | NC_000913 | = 1320406 | 98 (0.610) | coding (979/1596 nt) | trpD | fused glutamine amidotransferase (component II) of anthranilate synthase/anthranilate phosphoribosyl transferase | |||||
| * | ? | NC_000913 | 1718531 = | 118 (0.730) | 4 (0.030) | 4/486 | NT | 3.4% | coding (1072/1110 nt) | anmK | anhydro‑N‑acetylmuramic acid kinase |
| ? | NC_000913 | 1718600 = | 112 (0.720) | coding (1003/1110 nt) | anmK | anhydro‑N‑acetylmuramic acid kinase | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 91 (0.560) | 54/506 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 168 (1.030) | 75/506 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 2288917 = | NA (NA) | 110 (0.680) | 72/506 | NT | 54.2% | intergenic (‑5/+146) | yejO/insH1 | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator |
| ? | NC_000913 | 3526447 = | 93 (0.570) | intergenic (‑300/‑20) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913 | = 2290110 | NA (NA) | 64 (0.400) | 48/504 | NT | 41.4% | intergenic (‑31/+2) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
| ? | NC_000913 | = 3526451 | 91 (0.560) | intergenic (‑304/‑16) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913 | = 2331856 | 178 (1.100) | 5 (0.030) | 5/490 | NT | 2.8% | pseudogene (2545/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family, putative membrane protein |
| ? | NC_000913 | = 2331857 | 175 (1.110) | pseudogene (2544/4605 nt) | yfaS | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family, putative membrane protein | |||||
| * | ? | NC_000913 | 3845530 = | 139 (0.860) | 109 (0.700) | 72/486 | NT | 45.0% | coding (1568/1767 nt) | adeD | cryptic adenine deaminase |
| ? | NC_000913 | = 3992759 | 133 (0.850) | coding (1608/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | 3927417 = | 241 (1.480) | 8 (0.050) | 8/482 | NT | 3.5% | coding (264/993 nt) | asnA | asparagine synthetase A |
| ? | NC_000913 | 3927456 = | 215 (1.390) | coding (303/993 nt) | asnA | asparagine synthetase A | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 11 (0.080) | 7/428 | NT | NA | intergenic (+38/+606) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | = 4296395 | NA (NA) | noncoding (562/602 nt) | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | |||||