mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 |
| RA | 12,484 | C→A | 19.6% | Q108K (CAG→AAG) | dnaK → | chaperone Hsp70, with co‑chaperone DnaJ |
| RA | 134,775 | T→C | 19.4% | intergenic (+25/+13) | yacL → / ← speD | UPF0231 family protein/S‑adenosylmethionine decarboxylase |
| RA | 249,538 | T→G | 28.9% | pseudogene (533/1713 nt) | lfhA ← | pseudogene, flagellar system protein, promoterless fragment, flagellar biosynthesis |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 351,510 | T→C | 24.7% | L99P (CTC→CCC) | prpD → | 2‑methylcitrate dehydratase |
| RA | 365,783 | T→C | 25.8% | S175G (AGC→GGC) | lacZ ← | beta‑D‑galactosidase |
| RA | 540,558 | T→G | 24.6% | intergenic (+50/‑7) | allB → / → ybbY | allantoinase/putative uracil/xanthine transporter |
| RA | 540,577 | G→T | 17.1% | A5S (GCA→TCA) | ybbY → | putative uracil/xanthine transporter |
| RA | 602,200 | A→G | 17.4% | E81G (GAG→GGG) | pheP → | phenylalanine transporter |
| RA | 715,338 | T→A | 14.2% | intergenic (+140/‑74) | pgm → / → ybfP | phosphoglucomutase/lipoprotein |
| RA | 1,080,508 | A→G | 26.8% | S402G (AGC→GGC) | putP → | proline:sodium symporter |
| JC | 1,195,194 | Δ3 bp | 3.1% | coding (72‑74/1251 nt) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,196,131 | G→A | 20.3% | A337T (GCC→ACC) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,196,305 | C→T | 55.7% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,325,980 | A→T | 17.5% | Y412F (TAC→TTC) | yciQ → | enhancer of membrane protein expression, putative inner membrane protein |
| RA | 1,388,666 | A→C | 16.9% | V49G (GTG→GGG) | tpx ← | lipid hydroperoxide peroxidase |
| RA | 1,445,981 | T→G | 27.2% | G34G (GGT→GGG) | ydbL → | DUF1318 family protein |
| RA | 1,695,755 | T→C | 12.7% | E106G (GAG→GGG) | uidA ← | beta‑D‑glucuronidase |
| RA | 1,734,567 | G→A | 15.1% | D45N (GAT→AAT) | mepH → | murein DD‑endopeptidase, space‑maker hydrolase |
| RA | 1,858,941:1 | +A | 4.0% | coding (1289/1380 nt) | ydjK ← | putative MFS sugar transporter, membrane protein |
| RA | 2,079,975 | A→G | 18.6% | L206P (CTC→CCC) | yeeA ← | putative transporter, FUSC family inner membrane protein |
| RA | 2,080,362 | A→C | 27.6% | V77G (GTG→GGG) | yeeA ← | putative transporter, FUSC family inner membrane protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,149,901 | G→C | 46.2% | A362G (GCG→GGG) | yegI ← | protein kinase‑related putative non‑specific DNA‑binding protein |
| RA | 2,235,396 | T→G | 21.7% | V45G (GTG→GGG) | preA → | dihydropyrimidine dehydrogenase, NADH‑dependent, subunit C |
| RA | 2,389,434 | T→C | 15.4% | A107A (GCT→GCC) | yfbP → | TPR‑like repeats‑containing protein |
| RA | 2,525,296 | C→T | 14.0% | L58F (CTT→TTT) | yfeN → | putative outer membrane protein |
| RA | 2,541,881 | A→C | 19.1% | G210G (GGT→GGG) | cysU ← | sulfate/thiosulfate ABC transporter permease |
| RA | 2,739,601 | T→C | 13.8% | E156G (GAG→GGG) | tyrA ← | fused chorismate mutase T/prephenate dehydrogenase |
| RA | 2,782,495 | C→T | 21.9% | S77N (AGT→AAT) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,820,019 | T→C | 20.9% | E664G (GAG→GGG) | alaS ← | alanyl‑tRNA synthetase |
| RA | 2,909,227 | A→C | 33.0% | G146G (GGT→GGG) | pyrG ← | CTP synthetase |
| RA | 2,942,817 | C→T | 15.3% | noncoding (124/206 nt) | gcvB → | sRNA antisense regulator represses oppA, dppA, gltI and livJ expression, Hfq‑dependent |
| RA | 3,075,552 | G→C | 22.6% | A210G (GCG→GGG) | yggF ← | fructose 1,6 bisphosphatase isozyme |
| RA | 3,079,068 | A→C | 14.0% | G87G (GGT→GGG) | cmtB ← | putative mannitol‑specific enzyme IIA component of PTS |
| RA | 3,151,563 | A→G | 11.3% | S140S (TCT→TCC) | exbB ← | membrane spanning protein in TonB‑ExbB‑ExbD complex |
| RA | 3,206,436 | G→A | 24.3% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,277,454 | T→A | 10.6% | Y40* (TAT→TAA) | yhaV → | toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system |
| RA | 3,277,497 | G→A | 14.4% | V55M (GTG→ATG) | yhaV → | toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system |
| RA | 3,527,720 | A→C | 16.2% | S418S (TCA→TCC) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,646,108 | T→G | 27.8% | V242G (GTG→GGG) | rlmJ → | 23S rRNA m(6)A2030 methyltransferase, SAM‑dependent |
| RA | 3,665,697 | T→C | 26.0% | D38G (GAT→GGT) | gadX ← | acid resistance regulon transcriptional activator, autoactivator |
| RA | 3,665,701 | C→A | 36.1% | A37S (GCG→TCG) | gadX ← | acid resistance regulon transcriptional activator, autoactivator |
| RA | 3,719,840 | G→A | 14.6% | intergenic (+73/‑208) | yiaG → / → cspA | HTH_CROC1 family putative transcriptional regulator/RNA chaperone and antiterminator, cold‑inducible |
| RA | 3,749,428 | T→G | 20.3% | G66G (GGT→GGG) | sgbU → | putative L‑xylulose 5‑phosphate 3‑epimerase |
| RA | 3,767,038 | A→T | 6.1% | N235Y (AAT→TAT) | yibA → | putative immunity protein for polymorphic toxin RhsA, HEAT‑domain protein, lethality reduction protein |
| RA | 3,790,968 | A→C | 10.2% | V126G (GTG→GGG) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,796,589 | T→G | 6.8% | G204G (GGT→GGG) | waaC → | ADP‑heptose:LPS heptosyl transferase I |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,857,244 | T→C | 7.8% | D387G (GAT→GGT) | yidJ ← | sulfatase/phosphatase superfamily protein |
| RA | 3,891,652 | A→C | 17.4% | L13F (TTA→TTC) | mdtL → | multidrug efflux system protein |
| RA | 3,895,484 | G→C | 21.6% | R375R (CGC→CGG) | adeP ← | adenine permease, high affinity, adenine:H+ symporter |
| RA | 3,917,801 | A→C | 13.2% | V155G (GTG→GGG) | atpG ← | F1 sector of membrane‑bound ATP synthase, gamma subunit |
| RA | 3,978,861 | A→C | 26.2% | T88P (ACC→CCC) | wzyE → | putative ECA polysaccharide chain elongation protein |
| JC | 4,001,644 | Δ5 bp | 96.5% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,015,350 | T→C | 13.1% | intergenic (+37/+3) | metE → / ← ysgA | 5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase/putative carboxymethylenebutenolidase |
| RA | 4,017,124 | A→G | 12.1% | E232G (GAG→GGG) | udp → | uridine phosphorylase |
| RA | 4,065,579 | T→A | 16.0% | T63S (ACC→TCC) | yihO ← | putative sulphoquinovose importer |
| RA | 4,125,339 | T→G | 16.0% | T491P (ACC→CCC) | priA ← | Primosome factor n' (replication factor Y) |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,241,828 | T→A | 12.9% | L142F (TTA→TTT) | xylE ← | D‑xylose transporter |
| RA | 4,253,508 | T→G | 11.9% | V165G (GTG→GGG) | ubiA → | p‑hydroxybenzoate octaprenyltransferase |
| RA | 4,253,516 | A→G | 12.7% | S168G (AGT→GGT) | ubiA → | p‑hydroxybenzoate octaprenyltransferase |
| RA | 4,366,216 | T→G | 23.4% | T187P (ACT→CCT) | dcuA ← | C4‑dicarboxylate antiporter |
| RA | 4,386,018 | G→T | 13.2% | *105L (TGA→TTA) | yjeO → | inner membrane protein |
| RA | 4,430,340 | A→G | 20.3% | E159G (GAG→GGG) | cycA → | D‑alanine/D‑serine/glycine transporter |
| RA | 4,464,860 | A→C | 14.5% | V441G (GTG→GGG) | treB ← | trehalose‑specific PTS enzyme: IIB and IIC component |
| RA | 4,471,964 | T→G | 17.9% | T145P (ACT→CCT) | pyrB ← | aspartate carbamoyltransferase, catalytic subunit |
| RA | 4,480,112 | C→T | 14.3% | L128F (CTC→TTC) | yjgN → | DUF898 family inner membrane protein |
| RA | 4,596,481 | A→G | 22.9% | E164G (GAG→GGG) | lgoD → | L‑galactonate oxidoreductase, L‑gulonate oxidoreductase |
| RA | 4,609,768 | T→G | 24.0% | G118G (GGT→GGG) | prfC → | peptide chain release factor RF‑3 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2192244 | 2192433 | 190 | 14 [13] | [12] 14 | yehD/yehE | putative fimbrial‑like adhesin protein/DUF2574 family protein |
| * | * | ÷ | NC_000913 | 2469142 | 2469773 | 632 | 14 [12] | [13] 15 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | NC_000913 | 2470087 | 2470357 | 271 | 14 [13] | [13] 14 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | NC_000913 | 3769577 | 3769903 | 327 | 19 [10] | [12] 17 | [yibV]–yibV | [yibV], yibV |
| * | * | ÷ | NC_000913 | 4233772 | 4235422 | 1651 | 14 [12] | [13] 14 | [pgi] | [pgi] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 67 (1.100) | 46/418 | 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 | 458787 = | 28 (0.460) | 25 (0.420) | 21/412 | NT | 47.5% | intergenic (+87/‑101) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | 608011 = | NA (NA) | intergenic (+23/‑54) | hokE/insL1 | toxic polypeptide, small/IS186 transposase | |||||
| * | ? | NC_000913 | = 458799 | 24 (0.390) | 32 (0.540) | 24/410 | NT | 57.6% | intergenic (+99/‑89) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | = 609347 | NA (NA) | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | NC_000913 | 1207790 = | 5 (0.080) | 65 (1.150) | 43/386 | NT | 90.5% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 9 (0.160) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 5 (0.080) | 56 (0.990) | 36/386 | NT | 89.2% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 9 (0.160) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 1 (0.020) | 67 (1.100) | 47/418 | NT | 98.5% | 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 | = 1299498 | 0 (0.000) | 42 (0.700) | 29/410 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 39 (0.670) | 32/402 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 32 (0.530) | 25/418 | 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) | 66 (1.080) | 44/418 | 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 | |||||