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 |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 124,241 | C→T | Q409* (CAG→TAG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 135,167 | G→T | T139N (ACC→AAC) | speD ← | S‑adenosylmethionine decarboxylase proenzyme |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 674,768 | G→T | R6S (CGC→AGC) | leuS ← | leucine‑‑tRNA ligase |
| RA | 696,470 | C→T | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 754,446 | A→G | L8P (CTC→CCC) | gltA ← | citrate synthase |
| RA | 760,485 | G→A | G594S (GGC→AGC) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 1,151,736 | T→C | V41A (GTT→GCT) | acpP → | acyl carrier protein |
| JC JC | 1,293,032 | IS1 (–) +8 bp | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| JC JC | 1,572,474 | IS5 (+) +4 bp | coding (2726‑2729/2796 nt) | pqqL ← | putative zinc peptidase |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,132,787 | A→C | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,368,101 | T→C | A21A (GCT→GCC) | arnA → | fused UDP‑4‑amino‑4‑deoxy‑L‑arabinose formyltransferase/UDP‑glucuronate dehydrogenase |
| RA | 2,661,821 | C→G | C104S (TGC→TCC) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,737,631 | +A | coding (33/48 nt) | pheL → | phe operon leader peptide |
| RA | 3,041,634 | A→C | T108P (ACC→CCC) | ygfZ → | folate‑binding protein |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| MC JC | 3,815,859 | Δ82 bp | [rph] | [rph] | |
| MC JC | 4,001,645 | Δ5 bp | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,033,610 | G→A | G156S (GGT→AGT) | trkH → | K(+) transporter TrkH |
| RA | 4,184,543 | C→A | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,196,219 | A→C | intergenic (‑120/+113) | thiC ← / ← rsd | phosphomethylpyrimidine synthase/regulator of sigma D |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1209603 | 1209618 | 16 | 54 [0] | [0] 49 | stfE | e14 prophage; putative side tail fiber protein fragment |
| * | * | ÷ | NC_000913 | 3423729–3424543 | 3424543 | 1–815 | 24 [22] | [23] 24 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 566777 = | NA (NA) | 2589 (43.020) | 270/280 | 0.0 | 97.9% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 56 (0.920) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | = 572471 | 56 (0.920) | 20 (0.430) +34 bp |
15/214 | 2.3 | 36.4% | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein |
| ? | NC_000913 | = 2170235 | 36 (0.590) | noncoding (65/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 2 (0.030) | 42 (0.780) | 37/250 | 0.3 | 97.9% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 0 (0.000) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 3 (0.050) | 48 (0.890) | 41/250 | 0.2 | 97.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 0 (0.000) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1411899 = | 88 (1.450) | 62 (1.250) | 47/230 | 0.0 | 49.6% | coding (50/936 nt) | ttcA | tRNA cytosine(32) 2‑sulfurtransferase TtcA |
| ? | NC_000913 | = 1434958 | 54 (1.090) | pseudogene (51/51 nt) | ttcC | putative tRNA 2‑thiocytidine (s(2)C32) synthase | |||||