mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 43 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | JE3692‑4 | 1,327,121 | 0 | C | T | 58.1% | 3.6 / 175.8 | 129 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | JE3692‑4 | 699,722 | 0 | A | G | 52.0% | ‑5.8 / 112.9 | 75 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | JE3692‑4 | 4,360,849 | 0 | A | G | 40.9% | 146.5 / 203.0 | 155 | intergenic (‑70/+404) | PP_3820/PP_3821 | Group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | JE3692‑4 | 3,636,954 | 0 | G | C | 38.2% | 43.1 / 39.6 | 62 | G226G (GGC→GGG) | PP_3195 | conserved protein of unknown function |
| * | JE3692‑4 | 2,184,203 | 0 | T | C | 36.6% | 122.2 / 68.2 | 93 | N269N (AAT→AAC) | PP_1931 | conserved protein of unknown function |
| * | JE3692‑4 | 196,351 | 0 | C | G | 35.3% | 289.6 / 255.3 | 201 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 195,634 | 0 | C | T | 34.8% | 298.3 / 195.7 | 181 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 324,670 | 0 | C | T | 33.6% | 141.5 / 65.8 | 107 | intergenic (‑430/‑45) | PP_0267/PP_0268 | putative Outer membrane ferric siderophore receptor/outer‑membrane porin D |
| * | JE3692‑4 | 1,927,172 | 0 | T | C | 32.6% | 77.8 / 20.0 | 49 | intergenic (+15/+46) | PP_1720/PP_1721 | Alcohol dehydrogenase, zinc‑containing/putative phosphoserine phosphatase |
| * | JE3692‑4 | 4,864,608 | 0 | G | C | 32.4% | 60.2 / 20.4 | 39 | intergenic (‑135/+162) | PP_4267/PP_4268 | Recombination protein RecR/nucleoid‑associated broad specificity regulator |
| * | JE3692‑4 | 2,184,204 | 0 | G | C | 31.0% | 178.9 / 48.4 | 93 | V270L (GTC→CTC) | PP_1931 | conserved protein of unknown function |
| * | JE3692‑4 | 196,390 | 0 | T | C | 30.8% | 272.4 / 141.9 | 156 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 97,588 | 0 | C | G | 29.2% | 111.1 / 33.8 | 69 | intergenic (+17/+19) | PP_0090/PP_0091 | conserved exported protein of unknown function/putative lipoprotein |
| * | JE3692‑4 | 4,864,581 | 0 | C | T | 29.1% | 110.1 / 13.9 | 55 | intergenic (‑108/+189) | PP_4267/PP_4268 | Recombination protein RecR/nucleoid‑associated broad specificity regulator |
| * | JE3692‑4 | 884,007 | 0 | C | T | 29.0% | 150.3 / 29.6 | 99 | intergenic (+245/‑83) | PP_0766/PP_0767 | conserved exported protein of unknown function/Transcriptional regulator, LuxR family |
| * | JE3692‑4 | 2,184,200 | 0 | G | A | 28.4% | 172.1 / 25.0 | 93 | T268T (ACG→ACA) | PP_1931 | conserved protein of unknown function |
| * | JE3692‑4 | 4,793,175 | 0 | G | C | 27.7% | 185.4 / 41.2 | 89 | R2095G (CGC→GGC) | PP_4220 | non‑ribosomal peptide synthetase (subunit of ferribactin synthase) |
| * | JE3692‑4 | 1,904,632 | 0 | A | C | 27.5% | 160.1 / 23.5 | 81 | intergenic (+70/‑450) | PP_t18/PP_1703 | tRNA‑Asp/assimilatory nitrate reductase/sulfite reductase |
| * | JE3692‑4 | 2,504,475 | 0 | C | T | 27.0% | 176.6 / 19.9 | 90 | Y248Y (TAC→TAT) | PP_2193 | Outer membrane ferric siderophore receptor |
| * | JE3692‑4 | 363,987 | 0 | C | G | 25.5% | 243.2 / 47.1 | 108 | G183R (GGC→CGC) | PP_0303 | dehydrocarnitine cleavage enzyme |
| Marginal new junction evidence (lowest skew 10 of 831 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | JE3692‑4 | = 652783 | 94 (0.830) | 32 (0.440) | 19/126 | 4.4 | 51.6% | coding (1960/1962 nt) | PP_0562 | Methyl‑accepting chemotaxis protein CtpL |
| ? | JE3692‑4 | 4820353 = | 0 (0.000) | intergenic (‑318/‑237) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | JE3692‑4 | 1297692 = | NA (NA) | 21 (0.190) | 17/190 | 8.7 | NA | noncoding (1208/2040 nt) | mobile_element | repeat region |
| ? | JE3692‑4 | 1297721 = | NA (NA) | noncoding (1237/2040 nt) | mobile_element | repeat region | |||||
| * | ? | JE3692‑4 | 174577 = | NA (NA) | 14 (0.130) | 13/186 | 10.1 | NA | noncoding (1375/2902 nt) | PP_23SA | 23S ribosomal RNA |
| ? | JE3692‑4 | 174595 = | NA (NA) | noncoding (1393/2902 nt) | PP_23SA | 23S ribosomal RNA | |||||
| * | ? | JE3692‑4 | = 611136 | NA (NA) | 14 (0.130) | 13/190 | 10.3 | NA | noncoding (237/1314 nt) | mobile_element | repeat region |
| ? | JE3692‑4 | = 611169 | NA (NA) | noncoding (270/1314 nt) | mobile_element | repeat region | |||||
| * | ? | JE3692‑4 | = 175970 | NA (NA) | 24 (0.230) | 12/182 | 10.3 | NA | noncoding (2768/2902 nt) | PP_23SA | 23S ribosomal RNA |
| ? | JE3692‑4 | = 175984 | NA (NA) | noncoding (2782/2902 nt) | PP_23SA | 23S ribosomal RNA | |||||
| * | ? | JE3692‑4 | = 611115 | NA (NA) | 17 (0.160) | 11/186 | 11.0 | NA | noncoding (216/1314 nt) | mobile_element | repeat region |
| ? | JE3692‑4 | = 611138 | NA (NA) | noncoding (239/1314 nt) | mobile_element | repeat region | |||||
| * | ? | JE3692‑4 | 175943 = | NA (NA) | 13 (0.120) | 11/186 | 11.0 | NA | noncoding (2741/2902 nt) | PP_23SA | 23S ribosomal RNA |
| ? | JE3692‑4 | 175972 = | NA (NA) | noncoding (2770/2902 nt) | PP_23SA | 23S ribosomal RNA | |||||
| * | ? | JE3692‑4 | 175338 = | NA (NA) | 17 (0.160) | 11/188 | 11.1 | NA | noncoding (2136/2902 nt) | PP_23SA | 23S ribosomal RNA |
| ? | JE3692‑4 | 175379 = | NA (NA) | noncoding (2177/2902 nt) | PP_23SA | 23S ribosomal RNA | |||||
| * | ? | JE3692‑4 | = 2554224 | NA (NA) | 12 (0.110) | 11/190 | 11.2 | NA | intergenic (‑391/‑98) | PP_2239/PP_16SF | threonine and homoserine exporter/16S ribosomal RNA |
| ? | JE3692‑4 | = 2554260 | NA (NA) | intergenic (‑427/‑62) | PP_2239/PP_16SF | threonine and homoserine exporter/16S ribosomal RNA | |||||
| * | ? | JE3692‑4 | = 178786 | NA (NA) | 16 (0.150) | 10/186 | 11.5 | NA | noncoding (154/2902 nt) | PP_23SB | 23S ribosomal RNA |
| ? | JE3692‑4 | = 178803 | NA (NA) | noncoding (171/2902 nt) | PP_23SB | 23S ribosomal RNA | |||||