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 |
| Marginal read alignment evidence (highest frequency 20 of 178 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 1,548,257 | 0 | T | G | 39.1% | 93.8 / 19.6 | 70 | Y557S (TAC→TCC) | maeA | malate dehydrogenase |
| * | NZ_CP009273 | 295,837 | 0 | A | G | 39.1% | 76.5 / 19.9 | 67 | L270P (CTC→CCC) | paoC | aldehyde oxidoreductase molybdenum‑binding subunit PaoC |
| * | NZ_CP009273 | 2,319,929 | 0 | T | G | 38.5% | 92.5 / 17.7 | 52 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NZ_CP009273 | 807,177 | 0 | T | G | 38.3% | 95.1 / 12.5 | 61 | V67G (GTG→GGG) | bioC | malonyl‑ACP O‑methyltransferase BioC |
| * | NZ_CP009273 | 2,145,134 | 0 | G | T | 38.2% | 64.5 / 15.0 | 34 | intergenic (+7/+58) | yegJ/pphC | DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC |
| * | NZ_CP009273 | 2,145,167 | 0 | G | T | 38.2% | 25.6 / 11.8 | 34 | intergenic (+40/+25) | yegJ/pphC | DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC |
| * | NZ_CP009273 | 2,871,023 | 0 | A | G | 37.6% | 131.3 / 28.1 | 93 | intergenic (+46/+905) | iap/cas2e | alkaline phosphatase isozyme conversion aminopeptidase/type I‑E CRISPR‑associated endoribonuclease Cas2e |
| * | NZ_CP009273 | 3,199,803 | 0 | T | A | 35.3% | 112.6 / 30.4 | 85 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| * | NZ_CP009273 | 595,032 | 0 | T | G | 33.3% | 64.5 / 16.8 | 43 | V288G (GTG→GGG) | cusA | Cu(+)/Ag(+) efflux RND transporter permease subunit CusA |
| * | NZ_CP009273 | 4,501,865 | 0 | A | C | 31.9% | 150.1 / 14.2 | 72 | L123V (TTG→GTG) | fecD | Fe(3+) dicitrate ABC transporter permease subunit FecD |
| * | NZ_CP009273 | 368,096 | 0 | T | G | 31.8% | 140.0 / 10.5 | 63 | L176V (TTA→GTA) | mhpD | 2‑keto‑4‑pentenoate hydratase |
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 31.6% | 174.0 / 30.1 | 79 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| * | NZ_CP009273 | 748,581 | 0 | T | A | 31.6% | 156.4 / 19.8 | 76 | intergenic (‑330/+60) | ybgD/gltA | fimbrial protein/citrate synthase |
| * | NZ_CP009273 | 341,039 | 0 | C | A | 31.4% | 215.9 / 37.1 | 86 | intergenic (+337/‑76) | BW25113_RS01680/BW25113_RS01685 | protein YahL/protein YahM |
| * | NZ_CP009273 | 360,751 | 0 | C | G | 31.0% | 138.5 / 18.0 | 58 | V331V (GTG→GTC) | lacI | DNA‑binding transcriptional repressor LacI |
| * | NZ_CP009273 | 2,897,074 | 0 | G | A | 30.8% | 144.0 / 44.4 | 79 | intergenic (+341/+1032) | ygcE/queE | FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE |
| * | NZ_CP009273 | 630,548 | 0 | A | T | 30.3% | 133.3 / 19.9 | 66 | D95E (GAT→GAA) | ybdM | ParB/RepB/Spo0J family partition protein |
| * | NZ_CP009273 | 360,759 | 0 | T | G | 30.2% | 105.6 / 19.8 | 53 | T329P (ACC→CCC) | lacI | DNA‑binding transcriptional repressor LacI |
| * | NZ_CP009273 | 4,326,718 | 0 | T | A | 30.0% | 154.4 / 21.2 | 83 | Y44F (TAT→TTT) | adiC | arginine/agmatine antiporter |
| * | NZ_CP009273 | 2,503,359 | 0 | A | C | 29.7% | 156.6 / 10.7 | 76 | D84A (GAC→GCC) | yfeO | ion channel protein |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | 19796 = | NA (NA) | 43 (0.440) | 43/496 | 3.3 | 43.4% | intergenic (‑1/+15) | BW25113_RS25960/BW25113_RS00100 | fimbrial family protein/IS1‑like element IS1A family transposase |
| ? | NZ_CP009273 | = 651723 | 56 (0.570) | intergenic (‑299/‑290) | dcuC/pagP | anaerobic C4‑dicarboxylate transporter DcuC/lipid IV(A) palmitoyltransferase PagP | |||||
| * | ? | NZ_CP009273 | = 20563 | NA (NA) | 32 (0.330) | 32/496 | 5.2 | 34.8% | intergenic (‑55/+252) | BW25113_RS00100/rpsT | IS1‑like element IS1A family transposase/30S ribosomal protein S20 |
| ? | NZ_CP009273 | 651716 = | 60 (0.610) | intergenic (‑292/‑297) | dcuC/pagP | anaerobic C4‑dicarboxylate transporter DcuC/lipid IV(A) palmitoyltransferase PagP | |||||
| * | ? | NZ_CP009273 | = 651723 | 56 (0.570) | 21 (0.210) | 21/496 | 8.1 | 19.5% | intergenic (‑299/‑290) | dcuC/pagP | anaerobic C4‑dicarboxylate transporter DcuC/lipid IV(A) palmitoyltransferase PagP |
| ? | NZ_CP009273 | = 1046001 | 117 (1.190) | intergenic (+15/+418) | BW25113_RS05135/cspH | IS1‑like element IS1D family transposase/cold shock‑like protein CspH | |||||
| * | ? | NZ_CP009273 | 286345 = | NA (NA) | 15 (0.150) | 15/496 | 10.3 | 21.1% | intergenic (+2/+15) | BW25113_RS23270/BW25113_RS01405 | YfjI family protein/IS1‑like element IS1B family transposase |
| ? | NZ_CP009273 | = 651723 | 56 (0.570) | intergenic (‑299/‑290) | dcuC/pagP | anaerobic C4‑dicarboxylate transporter DcuC/lipid IV(A) palmitoyltransferase PagP | |||||
| * | ? | NZ_CP009273 | = 287112 | NA (NA) | 14 (0.140) | 14/496 | 10.7 | 18.9% | intergenic (‑55/‑99) | BW25113_RS01405/BW25113_RS01410 | IS1‑like element IS1B family transposase/protein YagJ |
| ? | NZ_CP009273 | 651716 = | 60 (0.610) | intergenic (‑292/‑297) | dcuC/pagP | anaerobic C4‑dicarboxylate transporter DcuC/lipid IV(A) palmitoyltransferase PagP | |||||
| * | ? | NZ_CP009273 | 1203246 = | 78 (0.790) | 9 (0.100) | 9/464 | 12.4 | 9.7% | coding (290/630 nt) | BW25113_RS05990 | protein StfP |
| ? | NZ_CP009273 | 1205075 = | 94 (1.020) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 692197 | 55 (0.560) | 5 (0.070) | 4/340 | 12.6 | 10.1% | intergenic (‑1/+15) | BW25113_RS03450/BW25113_RS03455 | tRNA‑Met/tRNA‑Gln |
| ? | NZ_CP009273 | 692591 = | 51 (0.760) | intergenic (‑2/+378) | BW25113_RS03470/asnB | tRNA‑Met/asparagine synthase B | |||||
| * | ? | NZ_CP009273 | = 1203261 | 75 (0.760) | 9 (0.100) | 8/464 | 13.0 | 9.9% | coding (305/630 nt) | BW25113_RS05990 | protein StfP |
| ? | NZ_CP009273 | = 1205058 | 94 (1.020) | coding (57/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 4532507 | 120 (1.220) | 7 (0.070) | 7/478 | 13.9 | 5.7% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 117 (1.240) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NZ_CP009273 | 4532499 = | 123 (1.250) | 6 (0.060) | 6/478 | 14.6 | 4.8% | intergenic (+49/‑433) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | 4532813 = | 117 (1.240) | intergenic (+363/‑119) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||