mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 30 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 699,722 | 0 | A | G | 55.2% | 5.3 / 81.7 | 69 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 4,353,218 | 0 | G | C | 54.5% | 3.1 / 11.8 | 12 | R115P (CGT→CCT) | yrpB | 2‑nitropropane dioxygenase |
| * | NC_002947 | 1,327,121 | 0 | C | T | 53.8% | 7.3 / 119.5 | 91 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 196,879 | 0 | G | A | 44.4% | 8.4 / 16.9 | 18 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 1,544,494 | 0 | C | G | 42.9% | 4.4 / 13.0 | 14 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,489 | 0 | C | A | 41.7% | 0.6 / 11.1 | 12 | intergenic (+48/+66) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 4,022,618 | 0 | T | G | 40.6% | 21.4 / 28.7 | 32 | intergenic (‑313/+355) | PP_3547/emrB | NAD(P)‑binding oxidoreductase/multidrug transporter permease |
| * | NC_002947 | 4,348,705 | 0 | A | G | 40.4% | 38.4 / 55.6 | 52 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,544,504 | 0 | T | G | 40.0% | ‑1.3 / 12.5 | 15 | intergenic (+63/+51) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,492 | 0 | G | C | 38.5% | 4.6 / 11.7 | 13 | intergenic (+51/+63) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 4,022,611 | 0 | A | G | 38.2% | 20.8 / 30.4 | 34 | intergenic (‑306/+362) | PP_3547/emrB | NAD(P)‑binding oxidoreductase/multidrug transporter permease |
| * | NC_002947 | 195,634 | 0 | C | T | 37.8% | 39.5 / 40.8 | 47 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,022,596 | 0 | A | C | 36.1% | 31.1 / 27.2 | 36 | intergenic (‑291/+377) | PP_3547/emrB | NAD(P)‑binding oxidoreductase/multidrug transporter permease |
| * | NC_002947 | 1,544,499 | 0 | C | G | 35.7% | 2.8 / 11.6 | 14 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 1,544,501 | 0 | G | C | 35.7% | 2.7 / 11.5 | 14 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947 | 4,791,927 | 0 | G | T | 31.0% | 38.9 / 13.1 | 29 | S638Y (TCC→TAC) | pvdI | non‑ribosomal peptide synthetase |
| * | NC_002947 | 4,022,633 | 0 | C | T | 29.6% | 34.1 / 16.4 | 27 | intergenic (‑328/+340) | PP_3547/emrB | NAD(P)‑binding oxidoreductase/multidrug transporter permease |
| * | NC_002947 | 4,791,923 | 0 | G | A | 29.6% | 37.3 / 11.9 | 28 | G639G (GGC→GGT) | pvdI | non‑ribosomal peptide synthetase |
| * | NC_002947 | 4,791,931 | 0 | G | A | 29.6% | 36.3 / 11.9 | 27 | H637Y (CAC→TAC) | pvdI | non‑ribosomal peptide synthetase |
| * | NC_002947 | 4,791,916 | 0 | C | A | 29.0% | 42.2 / 18.2 | 31 | A642S (GCT→TCT) | pvdI | non‑ribosomal peptide synthetase |
| Marginal new junction evidence (lowest skew 10 of 60 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 2957080 | 19 (0.590) | 6 (0.190) | 6/280 | 3.3 | 24.3% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947 | 2957165 = | 19 (0.610) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947 | = 4647595 | 17 (0.530) | 3 (0.130) | 3/212 | 3.6 | 20.4% | intergenic (+48/+83) | fusB/PP_4112 | elongation factor G 2/sulfate transporter |
| ? | NC_002947 | = 4647625 | 11 (0.470) | intergenic (+78/+53) | fusB/PP_4112 | elongation factor G 2/sulfate transporter | |||||
| * | ? | NC_002947 | = 2958779 | 15 (0.470) | 5 (0.160) | 5/278 | 3.6 | 24.8% | intergenic (+45/+97) | PP_2589/PP_2590 | aldehyde dehydrogenase family protein/ferric siderophore receptor |
| ? | NC_002947 | 2958841 = | 16 (0.520) | intergenic (+107/+35) | PP_2589/PP_2590 | aldehyde dehydrogenase family protein/ferric siderophore receptor | |||||
| * | ? | NC_002947 | 5382398 = | 18 (0.560) | 3 (0.120) | 3/220 | 3.7 | 18.9% | intergenic (+18/+115) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR |
| ? | NC_002947 | 5382496 = | 12 (0.490) | intergenic (+116/+17) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR | |||||
| * | ? | NC_002947 | = 174906 | NA (NA) | 6 (0.190) | 5/280 | 3.7 | NA | noncoding (1704/2902 nt) | PP_23SA | 23S ribosomal RNA |
| ? | NC_002947 | = 174936 | NA (NA) | noncoding (1734/2902 nt) | PP_23SA | 23S ribosomal RNA | |||||
| * | ? | NC_002947 | = 5988757 | 19 (0.590) | 4 (0.130) | 4/274 | 4.0 | 15.4% | intergenic (+51/‑495) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947 | 5988979 = | 26 (0.860) | intergenic (+273/‑273) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 4893579 | 22 (0.690) | 3 (0.120) | 3/236 | 4.0 | 16.3% | intergenic (+54/‑154) | pyk/PP_4302 | pyruvate kinase/urea transporter |
| ? | NC_002947 | = 4893604 | 13 (0.500) | intergenic (+79/‑129) | pyk/PP_4302 | pyruvate kinase/urea transporter | |||||
| * | ? | NC_002947 | = 428054 | 40 (1.250) | 3 (0.110) +26 bp |
3/238 | 4.0 | 8.7% | coding (953/957 nt) | PP_0351 | transmembrane sensor |
| ? | NC_002947 | 3279267 = | 37 (1.150) | coding (17/183 nt) | PP_2878 | hypothetical protein | |||||
| * | ? | NC_002947 | 3279267 = | 37 (1.150) | 3 (0.110) +21 bp |
3/248 | 4.1 | 11.7% | coding (17/183 nt) | PP_2878 | hypothetical protein |
| ? | NC_002947 | 5756593 = | 16 (0.500) | intergenic (+270/‑418) | glnG/PP_5050 | two‑component system DNA‑binding response regulator GlnL/GlnG/transposase | |||||
| * | ? | NC_002947 | = 2988809 | 29 (0.910) | 4 (0.130) | 4/282 | 4.1 | 12.3% | coding (533/951 nt) | PP_2613 | hypothetical protein |
| ? | NC_002947 | = 2988905 | 29 (0.930) | coding (437/951 nt) | PP_2613 | hypothetical protein | |||||