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 197,968 G→A 8.5% S14N (AGC→AAC)  bamA → BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 264,098 G→T 100% L50L (CTC→CTA)  ykfH ← uncharacterized protein
RA 269,605 A→T 9.4% V193E (GTG→GAG)  perR ← CP4‑6 prophage; putative DNA‑binding transcriptional regulator
RA 275,065 G→A 100% T18I (ACC→ATC)  insH1 ← IS5 transposase and trans‑activator
RA 282,138 A→G 10.9% intergenic (‑155/‑140) yagA ← / → yagE CP4‑6 prophage; putative DNA‑binding transcriptional regulator/2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage
RA 430,866 G→A 10.2% A88T (GCA→ACA)  yajD → HNH nuclease family protein
RA 482,230 G→A 100% P725L (CCG→CTG)  acrB ← multidrug efflux system protein
RA 990,097 C→A 7.1% W87L (TGG→TTG)  pncB ← nicotinate phosphoribosyltransferase
RA 1,197,502 C→T 100% G11R (GGA→AGA)  ymfD ← e14 prophage; putative SAM‑dependent methyltransferase
RA 1,197,717 C→A 20.7% C174F (TGC→TTC)  ymfE ← e14 prophage; putative inner membrane protein
RA 1,544,022 1 bp→AA 100% coding (39/1389 nt) narU ← nitrate/nitrite transporter
RA 1,774,576 G→A 100% G263E (GGG→GAG)  ydiB → quinate/shikimate 5‑dehydrogenase, NAD(P)‑binding
MC JC 1,978,503 Δ776 bp 100% insB1–insA insB1, insA
RA 2,106,741 A→T 100% S162S (TCT→TCA)  wbbH ← O‑antigen polymerase
RA 2,168,532 G→T 17.1% intergenic (‑226/‑180) yegR ← / → yegS uncharacterized protein/phosphatidylglycerol kinase, metal‑dependent
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 2,637,439 C→A 9.8% intergenic (‑83/+35) der ← / ← bamB GTPase; multicopy suppressor of ftsJ/BamABCDE complex OM biogenesis lipoprotein
RA 2,679,525 G→T 100% A1074D (GCT→GAT)  yphG ← DUF4380 domain‑containing TPR repeat protein
RA 2,795,396 C→A 100% Q382K (CAG→AAG)  gabP → gamma‑aminobutyrate transporter
RA 2,817,170 C→A 100% E112* (GAA→TAA)  yqaB ← fructose‑1‑P and 6‑phosphogluconate phosphatase
RA 2,893,414 A→T 8.2% K253I (AAA→ATA)  ygcN → putative oxidoreductase
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
RA 3,601,171 C→T 14.8% A306T (GCA→ACA)  ftsX ← putative ABC transporter permease
RA 4,002,902 A→T 6.4% S98T (TCA→ACA)  yigG ← PRK11371 family inner membrane protein
RA 4,002,903 A→T 6.5% C97* (TGT→TGA)  yigG ← PRK11371 family inner membrane protein
RA 4,111,662 G→A 100% L179L (CTG→TTG)  yiiQ ← DUF1454 family putative periplasmic protein
RA 4,296,042 C→T 21.2% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,362:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,513,088 C→G 9.2% A102P (GCG→CCG)  fecC ← ferric citrate ABC transporter permease
RA 4,604,698 C→A 100% A186E (GCA→GAA)  bglJ → bgl operon transcriptional activator

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913_3_hsa_tpiA 3423760–3424544 3424544 1–785 15 [14] [14] 15 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_hsa_tpiA = 12994980 (0.000)44 (1.180) 35/264 NT 100% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913_3_hsa_tpiA 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913_3_hsa_tpiA = 230471917 (0.440)3 (0.080) 3/268 NT 13.1% noncoding (303/655 nt) REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
?NC_000913_3_hsa_tpiA = 2304926 23 (0.610)noncoding (510/655 nt) REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences
* ? NC_000913_3_hsa_tpiA 3426836 =NA (NA)5 (0.140) 4/258 NT NA intergenic (‑53/+122) rrlD/alaU 23S ribosomal RNA of rrnD operon/tRNA‑Ala
?NC_000913_3_hsa_tpiA 3426854 = NA (NA)intergenic (‑71/+104) rrlD/alaU 23S ribosomal RNA of rrnD operon/tRNA‑Ala
* ? NC_000913_3_hsa_tpiA 3730307 =31 (0.810)4 (0.110) 4/264 NT 11.9% coding (459/1323 nt) xylA D‑xylose isomerase
?NC_000913_3_hsa_tpiA 3730327 = 29 (0.780)coding (439/1323 nt) xylA D‑xylose isomerase
* ? NC_000913_3_hsa_tpiA = 454267230 (0.780)3 (0.080) 3/254 NT 9.8% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913_3_hsa_tpiA = 4542968 27 (0.750)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)