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 34 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,229,191 | 0 | C | A | 58.3% | 4.3 / 12.1 | 13 | intergenic (+126/+247) | yohP/dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| * | NC_000913 | 4,296,060 | 0 | C | T | 47.3% | ‑1.0 / 84.3 | 56 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 1,041,386 | 0 | G | C | 45.2% | 20.3 / 26.5 | 32 | G257A (GGA→GCA) | appA | phosphoanhydride phosphorylase |
| * | NC_000913 | 3,770,231 | 0 | C | G | 44.4% | 28.8 / 21.3 | 27 | intergenic (+85/+12) | yibU/yibH | pseudogene, H repeat‑associated protein/putative membrane fusion protein (MFP) component of efflux pump |
| * | NC_000913 | 4,164,132 | 0 | G | C | 41.7% | 17.8 / 13.1 | 24 | G165A (GGA→GCA) | btuB | vitamin B12/cobalamin outer membrane transporter |
| * | NC_000913 | 2,375,835 | 0 | C | G | 40.0% | 20.8 / 11.9 | 20 | G43A (GGG→GCG) | menC | O‑succinylbenzoyl‑CoA synthase |
| * | NC_000913 | 3,770,229 | 0 | C | G | 37.0% | 38.4 / 15.8 | 27 | intergenic (+83/+14) | yibU/yibH | pseudogene, H repeat‑associated protein/putative membrane fusion protein (MFP) component of efflux pump |
| * | NC_000913 | 3,770,233 | 0 | C | G | 37.0% | 38.8 / 14.4 | 27 | intergenic (+87/+10) | yibU/yibH | pseudogene, H repeat‑associated protein/putative membrane fusion protein (MFP) component of efflux pump |
| * | NC_000913 | 1,667,883 | 0 | C | G | 36.4% | 52.5 / 20.1 | 34 | V228L (GTC→CTC) | mlc | glucosamine anaerobic growth regulon transcriptional repressor; autorepressor |
| * | NC_000913 | 3,982,343 | 0 | G | C | 36.0% | 29.7 / 10.7 | 25 | intergenic (+71/‑32) | yifK/argX | putative APC family amino acid transporter/tRNA‑Arg |
| * | NC_000913 | 2,253,023 | 0 | C | G | 35.7% | 44.3 / 20.9 | 28 | A375P (GCG→CCG) | nupX | nucleoside permease |
| * | NC_000913 | 476,554 | 0 | C | G | 34.6% | 42.2 / 12.0 | 27 | noncoding (107/114 nt) | ffs | 4.5S sRNA component of Signal Recognition Particle (SRP) |
| * | NC_000913 | 1,563,398 | 0 | G | C | 34.6% | 30.1 / 15.5 | 27 | S779C (TCC→TGC) | dosP | oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator |
| * | NC_000913 | 1,984,188 | 0 | C | G | 34.6% | 34.9 / 21.8 | 27 | G294G (GGG→GGC) | araG | L‑arabinose ABC transporter ATPase |
| * | NC_000913 | 1,507,407 | 0 | G | C | 32.3% | 56.6 / 12.2 | 31 | V209V (GTG→GTC) | ydcP | putative peptidase |
| * | NC_000913 | 2,035,587 | 0 | C | G | 31.8% | 69.6 / 20.8 | 44 | intergenic (+344/‑248) | yedS/hchA | pseudogene, outer membrane protein homology; putative outer membrane protein/glyoxalase III and Hsp31 molecular chaperone |
| * | NC_000913 | 34,508 | 0 | G | C | 30.4% | 93.6 / 24.9 | 46 | G70A (GGA→GCA) | caiF | cai operon transcriptional activator |
| * | NC_000913 | 1,209,420 | 0 | C | G | 30.3% | 53.7 / 12.7 | 36 | pseudogene (200/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related |
| * | NC_000913 | 1,135,975 | 0 | G | C | 30.0% | 52.8 / 14.4 | 31 | A138P (GCC→CCC) | flgH | flagellar protein of basal‑body outer‑membrane L ring |
| * | NC_000913 | 2,764,594 | 0 | T | A | 29.7% | 56.7 / 10.5 | 38 | Q187L (CAA→CTA) | yfjL | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| Marginal new junction evidence (lowest skew 10 of 134 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 3255241 = | NA (NA) | 8 (0.240) | 7/110 | 1.9 | 16.7% | noncoding (25/103 nt) | REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | 3255294 = | 40 (1.220) | noncoding (78/103 nt) | REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP236 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913 | 2275832 = | 42 (1.080) | 5 (0.150) | 5/114 | 2.6 | 13.2% | coding (560/1026 nt) | yejE | microcin C ABC transporter permease |
| ? | NC_000913 | 2275868 = | 29 (0.850) | coding (596/1026 nt) | yejE | microcin C ABC transporter permease | |||||
| * | ? | NC_000913 | 3858193 = | 52 (1.340) | 7 (0.230) | 4/104 | 2.7 | 19.3% | coding (212/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein |
| ? | NC_000913 | 3858242 = | 17 (0.550) | coding (163/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein | |||||
| * | ? | NC_000913 | = 633243 | 31 (0.800) | 6 (0.170) | 5/116 | 2.7 | 15.7% | coding (235/1089 nt) | ybdH | putative oxidoreductase |
| ? | NC_000913 | = 633311 | 37 (1.070) | coding (167/1089 nt) | ybdH | putative oxidoreductase | |||||
| * | ? | NC_000913 | = 1328562 | 29 (0.750) | 6 (0.170) | 5/120 | 2.8 | 16.5% | coding (551/759 nt) | yciK | putative EmrKY‑TolC system oxoacyl‑(acyl carrier protein) reductase |
| ? | NC_000913 | = 1328705 | 34 (0.950) | coding (408/759 nt) | yciK | putative EmrKY‑TolC system oxoacyl‑(acyl carrier protein) reductase | |||||
| * | ? | NC_000913 | = 2962659 | 40 (1.030) | 5 (0.130) | 5/126 | 2.9 | 11.7% | coding (106/324 nt) | ppdC | putative prepilin peptidase‑dependent protein |
| ? | NC_000913 | = 2962936 | 37 (0.980) | coding (221/408 nt) | ygdB | DUF2509 family protein | |||||
| * | ? | NC_000913 | 2748976 = | 47 (1.210) | 4 (0.120) | 4/112 | 2.9 | 10.3% | coding (203/1287 nt) | yfjD | UPF0053 family inner membrane protein |
| ? | NC_000913 | 2749114 = | 29 (0.870) | coding (341/1287 nt) | yfjD | UPF0053 family inner membrane protein | |||||
| * | ? | NC_000913 | = 2508694 | 36 (0.930) | 4 (0.120) | 4/110 | 2.9 | 11.7% | coding (733/966 nt) | glk | glucokinase |
| ? | NC_000913 | = 2508732 | 30 (0.910) | coding (695/966 nt) | glk | glucokinase | |||||
| * | ? | NC_000913 | 4618175 = | 37 (0.950) | 4 (0.120) | 4/116 | 3.0 | 9.3% | noncoding (59/82 nt) | REP353 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP353 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | 4618735 = | 45 (1.300) | coding (507/1323 nt) | deoA | thymidine phosphorylase | |||||
| * | ? | NC_000913 | 4148708 = | 44 (1.130) | 4 (0.120) | 4/114 | 3.0 | 7.1% | coding (1558/1734 nt) | eptC | LPS heptose I phosphoethanolamine transferase |
| ? | NC_000913 | 4149027 = | 66 (1.940) | coding (1239/1734 nt) | eptC | LPS heptose I phosphoethanolamine transferase | |||||