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 |
| Marginal read alignment evidence (highest frequency 20 of 22 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009273 | 2,045,540 | 0 | T | . | 57.1% | ‑4.8 / 11.5 | 7 | intergenic (+45/+217) | yeeJ/yeeL | putative adhesin/pseudogene, glycosyltransferase homology |
| * | CP009273 | 4,617,910 | 1 | . | G | 46.2% | ‑6.0 / 28.9 | 13 | coding (779/1233 nt) | nadR | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| * | CP009273 | 4,617,910 | 2 | . | T | 46.2% | 18.3 / 28.1 | 13 | coding (779/1233 nt) | nadR | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| * | CP009273 | 4,617,910 | 3 | . | G | 46.2% | ‑6.0 / 29.0 | 13 | coding (779/1233 nt) | nadR | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| * | CP009273 | 4,617,910 | 4 | . | G | 46.2% | 13.3 / 30.3 | 13 | coding (779/1233 nt) | nadR | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| * | CP009273 | 4,178,500 | 0 | C | T | 45.5% | 2.1 / 28.8 | 22 | R1075C (CGT→TGT) | rpoC | RNA polymerase, beta prime subunit |
| * | CP009273 | 1,623,362 | 0 | A | . | 33.3% | 25.0 / 12.0 | 12 | intergenic (+67/‑110) | rspR/ydfZ | transcriptional repressor for rspAB/selenoprotein, function unknown |
| * | CP009273 | 910,669 | 0 | A | T | 25.3% | 132.0 / 16.5 | 85 | intergenic (‑356/+139) | ybjE/aqpZ | putative transporter/aquaporin Z |
| * | CP009273 | 2,823,534 | 0 | G | T | 25.0% | 34.7 / 13.4 | 24 | A121A (GCG→GCT) | srlQ | D‑arabinose 5‑phosphate isomerase |
| * | CP009273 | 3,618,160 | 0 | A | G | 23.8% | 81.5 / 25.9 | 42 | G141G (GGA→GGG) | yhhI | putative transposase |
| * | CP009273 | 2,257,707 | 0 | T | A | 20.7% | 74.1 / 15.1 | 29 | A122A (GCT→GCA) | setB | lactose/glucose efflux system |
| * | CP009273 | 3,452,005 | 0 | A | . | 20.7% | 89.1 / 19.5 | 29 | coding (308/1482 nt) | gspE | general secretory pathway component, cryptic |
| * | CP009273 | 2,147,286 | 0 | G | A | 20.5% | 96.3 / 18.2 | 39 | intergenic (+26/‑211) | sibB/mdtA | sRNA antisense regulator of toxic IbsB protein/multidrug efflux system, subunit A |
| * | CP009273 | 3,451,996 | 0 | T | . | 20.0% | 87.1 / 19.3 | 30 | coding (299/1482 nt) | gspE | general secretory pathway component, cryptic |
| * | CP009273 | 3,451,997 | 0 | G | . | 20.0% | 78.8 / 21.7 | 30 | coding (300/1482 nt) | gspE | general secretory pathway component, cryptic |
| * | CP009273 | 3,451,998 | 0 | A | . | 20.0% | 89.6 / 19.4 | 30 | coding (301/1482 nt) | gspE | general secretory pathway component, cryptic |
| * | CP009273 | 3,451,999 | 0 | A | . | 20.0% | 91.0 / 19.4 | 30 | coding (302/1482 nt) | gspE | general secretory pathway component, cryptic |
| * | CP009273 | 3,452,000 | 0 | T | . | 20.0% | 88.3 / 19.3 | 30 | coding (303/1482 nt) | gspE | general secretory pathway component, cryptic |
| * | CP009273 | 3,452,001 | 0 | G | . | 20.0% | 78.8 / 21.7 | 30 | coding (304/1482 nt) | gspE | general secretory pathway component, cryptic |
| * | CP009273 | 3,452,002 | 0 | A | . | 20.0% | 92.3 / 19.4 | 30 | coding (305/1482 nt) | gspE | general secretory pathway component, cryptic |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 370385 | 43 (1.820) | 3 (0.140) | 3/182 | 1.6 | 7.1% | intergenic (+48/‑530) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| ? | CP009273 | = 372977 | NA (NA) | noncoding (187/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | = 2806584 | 21 (0.660) | 4 (0.130) | 4/266 | 1.9 | 16.1% | coding (610/1539 nt) | emrB | multidrug efflux system protein |
| ? | CP009273 | 3124314 = | NA (NA) | coding (778/1017 nt) | insH1 | IS5 transposase and trans‑activator | |||||
| * | ? | CP009273 | 370704 = | 42 (1.330) | 8 (0.290) | 3/230 | 1.9 | 20.0% | noncoding (319/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | 372963 = | 28 (1.030) | noncoding (173/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | 353187 = | NA (NA) | 4 (0.130) +C |
4/266 | 1.9 | 14.4% | intergenic (+22/+315) | codA/cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| ? | CP009273 | = 353585 | 24 (0.760) | coding (817/900 nt) | cynR | transcriptional activator of cyn operon; autorepressor | |||||
| * | ? | CP009273 | = 1802194 | 39 (1.230) | 3 (0.100) | 3/254 | 2.1 | 7.7% | coding (142/861 nt) | yniA | fructosamine kinase family protein |
| ? | CP009273 | 3487049 = | 35 (1.170) | coding (1123/1182 nt) | tsgA | putative transporter | |||||
| * | ? | CP009273 | = 3417837 | NA (NA) | 3 (0.100) | 3/262 | 2.2 | 18.0% | noncoding (2306/2904 nt) | rrlD | 23S ribosomal RNA of rrnD operon |
| ? | CP009273 | 3667374 = | 14 (0.440) | coding (653/1014 nt) | yhjD | inner membrane putative BrbK family alternate lipid exporter | |||||
| * | ? | CP009273 | = 2250177 | 19 (0.600) | 3 (0.100) | 3/264 | 2.2 | 8.5% | coding (638/1251 nt) | psuT | putative nucleoside transporter |
| ? | CP009273 | 3883404 = | 46 (1.480) | coding (1315/1416 nt) | tnaA | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent | |||||
| * | ? | CP009273 | = 55775 | 21 (0.660) | 5 (0.160) | 3/266 | 2.2 | 19.4% | coding (1335/2355 nt) | lptD | LPS assembly OM complex LptDE, beta‑barrel component |
| ? | CP009273 | = 270051 | NA (NA) | noncoding (810/1195 nt) | IS5 | repeat region | |||||