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 | 375,121 | T→G | 5.6% | intergenic (+240/‑338) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 636,505 | C→T | 6.8% | W22* (TGG→TAG) | ybdN ← | PAPS reductase‑like domain protein |
| RA | 762,818 | G→T | 4.6% | intergenic (+79/‑196) | sucB → / → sucC | dihydrolipoyltranssuccinase/succinyl‑CoA synthetase, beta subunit |
| RA | 778,143 | A→T | 3.8% | K135I (AAA→ATA) | tolB → | periplasmic protein |
| RA | 1,085,712 | Δ1 bp | 3.7% | coding (721/1065 nt) | phoH → | ATP‑binding protein, putative PhoH family P‑loop ATPase |
| RA | 1,089,012 | C→T | 3.1% | S282S (TCG→TCA) | pgaB ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein |
| RA | 1,286,965 | A→G | 15.5% | intergenic (+439/+101) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| 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 | 1,379,604 | A→G | 3.9% | Q574R (CAA→CGA) | ycjT → | putative family 65 glycosyl hydrolase |
| RA | 1,390,719 | C→T | 3.6% | intergenic (‑121/+6) | mpaA ← / ← ymjC | murein peptide amidase A/pseudogene |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,110,523 | T→C | 7.0% | E166G (GAA→GGA) | rfbA ← | glucose‑1‑phosphate thymidylyltransferase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,281,090 | T→C | 5.0% | F154S (TTT→TCT) | yejH → | putative ATP‑dependent DNA or RNA helicase |
| RA | 2,304,796 | T→C | 10.3% | intergenic (+405/+310) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,780,625 | Δ1 bp | 3.9% | coding (2100/4581 nt) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,893,202 | T→C | 4.7% | L183P (CTG→CCG) | ygcN → | putative oxidoreductase |
| RA | 3,528,106 | T→G | 50.3% | L547R (CTG→CGG) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,688,286 | A→C | 15.4% | V296G (GTG→GGG) | bcsC ← | cellulose synthase subunit |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,945,480 | T→C | 3.2% | noncoding (1778/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,992,437 | T→G | 16.9% | L429* (TTA→TGA) | cyaA → | adenylate cyclase |
| JC | 3,992,468 | Δ4 bp | 5.2% | coding (1317‑1320/2547 nt) | cyaA → | adenylate cyclase |
| JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,144,368 | A→G | 3.5% | K125K (AAA→AAG) | pflD → | putative glycine radical domain‑containing pyruvate formate‑lyase |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,189,162 | T→A | 4.5% | S1272T (TCC→ACC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,257,229 | C→T | 3.2% | S39F (TCC→TTC) | lexA → | transcriptional repressor of SOS regulon |
| RA | 4,295,928 | T→C | 4.6% | intergenic (+135/+509) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,295,964 | A→C | 7.7% | intergenic (+171/+473) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 46.2% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 47.2% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,578,562 | A→G | 5.5% | F259F (TTT→TTC) | mcrB ← | 5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrB |
| RA | 4,625,904 | Δ1 bp | 5.7% | intergenic (+40/‑9) | serB → / → radA | 3‑phosphoserine phosphatase/DNA repair protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2533726 | 2536429 | 2704 | 41 [37] | [38] 39 | ptsH–[pdxK] | ptsH, ptsI, crr, [pdxK] |
| * | * | ÷ | NC_000913 | 3423877–3424229 | 3424447–3424237 | 9–571 | 40 [38] | [38] 39 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 107 (1.120) | 77/510 | NT | 100% | 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 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 373065 | 75 (0.790) | 4 (0.050) | 4/474 | NT | 5.5% | coding (145/951 nt) | mhpF | acetaldehyde‑CoA dehydrogenase II, NAD‑binding |
| ? | NC_000913 | = 373047 | 69 (0.780) | coding (127/951 nt) | mhpF | acetaldehyde‑CoA dehydrogenase II, NAD‑binding | |||||
| * | ? | NC_000913 | 1207790 = | 42 (0.440) | 31 (0.350) | 27/478 | NT | 42.9% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 43 (0.480) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 40 (0.420) | 58 (0.650) | 41/478 | NT | 59.0% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 43 (0.480) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 5 (0.050) | 108 (1.130) | 74/510 | NT | 95.6% | 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 | 1508853 = | 90 (0.940) | 3 (0.030) | 3/488 | NT | 3.6% | coding (212/231 nt) | yncJ | uncharacterized protein |
| ? | NC_000913 | 1508894 = | 76 (0.830) | coding (171/231 nt) | yncJ | uncharacterized protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 47 (0.490) | 34/510 | 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) | 109 (1.140) | 65/510 | 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) | 70 (0.730) | 50/510 | NT | 68.6% | 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 = | 32 (0.340) | 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) | 52 (0.550) | 40/508 | NT | 62.0% | 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 | 32 (0.340) | intergenic (‑304/‑16) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913 | 2852104 = | 90 (0.940) | 3 (0.030) | 3/494 | NT | 3.6% | coding (243/273 nt) | hypC | hydrogenase maturation protein |
| ? | NC_000913 | 2852164 = | 74 (0.800) | coding (31/1122 nt) | hypD | hydrogenase maturation protein | |||||
| * | ? | NC_000913 | = 3000943 | 60 (0.630) | 3 (0.030) | 3/502 | NT | 4.7% | coding (601/2259 nt) | xdhA | xanthine dehydrogenase, molybdenum binding subunit |
| ? | NC_000913 | = 3001008 | 63 (0.670) | coding (666/2259 nt) | xdhA | xanthine dehydrogenase, molybdenum binding subunit | |||||
| * | ? | NC_000913 | 3845530 = | 103 (1.080) | 47 (0.510) | 42/490 | NT | 31.5% | coding (1568/1767 nt) | adeD | cryptic adenine deaminase |
| ? | NC_000913 | = 3992759 | 105 (1.140) | coding (1608/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | 4036030 = | NA (NA) | 3 (0.030) | 3/500 | NT | 100% | noncoding (501/1542 nt) | rrsA | 16S ribosomal RNA of rrnA operon |
| ? | NC_000913 | = 4036026 | 0 (0.000) | noncoding (497/1542 nt) | rrsA | 16S ribosomal RNA of rrnA operon | |||||
| * | ? | NC_000913 | = 4094858 | 146 (1.530) | 3 (0.030) | 3/504 | NT | 2.5% | coding (1124/1260 nt) | rhaA | L‑rhamnose isomerase |
| ? | NC_000913 | = 4095494 | 88 (0.930) | coding (488/1260 nt) | rhaA | L‑rhamnose isomerase | |||||
| * | ? | NC_000913 | = 4233841 | 99 (1.040) | 4 (0.040) | 4/490 | NT | 3.8% | coding (85/1650 nt) | pgi | glucosephosphate isomerase |
| ? | NC_000913 | = 4233857 | 110 (1.200) | coding (101/1650 nt) | pgi | glucosephosphate isomerase | |||||
| * | ? | NC_000913 | 4409175 = | NA (NA) | 4 (0.040) | 4/480 | NT | 6.3% | noncoding (22/98 nt) | RIP331 (repetitive extragenic palindromic) element, contains 2 REP sequences and 1 IHF site | RIP331 (repetitive extragenic palindromic) element, contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 4409236 = | 59 (0.660) | noncoding (83/98 nt) | RIP331 (repetitive extragenic palindromic) element, contains 2 REP sequences and 1 IHF site | RIP331 (repetitive extragenic palindromic) element, contains 2 REP sequences and 1 IHF site | |||||