mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 165,749 | Δ1 bp | intergenic (+42/‑5) | rrnI‑5S → / → trnI‑Asn | ribosomal RNA‑5S/tRNA‑Asn |
| RA | 165,751 | Δ1 bp | intergenic (+44/‑3) | rrnI‑5S → / → trnI‑Asn | ribosomal RNA‑5S/tRNA‑Asn |
| RA | 165,826 | +C | intergenic (+1/‑4) | trnI‑Asn → / → trnI‑Thr | tRNA‑Asn/tRNA‑Thr |
| RA | 166,037 | +T | intergenic (+4/‑27) | trnI‑Gly → / → trnI‑Arg | tRNA‑Gly/tRNA‑Arg |
| RA | 166,345 | Δ1 bp | intergenic (+17/‑155) | trnI‑Ala → / → rrnH‑16S | tRNA‑Ala/ribosomal RNA‑16S |
| RA | 490,812 | G→T | P78T (CCT→ACT) | ydzK ← | hypothetical protein |
| RA | 557,870 | (T)5→6 | intergenic (+421/‑3) | yddT → / → ydzN | putative exported phage protein/hypothetical protein |
| RA | 608,219 | (A)5→6 | intergenic (‑144/+27) | ydgF ← / ← dinB | putative amino acid permease/nuclease inhibitor |
| RA | 756,382 | C→A | P82T (CCA→ACA) | cotJB → | component of the inner spore coat |
| RA | 1,176,825 | A→G | L143L (CTT→CTC) | yitG ← | putative efflux transporter |
| RA | 1,176,945 | A→G | Y103Y (TAT→TAC) | yitG ← | putative efflux transporter |
| RA | 1,177,136 | G→A | L40F (CTT→TTT) | yitG ← | putative efflux transporter |
| RA | 1,194,908 | (T)8→9 | intergenic (+81/‑126) | yitZ → / → argC | putative transport protein/N‑acetylglutamate gamma‑semialdehyde dehydrogenase |
| RA | 1,195,173 | A→G | H47R (CAT→CGT) | argC → | N‑acetylglutamate gamma‑semialdehyde dehydrogenase |
| RA | 1,195,446 | T→C | I138T (ATT→ACT) | argC → | N‑acetylglutamate gamma‑semialdehyde dehydrogenase |
| RA | 1,317,152 | +GT | intergenic (+23/+5) | phrA → / ← yjpA | secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
| RA | 1,317,158 | (T)5→6 | coding (257/258 nt) | yjpA ← | putative enzyme |
| RA | 2,097,087 | (A)7→8 | intergenic (‑111/+39) | azoJ ← / ← yocK | FMN‑dependent NADH‑azoreductase/putative general stress protein |
| RA | 2,271,424 | T→C | R78R (AGA→AGG) | uvrX ← | lesion bypass phage DNA polymerase; phage SPbeta |
| RA | 2,271,505 | C→T | V51V (GTG→GTA) | uvrX ← | lesion bypass phage DNA polymerase; phage SPbeta |
| RA | 2,271,523 | A→C | D45E (GAT→GAG) | uvrX ← | lesion bypass phage DNA polymerase; phage SPbeta |
| RA | 2,480,646 | 2 bp→AT | intergenic (+21/+103) | zwf → / ← gndA | glucose‑6‑phosphate 1‑dehydrogenase (NADP‑dependent)/NADP+‑dependent 6‑P‑gluconate dehydrogenase |
| RA | 2,480,654 | Δ1 bp | intergenic (+29/+96) | zwf → / ← gndA | glucose‑6‑phosphate 1‑dehydrogenase (NADP‑dependent)/NADP+‑dependent 6‑P‑gluconate dehydrogenase |
| RA | 2,480,667 | Δ1 bp | intergenic (+42/+83) | zwf → / ← gndA | glucose‑6‑phosphate 1‑dehydrogenase (NADP‑dependent)/NADP+‑dependent 6‑P‑gluconate dehydrogenase |
| RA | 2,581,732 | (T)6→7 | intergenic (‑115/+39) | pstS ← / ← pbpA | phosphate ABC transporter (phosphate binding lipoprotein)/transpeptidase (penicillin‑binding protein 2A) |
| RA | 3,770,066 | (A)8→9 | intergenic (‑613/+38) | ywzE ← / ← csbD | conserved protein of unknown function (putative phage interference protein)/stress response protein |
| RA | 3,935,825 | Δ1 bp | coding (1190/1191 nt) | rlmI ← | large subunit ribosomal RNA m5C1962 methyltransferase |
| RA | 3,948,008 | T→A | L284H (CTT→CAT) | tyrZ → | tyrosyl‑tRNA synthetase |
| RA | 4,155,395 | (A)5→6 | intergenic (‑186/+38) | trnY‑Lys ← / ← purA | tRNA‑Lys/adenylosuccinate synthetase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000964 | 161166–161240 | 161471 | 232–306 | 4 [3] | [3] 4 | rrnI‑16S | ribosomal RNA‑16S |
| * | * | ÷ | NC_000964 | 161535–164898 | 165474–164903 | 6–3940 | 4 [3] | [3] 6 | [rrnI‑16S]–[rrnI‑23S] | [rrnI‑16S],[rrnI‑23S] |
| * | * | ÷ | NC_000964 | 166747 | 171073–170393 | 3647–4327 | 4 [3] | [3] 4 | [rrnH‑16S]–[rrnH‑23S] | [rrnH‑16S],[rrnH‑23S] |
| * | * | ÷ | NC_000964 | 171577–171679 | 176091–172533 | 855–4515 | 4 [3] | [3] 5 | [rrnG‑16S]–[rrnG‑23S] | [rrnG‑16S],[rrnG‑23S] |
| * | * | ÷ | NC_000964 | 1177359 | 1194824 | 17466 | 4 [3] | [0] 21 | yitH–[yitZ] | yitH,yitI,samT,yitK,yitL,yitM,yitO,yitP,yizB,yitQ,yitR,nprB,fakBB,yitT,ipi,yizC,ribZC,yitV,yitW,yitY,[yitZ] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000964 | = 1153702 | 10 (0.260) | 5 (0.140) | 5/478 | 2.8 | 34.8% | intergenic (+81/‑87) | yisL/wprA | putative integral membrane protein/cell wall‑associated protease |
| ? | NC_000964 | 1153714 = | 9 (0.240) | intergenic (+93/‑75) | yisL/wprA | putative integral membrane protein/cell wall‑associated protease | |||||
| * | ? | NC_000964 | 1194825 = | 0 (0.000) | 18 (0.550) +36 bp |
17/420 | 0.8 | 61.9% | coding (493/495 nt) | yitZ | putative transport protein |
| ? | NC_000964 | 3788113 = | 26 (0.680) | intergenic (‑110/+313) | atpI/upp | ATP synthase (subunit i)/uracil phosphoribosyltransferase | |||||