mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 40,450 | A→G | 8.9% | F494F (TTT→TTC) | caiT ← | putative transporter |
| RA | 234,230 | T→C | 9.7% | I185V (ATA→GTA) | gloB ← | hydroxyacylglutathione hydrolase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 738,600 | A→C | 5.2% | K170T (AAA→ACA) | ybfD → | H repeat‑associated putative transposase |
| RA | 738,604 | C→T | 5.3% | T171T (ACC→ACT) | ybfD → | H repeat‑associated putative transposase |
| RA | 828,729 | T→C | 6.2% | M85V (ATG→GTG) | ybhF ← | putative ABC transporter ATPase |
| JC JC | 1,110,159 | IS2 (–) +5 bp | 32.3% | coding (825‑829/1536 nt) | opgG → | OPG biosynthetic periplasmic beta‑1,6 branching glycosyltransferase |
| RA | 1,111,908 | C→A | 10.0% | S349* (TCG→TAG) | opgH → | OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist |
| RA | 1,217,099 | T→C | 7.3% | intergenic (+103/‑229) | ymgC → / → ycgG | Blue light, low temperature and stress induced protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| 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 | 1,395,146 | A→G | 6.7% | R259R (CGT→CGC) | ynaI ← | mechanosensitive channel protein, very small conductance |
| RA | 1,482,252 | C→T | 7.9% | intergenic (+51/+3) | ynbD → / ← azoR | putative phosphatase inner membrane protein/NADH‑azoreductase, FMN‑dependent |
| RA | 1,904,420 | A→T | 6.6% | I176F (ATC→TTC) | manZ → | mannose‑specific enzyme IID component of PTS |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,290,730 | T→A | 6.4% | D77E (GAT→GAA) | narP → | response regulator in two‑component regulatory system with NarQ |
| RA | 2,507,628 | G→T | 6.9% | D89E (GAC→GAA) | fryC ← | putative enzyme IIC component of PTS |
| JC JC | 2,536,312 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | 100% | coding (479‑484/510 nt) | crr → | glucose‑specific enzyme IIA component of PTS |
| RA | 2,708,133 | G→T | 5.8% | P208T (CCG→ACG) | rseB ← | anti‑sigma E factor, binds RseA |
| RA | 2,883,178 | T→C | 6.3% | N321D (AAT→GAT) | casA ← | CRISP RNA (crRNA) containing Cascade antiviral complex protein |
| JC | 2,977,562 | Δ33 bp | 34.7% | coding (964‑996/1032 nt) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| RA | 3,195,008 | C→G | 5.5% | intergenic (‑143/+91) | sibD ← / ← sibE | sRNA antisense regulator of toxic IbsD protein/sRNA antisense regulator of toxic IbsE protein |
| RA | 3,489,898 | C→A | 5.4% | E95* (GAG→TAG) | argD ← | bifunctional acetylornithine aminotransferase and succinyldiaminopimelate aminotransferase |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,959,991 | T→A | 11.5% | intergenic (‑178/+21) | ppiC ← / ← yifN | peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/PemK toxin family pseudogene |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,160,113 | G→T | 100% | H226Q (CAC→CAA) | sthA ← | pyridine nucleotide transhydrogenase, soluble |
| RA | 4,160,854 | C→T | 100% | intergenic (‑64/‑270) | sthA ← / → fabR | pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,246,288 | G→A | 5.2% | N44N (AAC→AAT) | malE ← | maltose transporter subunit |
| RA | 4,296,060 | C→T | 11.0% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→G | 26.7% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 26.8% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 30.4% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,433,829 | C→T | 8.5% | V66M (GTG→ATG) | qorB ← | NAD(P)H:quinone oxidoreductase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1812693 | 1812952 | 260 | 17 [15] | [16] 18 | ydjO | uncharacterized protein |
| * | * | ÷ | NC_000913 | 2103923 | 2104113 | 191 | 17 [16] | [16] 17 | wbbK | lipopolysaccharide biosynthesis protein |
| * | * | ÷ | NC_000913 | 3268879 | 3269654 | 776 | 17 [16] | [16] 18 | [yhaC] | [yhaC] |
| * | * | ÷ | NC_000913 | 3423902–3424231 | 3424408–3424240 | 10–507 | 17 [16] | [16] 17 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 3653693 | 3653823 | 131 | 17 [14] | [15] 17 | [yhiS] | [yhiS] |
| * | * | ÷ | NC_000913 | 3796931 | 3797412 | 482 | 19 [16] | [13] 17 | [waaC]–[waaL] | [waaC],[waaL] |
| * | * | ÷ | NC_000913 | 3798888 | 3799583 | 696 | 17 [16] | [16] 17 | [waaU]–[waaZ] | [waaU],[waaZ] |
| * | * | ÷ | NC_000913 | 3804231 | 3805234 | 1004 | 18 [13] | [15] 19 | [waaS]–[waaP] | [waaS],[waaP] |
| * | * | ÷ | NC_000913 | 4233681 | 4235848 | 2168 | 18 [16] | [14] 17 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 166404 = | 76 (1.310) | 5 (0.090) | 3/502 | NT | 7.1% | coding (1675/2535 nt) | mrcB | fused glycosyl transferase and transpeptidase |
| ? | NC_000913 | 166643 = | 58 (1.030) | coding (1914/2535 nt) | mrcB | fused glycosyl transferase and transpeptidase | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 3 (0.050) | 3/518 | NT | 8.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1109374 | 31 (0.530) | coding (40/1536 nt) | opgG | OPG biosynthetic periplasmic beta‑1,6 branching glycosyltransferase | |||||
| * | ? | NC_000913 | = 275988 | 42 (0.720) | 3 (0.050) | 3/504 | NT | 5.9% | coding (664/1404 nt) | mmuP | CP4‑6 prophage; putative S‑methylmethionine transporter |
| ? | NC_000913 | = 276355 | 55 (0.970) | coding (1031/1404 nt) | mmuP | CP4‑6 prophage; putative S‑methylmethionine transporter | |||||
| * | ? | NC_000913 | = 933725 | 50 (0.860) | 3 (0.050) | 3/506 | NT | 5.7% | coding (502/3990 nt) | ftsK | DNA translocase at septal ring sorting daughter chromsomes |
| ? | NC_000913 | = 933736 | 50 (0.880) | coding (513/3990 nt) | ftsK | DNA translocase at septal ring sorting daughter chromsomes | |||||
| * | ? | NC_000913 | 1207790 = | 17 (0.290) | 28 (0.510) | 24/486 | NT | 63.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 17 (0.310) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 16 (0.280) | 37 (0.680) | 33/486 | NT | 69.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 17 (0.310) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1932802 = | 48 (0.830) | 53 (0.920) | 39/514 | NT | 52.1% | coding (1803/1812 nt) | edd | 6‑phosphogluconate dehydratase |
| ? | NC_000913 | = 1969467 | 50 (0.870) | coding (1518/1602 nt) | tap | methyl‑accepting protein IV | |||||
| * | ? | NC_000913 | = 2570111 | 58 (1.000) | 4 (0.070) | 4/492 | NT | 8.9% | coding (227/837 nt) | eutJ | ethanolamine utilization protein, HSP70/actin superfamily protein |
| ? | NC_000913 | = 2570316 | 27 (0.490) | coding (22/837 nt) | eutJ | ethanolamine utilization protein, HSP70/actin superfamily protein | |||||
| * | ? | NC_000913 | = 3841541 | 28 (0.480) | 3 (0.050) | 3/508 | NT | 6.4% | coding (199/1191 nt) | nepI | putative transporter |
| ? | NC_000913 | = 3842379 | 61 (1.070) | coding (24/453 nt) | yicN | DUF1198 family protein | |||||