mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 125,085 | Δ1 bp | 100% | coding (2069/2664 nt) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| JC JC | 568,268 | IS1 (–) +9 bp | 100% | intergenic (+21/‑39) | renD → / → emrE | DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE |
| RA | 710,489 | G→C | 100% | A53G (GCT→GGT) | fur ← | DNA‑binding transcriptional dual regulator Fur |
| RA | 1,026,927 | A→T | 100% | V30E (GTG→GAG) | mgsA ← | methylglyoxal synthase |
| RA | 1,196,220 | C→T | 100% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | 100% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | 100% | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | 100% | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,913,579 | G→A | 18.2% | A413V (GCG→GTG) | prc ← | tail‑specific protease |
| RA | 1,940,584 | C→A | 100% | R351L (CGT→CTT) | mepM ← | peptidoglycan DD‑endopeptidase MepM |
| RA | 1,941,326 | C→T | 100% | D104N (GAT→AAT) | mepM ← | peptidoglycan DD‑endopeptidase MepM |
| RA | 1,956,975 | G→T | 100% | H11Q (CAC→CAA) | torZ ← | trimethylamine N‑oxide reductase 2 |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,270,605 | G→A | 15.1% | intergenic (+60/‑121) | mepS → / → pdeN | peptidoglycan DD‑endopeptidase/peptidoglycan LD‑carboxypeptidase/putative c‑di‑GMP phosphodiesterase PdeN |
| RA | 2,416,239 | C→T | 100% | T498M (ACG→ATG) | pta → | phosphate acetyltransferase |
| RA | 3,041,398 | T→G | 100% | L29R (CTT→CGT) | ygfZ → | folate‑binding protein |
| RA | 3,486,157 | A→C | 100% | E13A (GAA→GCA) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,060 | C→T | 23.2% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,366,854 | T→G | 9.7% | intergenic (‑81/+37) | dcuA ← / ← aspA | C4‑dicarboxylate transporter DcuA/aspartate ammonia‑lyase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 366214 | 366434 | 221 | 6 [4] | [4] 5 | [lacZ]–[lacI] | [lacZ],[lacI] |
| * | * | ÷ | NC_000913 | 1196277 | 1211449 | 15173 | 6 [4] | [4] 5 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 3423759–3424525 | 3424525 | 1–767 | 5 [4] | [4] 5 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3621201–3622296 | 3653115–3652031 | 29736–31915 | 5 [4] | [4] 5 | [rhsB]–[insH‑11] | [rhsB],yhhH,yhhI,yhhJ,rbbA,yhiI,yhiJ,yhiL,yhiM,yhiN,pitA,uspB,uspA,dtpB,rsmJ,prlC,rlmJ,gor,dinQ,agrA,agrB,arsR,arsB,arsC,yhiS,[insH‑11] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 381669 | NA (NA) | 3 (0.130) | 3/250 | NT | NA | noncoding (410/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381695 | NA (NA) | noncoding (436/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1048415 = | 21 (0.860) | 3 (0.130) | 3/252 | NT | 13.0% | coding (277/747 nt) | gfcC | capsule biosynthesis GfcC family protein |
| ? | NC_000913 | 1048443 = | 20 (0.860) | coding (249/747 nt) | gfcC | capsule biosynthesis GfcC family protein | |||||
| * | ? | NC_000913 | = 2354346 | 13 (0.530) | 3 (0.130) | 3/252 | NT | 17.4% | coding (82/1260 nt) | glpB | anaerobic glycerol‑3‑phosphate dehydrogenase subunit B |
| ? | NC_000913 | = 2354369 | 16 (0.690) | coding (105/1260 nt) | glpB | anaerobic glycerol‑3‑phosphate dehydrogenase subunit B | |||||
| * | ? | NC_000913 | = 3944978 | NA (NA) | 4 (0.170) | 3/252 | NT | 16.6% | noncoding (1275/2904 nt) | rrlC | 23S ribosomal RNA |
| ? | NC_000913 | = 4038811 | 21 (0.860) | noncoding (1293/2905 nt) | rrlA | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | 4295980 = | NA (NA) | 3 (0.130) | 3/250 | NT | NA | noncoding (32/37 nt) | other | REP321c |
| ? | NC_000913 | 4296062 = | NA (NA) | noncoding (1/37 nt) | other | REP321e | |||||