mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 1,405 | A→C | S357R (AGC→CGC) | thrA → | Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| RA | 23,544 | C→T | A385V (GCG→GTG) | ileS → | isoleucyl‑tRNA synthetase |
| RA | 111,051 | (A)5→4 | coding (8/390 nt) | mutT → | dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase |
| RA | 124,558 | T→G | D514E (GAT→GAG) | aceE → | pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding |
| RA | 136,092 | T→G | N125H (AAC→CAC) | speE ← | spermidine synthase (putrescine aminopropyltransferase) |
| RA | 172,978 | C→T | A506V (GCG→GTG) | fhuB → | iron(3+)‑hydroxamate import ABC transporter permease |
| RA | 184,675 | A→C | L132* (TTA→TGA) | yaeI ← | phosphodiesterase with model substrate bis‑pNPP |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 450,073 | C→T | W190* (TGG→TAG) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 559,691 | C→T | intergenic (+25/‑6) | sfmC → / → sfmD | putative periplasmic pilus chaperone/putative outer membrane export usher protein |
| RA | 722,870 | T→G | L515F (TTA→TTC) | kdpD ← | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| RA | 723,486 | T→G | Q310P (CAG→CCG) | kdpD ← | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| RA | 776,710 | C→T | A123A (GCC→GCT) | tolA → | membrane anchored protein in TolA‑TolQ‑TolR complex |
| RA | 849,300 | T→G | L266L (CTA→CTC) | rhtA ← | threonine and homoserine efflux system |
| RA | 850,651 | T→G | Y68D (TAC→GAC) | ompX → | outer membrane protein X |
| RA | 856,402 | A→C | E147A (GAA→GCA) | ybiT → | ABC‑F family putative regulatory ATPase |
| RA | 926,224 | A→C | intergenic (‑253/+1) | serW ← / ← infA | tRNA‑Ser/translation initiation factor IF‑1 |
| RA | 932,321 | C→T | intergenic (‑271/‑274) | trxB ← / → lrp | thioredoxin reductase, FAD/NAD(P)‑binding/leucine‑responsive global transcriptional regulator |
| RA | 1,098,121 | A→C | E79A (GAA→GCA) | ghrA → | glyoxylate/hydroxypyruvate reductase A |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,245 | T→C | L375L (TTA→CTA) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,247 | A→G | L375L (TTA→TTG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,277 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,283 | A→G | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,283,279 | T→G | F1139C (TTC→TGC) | narG → | nitrate reductase 1, alpha subunit |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,429,709 | T→G | S221A (TCT→GCT) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,486,563 | A→C | K1168T (AAA→ACA) | hrpA → | putative ATP‑dependent helicase |
| RA | 1,522,825 | T→G | N81H (AAC→CAC) | yncD ← | putative iron outer membrane transporter |
| RA | 1,541,434 | A→C | V386G (GTA→GGA) | narZ ← | nitrate reductase 2 (NRZ), alpha subunit |
| RA | 1,593,099 | A→G | pseudogene (1027/1461 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,594,256 | (C)8→9 | pseudogene (3732/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,597,204 | T→G | pseudogene (784/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,598,297 | T→G | intergenic (‑310/+320) | yneO ← / ← lsrK | pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase |
| RA | 1,624,162 | G→A | G112G (GGC→GGT) | ydeI ← | hydrogen peroxide resistance OB fold protein; putative periplasmic protein |
| RA | 1,659,061 | T→G | I331M (ATT→ATG) | ynfE → | putative selenate reductase, periplasmic |
| RA | 1,797,961 | A→C | *328E (TAA→GAA) | pheS ← | phenylalanine tRNA synthetase, alpha subunit |
| RA | 1,818,103 | A→T | V133E (GTA→GAA) | chbF ← | phospho‑chitobiase; general 6‑phospho‑beta‑glucosidase activity |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,061,032 | C→T | W301* (TGG→TAG) | nac ← | nitrogen assimilation regulon transcriptional regulator; autorepressor |
| RA | 2,143,783 | T→G | L173R (CTG→CGG) | yegE → | putative diguanylate cyclase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,259,179 | C→T | G40S (GGT→AGT) | psuK ← | pseudouridine kinase |
| RA | 2,272,759 | T→G | T132T (ACT→ACG) | yejA → | microcin C ABC transporter periplasmic binding protein |
| RA | 2,372,256 | G→A | R450H (CGC→CAC) | arnT → | 4‑amino‑4‑deoxy‑L‑arabinose transferase |
| RA | 2,562,066 | A→G | intergenic (+73/‑45) | yffN → / → yffO | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,599,861 | (T)8→7 | intergenic (‑101/‑45) | dapA ← / → gcvR | dihydrodipicolinate synthase/transcriptional repressor, regulatory protein accessory to GcvA |
| RA | 2,612,344 | A→C | K149Q (AAA→CAA) | hyfR → | hydrogenase‑4 transcriptional activator |
| RA | 2,697,273 | T→G | F491L (TTT→TTG) | mltF → | membrane‑bound lytic transglycosylase F, murein hydrolase |
| RA | 2,740,932 | A→C | Y73* (TAT→TAG) | aroF ← | 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible |
| RA | 2,807,400 | A→C | H90P (CAT→CCT) | proX → | glycine betaine/proline ABC transporter periplasmic binding protein; cold shock protein |
| RA | 2,858,593 | T→G | Y501D (TAC→GAC) | mutS → | methyl‑directed mismatch repair protein |
| RA | 2,907,364 | A→T | L193Q (CTG→CAG) | eno ← | enolase |
| RA | 2,910,354 | A→G | V111A (GTG→GCG) | mazG ← | nucleoside triphosphate pyrophosphohydrolase |
| RA | 2,919,456 | T→G | I431L (ATC→CTC) | gudX ← | glucarate dehydratase‑related protein, substrate unknown |
| RA | 2,951,714 | T→C | S250G (AGC→GGC) | recD ← | exonuclease V (RecBCD complex), alpha chain |
| RA | 2,969,229 | A→C | intergenic (‑252/‑433) | rppH ← / → mutH | RNA pyrophosphohydrolase/methyl‑directed mismatch repair protein |
| RA | 3,028,941 | G→A | V24V (GTC→GTT) | ygfS ← | putative 4Fe‑4S ferredoxin‑type oxidoreductase subunit |
| RA | 3,110,040 | Δ1 bp | coding (488/708 nt) | yqgA → | DUF554 family putative inner membrane protein |
| RA | 3,266,892 | A→C | N58K (AAT→AAG) | tdcA ← | tdc operon transcriptional activator |
| RA | 3,299,392 | A→C | D140A (GAT→GCT) | yhbO → | stress‑resistance protein |
| RA | 3,375,330 | A→C | V154V (GTA→GTC) | dcuD → | putative transporter |
| RA | 3,376,226 | T→C | L453P (CTA→CCA) | dcuD → | putative transporter |
| RA | 3,560,455 | +G | 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 |
| RA | 3,633,194 | T→G | pseudogene (72/414 nt) | yhiL ← | pseudogene, DUF4049 family protein |
| RA | 3,658,425 | T→G | D20E (GAT→GAG) | gadE → | gad regulon transcriptional activator |
| RA | 3,792,236 | T→G | I106L (ATT→CTT) | kbl ← | glycine C‑acetyltransferase |
| RA | 3,835,453 | G→A | G159G (GGC→GGT) | yicJ ← | putative transporter |
| RA | 3,864,572 | A→G | Q225R (CAG→CGG) | yidP → | UTRA domain‑containing GntR family putative transcriptional regulator |
| RA | 3,874,610 | T→G | D184A (GAT→GCT) | dgoR ← | D‑galactonate catabolism operon transcriptional repressor |
| MC JC | 3,950,350 | Δ1,672 bp | [ilvL]–[ilvG] | [ilvL], ilvX, ilvG, [ilvG] | |
| RA | 3,955,324 | (G)6→7 | coding (1847/1851 nt) | ilvD → | dihydroxyacid dehydratase |
| RA | 3,988,430 | C→T | V213I (GTA→ATA) | hemX ← | putative uroporphyrinogen III methyltransferase |
| RA | 4,117,318 | T→G | H258P (CAT→CCT) | glpF ← | glycerol facilitator |
| RA | 4,182,878 | T→G | F545C (TTC→TGC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,236,154 | T→G | intergenic (+6/‑108) | yjbE → / → yjbF | extracellular polysaccharide production threonine‑rich protein/extracellular polysaccharide production lipoprotein |
| RA | 4,261,497 | T→G | intergenic (+191/‑172) | yjbM → / → dusA | uncharacterized protein/tRNA‑dihydrouridine synthase A |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,388,912 | A→C | N153K (AAT→AAG) | mscM ← | mechanosensitive channel protein, miniconductance |
| RA | 4,430,069 | T→G | F69C (TTC→TGC) | cycA → | D‑alanine/D‑serine/glycine transporter |
| RA | 4,436,026 | C→T | V180V (GTG→GTA) | cpdB ← | 2':3'‑cyclic‑nucleotide 2'‑phosphodiesterase |
| RA | 4,491,346 | T→G | N394H (AAC→CAC) | idnT ← | L‑idonate and D‑gluconate transporter |
| RA | 4,606,215 | (G)8→7 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196337 | 1211412 | 15076 | 3 [0] | [0] 4 | [icd]–mcrA | 24 genes [icd], ymfD, ymfE, lit, intE, xisE, ymfI, ymfJ, cohE, croE, ymfL, ymfM, oweE, aaaE, ymfR, beeE, jayE, ymfQ, stfP, tfaP, tfaE, stfE, pinE, mcrA |
| * | * | ÷ | NC_000913 | 1896928 | 1898281 | 1354 | 3 [2] | [0] 8 | [sdaA] | [sdaA] |
| * | * | ÷ | NC_000913 | 2684277 | 2685513 | 1237 | 4 [0] | [2] 6 | [glyA] | [glyA] |
| * | * | ÷ | NC_000913 | 2929579 | 2930928 | 1350 | 10 [0] | [0] 3 | sdaB | L‑serine dehydratase 2 |
| * | * | ÷ | NC_000913 | 3258300 | 3259646 | 1347 | 3 [0] | [0] 5 | tdcG | L‑serine dehydratase 3, anaerobic |
| * | * | ÷ | NC_000913 | 3423793–3424234 | 3424513–3424239 | 6–721 | 3 [2] | [2] 3 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381292 = | NA (NA) | 3 (0.160) | 3/280 | 2.1 | NA | noncoding (33/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381312 = | NA (NA) | noncoding (53/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 381689 | NA (NA) | 6 (0.310) | 5/280 | 1.5 | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 544389 | 7 (0.340) | 4 (0.200) | 3/298 | 2.2 | 36.4% | coding (904/1236 nt) | allC | allantoate amidohydrolase |
| ? | NC_000913 | 574591 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 2583809 | 12 (0.590) | 4 (0.210) | 3/282 | 2.1 | 28.2% | coding (1717/1980 nt) | aegA | putative oxidoreductase, FeS binding subunit/NAD/FAD‑binding subunit |
| ? | NC_000913 | = 2583847 | 9 (0.470) | coding (1679/1980 nt) | aegA | putative oxidoreductase, FeS binding subunit/NAD/FAD‑binding subunit | |||||
| * | ? | NC_000913 | 4227233 = | 19 (0.940) | 3 (0.160) | 3/280 | 2.1 | 20.1% | coding (3406/3684 nt) | metH | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| ? | NC_000913 | 4227352 = | 6 (0.310) | coding (3525/3684 nt) | metH | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent | |||||
| * | ? | NC_000913 | 4498180 = | NA (NA) | 24 (1.180) | 9/298 | 0.9 | NA | intergenic (+240/‑92) | intB/insC1 | pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA |
| ? | NC_000913 | = 4499511 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||