mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0b
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 444,779 | C→T | 85.7% | W440* (TGG→TAG) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 927,772 | Δ1 bp | 12.5% | intergenic (‑266/‑279) | trxB ← / → lrp | thioredoxin reductase, FAD/NAD(P)‑binding/leucine‑responsive global transcriptional regulator |
| RA | 982,560 | T→A | 23.6% | intergenic (‑122/+481) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 1,414,184 | T→C | 12.7% | R105R (AGA→AGG) | racR ← | Rac prophage; putative DNA‑binding transcriptional regulator |
| RA | 2,088,157 | G→T | 44.7% | G48C (GGC→TGC) | hisH → | imidazole glycerol phosphate synthase, glutamine amidotransferase subunit with HisF |
| RA | 2,111,876 | G→C | 53.9% | L4V (CTT→GTT) | wcaK ← | colanic acid biosynthesis protein |
| RA | 2,279,621 | T→A | 9.3% | intergenic (+6/‑69) | yejM → / → proL | essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor/tRNA‑Pro |
| RA | 2,305,945 | C→G | 69.3% | R95P (CGT→CCT) | ompC ← | outer membrane porin protein C |
| JC JC | 2,400,257 | IS5 (+) +4 bp | 36.4% | intergenic (‑137/‑780) | lrhA ← / → alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2 |
| RA | 2,420,353 | A→C | 22.7% | intergenic (‑86/+135) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| RA | 2,420,394 | G→T | 33.4% | intergenic (‑127/+94) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| RA | 2,506,454 | C→T | 17.3% | intergenic (‑269/‑67) | mntH ← / → nupC | manganese/divalent cation transporter/nucleoside (except guanosine) transporter |
| RA | 2,642,401 | C→T | 8.8% | T1082T (ACG→ACA) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,683,180 | C→T | 10.8% | Q426Q (CAG→CAA) | glrK ← | sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR |
| RA | 2,854,442 | A→G | 11.8% | L51P (CTG→CCG) | ygbI ← | DeoR family putative transcriptional regulator |
| JC JC | 3,178,254 | IS5 (+) +4 bp | 15.8% | coding (56‑59/291 nt) | yqiC → | BMFP family putative fusogenic protein |
| RA | 3,370,206 | C→A | 17.8% | E192* (GAG→TAG) | sspA ← | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog |
| RA | 3,529,197 | A→G | 87.8% | S11P (TCA→CCA) | envZ ← | sensory histidine kinase in two‑component regulatory system with OmpR |
| JC | 3,676,871:1 | +TAA | 74.8% | intergenic (‑64/+119) | dctA ← / ← yhjK | C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase |
| RA | 3,855,442 | T→G | 10.3% | pseudogene (1522/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| RA | 4,327,926 | C→A | 16.1% | intergenic (‑180/+145) | adiY ← / ← adiA | adi system transcriptional activator/arginine decarboxylase |
| RA | 4,390,286 | C→A | 81.4% | T61N (ACT→AAT) | hfq → | global sRNA chaperone; HF‑I, host factor for RNA phage Q beta replication |
| RA | 4,515,090 | Δ1 bp | 11.1% | coding (531/789 nt) | yjhI ← | putative DNA‑binding transcriptional regulator |
| RA | 4,601,044 | C→A | 31.0% | intergenic (+224/‑169) | prfC → / → osmY | peptide chain release factor RF‑3/periplasmic protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | NA (NA) | 58 (1.680) | 42/270 | NT | NA | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | 360128 = | NA (NA) | 3 (0.090) | 4/254 | NT | 6.4% | intergenic (‑62/+533) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | 360133 = | 47 (1.360) | intergenic (‑67/+528) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | = 377125 | NA (NA) | 3 (0.090) | 3/256 | NT | NA | coding (319/366 nt) | insC1 | IS2 repressor TnpA |
| ? | CP009273 | = 377151 | NA (NA) | coding (345/366 nt) | insC1 | IS2 repressor TnpA | |||||
| * | ? | CP009273 | 1045234 = | 24 (0.690) | 23 (0.660) | 20/270 | NT | 60.5% | intergenic (‑34/‑55) | gfcA/insA | O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA |
| ? | CP009273 | = 1973123 | 6 (0.170) | intergenic (‑669/‑111) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | 1203246 = | 3 (0.090) | 13 (0.430) | 12/238 | NT | 87.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 1 (0.030) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 3 (0.090) | 18 (0.590) | 13/238 | NT | 90.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 1 (0.030) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1973115 = | 6 (0.170) | 30 (0.870) | 22/270 | NT | 83.3% | intergenic (‑661/‑119) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||
| * | ? | CP009273 | = 2096424 | NA (NA) | 4 (0.120) | 4/270 | NT | 12.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | CP009273 | = 2160623 | 28 (0.810) | intergenic (+113/+160) | yegQ/ogrK | putative peptidase/positive regulator of P2 growth (insertion of P2 ogr gene into the chromosome) | |||||
| * | ? | CP009273 | = 3721251 | 65 (1.880) | 3 (0.090) | 3/254 | NT | 4.6% | noncoding (619/1443 nt) | IS150 | repeat region |
| ? | CP009273 | = 3721265 | 63 (1.940) | noncoding (633/1443 nt) | IS150 | repeat region | |||||
| * | ? | CP009273 | = 4145500 | 18 (0.520) | 12 (0.370) | 10/256 | NT | 36.3% | coding (572/1005 nt) | argC | N‑acetyl‑gamma‑glutamylphosphate reductase, NAD(P)‑binding |
| ? | CP009273 | 4145821 = | 25 (0.760) | coding (893/1005 nt) | argC | N‑acetyl‑gamma‑glutamylphosphate reductase, NAD(P)‑binding | |||||
| * | ? | CP009273 | = 4602145 | 27 (0.780) | 3 (0.090) | 4/248 | NT | 10.2% | intergenic (+39/‑83) | ytjA/yjjU | uncharacterized protein/putative patatin‑like family phospholipase |
| ? | CP009273 | = 4602148 | 28 (0.880) | intergenic (+42/‑80) | ytjA/yjjU | uncharacterized protein/putative patatin‑like family phospholipase | |||||