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 49 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | JE3692‑4 | 699,722 | 0 | A | G | 53.1% | 6.3 / 130.6 | 82 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | JE3692‑4 | 4,365,337 | 0 | A | C | 52.4% | 25.0 / 47.3 | 42 | T107P (ACG→CCG) | PP_3827 | 2‑nitropropane dioxygenase |
| * | JE3692‑4 | 4,360,849 | 0 | A | G | 46.9% | 62.3 / 201.0 | 131 | intergenic (‑70/+404) | PP_3820/PP_3821 | Group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | JE3692‑4 | 1,327,121 | 0 | C | T | 46.6% | 76.3 / 183.4 | 123 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | JE3692‑4 | 1,927,183 | 0 | A | C | 43.5% | 62.1 / 12.9 | 48 | intergenic (+26/+35) | PP_1720/PP_1721 | Alcohol dehydrogenase, zinc‑containing/putative phosphoserine phosphatase |
| * | JE3692‑4 | 1,927,172 | 0 | T | C | 41.5% | 60.1 / 28.6 | 53 | intergenic (+15/+46) | PP_1720/PP_1721 | Alcohol dehydrogenase, zinc‑containing/putative phosphoserine phosphatase |
| * | JE3692‑4 | 718,473 | 0 | A | C | 37.7% | 78.6 / 17.8 | 63 | intergenic (+43/+34) | PP_0612/PP_0613 | FAD‑dependent glycine/D‑amino acid oxidase/Amidase family protein |
| * | JE3692‑4 | 195,634 | 0 | C | T | 35.2% | 250.8 / 181.9 | 162 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 718,459 | 0 | A | C | 33.9% | 89.3 / 15.1 | 59 | intergenic (+29/+48) | PP_0612/PP_0613 | FAD‑dependent glycine/D‑amino acid oxidase/Amidase family protein |
| * | JE3692‑4 | 4,365,327 | 0 | C | G | 30.6% | 47.0 / 15.9 | 39 | G103G (GGC→GGG) | PP_3827 | 2‑nitropropane dioxygenase |
| * | JE3692‑4 | 196,351 | 0 | C | G | 29.6% | 308.3 / 180.9 | 186 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 5,797,620 | 0 | G | C | 29.5% | 83.6 / 21.5 | 46 | intergenic (+87/‑44) | PP_5068/PP_5069 | conserved protein of unknown function, UPF0061 family/Thioredoxin 2 |
| * | JE3692‑4 | 196,390 | 0 | T | C | 28.9% | 249.1 / 119.7 | 142 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | JE3692‑4 | 1,541,581 | 0 | C | T | 28.4% | 150.4 / 36.5 | 89 | intergenic (‑57/‑44) | PP_1351/PP_1352 | putative 2‑dehydropantoate 2‑reductase/UPF0234 protein PP_1352 |
| * | JE3692‑4 | 4,069,519 | 0 | A | G | 28.4% | 154.2 / 13.2 | 74 | L96P (CTG→CCG) | PP_3575 | Outer membrane ferric siderophore receptor |
| * | JE3692‑4 | 2,942,043 | 0 | T | C | 27.1% | 124.7 / 16.5 | 59 | Y149H (TAC→CAC) | PP_2569 | Metabolite MFS transporter, MHS family |
| * | JE3692‑4 | 74,485 | 0 | T | G | 26.9% | 224.1 / 20.1 | 107 | intergenic (+73/+25) | PP_0063/PP_0064 | putative Lipid A biosynthesis lauroyl acyltransferase/conserved protein of unknown function |
| * | JE3692‑4 | 4,069,505 | 0 | C | T | 26.3% | 168.3 / 12.2 | 76 | V101M (GTG→ATG) | PP_3575 | Outer membrane ferric siderophore receptor |
| * | JE3692‑4 | 5,354,724 | 0 | T | C | 25.6% | 195.2 / 14.9 | 86 | intergenic (+26/‑181) | PP_4700/PP_4701 | pantothenate synthetase/glucose‑6‑phosphate isomerase |
| * | JE3692‑4 | 324,670 | 0 | C | T | 25.0% | 190.4 / 39.8 | 96 | intergenic (‑430/‑45) | PP_0267/PP_0268 | putative Outer membrane ferric siderophore receptor/outer‑membrane porin D |
| Marginal new junction evidence (lowest skew 10 of 917 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | JE3692‑4 | = 652783 | 93 (0.890) | 29 (0.440) | 16/126 | 4.4 | 48.6% | coding (1960/1962 nt) | PP_0562 | Methyl‑accepting chemotaxis protein CtpL |
| ? | JE3692‑4 | 4820353 = | 2 (0.030) | intergenic (‑318/‑237) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | JE3692‑4 | 4820318 = | 6 (0.060) | 32 (0.420) | 16/144 | 5.4 | 54.1% | intergenic (‑283/‑272) | PP_4234/PP_4235 | Aldehyde oxidase and xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | JE3692‑4 | 5999855 = | 50 (0.660) | intergenic (+73/‑473) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | JE3692‑4 | = 5999847 | 83 (0.800) | 21 (0.220) | 18/180 | 6.4 | 20.4% | intergenic (+65/‑481) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | JE3692‑4 | 6000039 = | 88 (0.920) | intergenic (+257/‑289) | PP_5246/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | JE3692‑4 | 176278 = | NA (NA) | 26 (0.260) | 15/186 | 7.7 | 84.6% | noncoding (42/120 nt) | PP_5SA | 5S ribosomal RNA |
| ? | JE3692‑4 | 176308 = | 5 (0.050) | noncoding (72/120 nt) | PP_5SA | 5S ribosomal RNA | |||||
| * | ? | JE3692‑4 | 2559423 = | NA (NA) | 25 (0.250) | 14/186 | 8.0 | 100% | noncoding (42/120 nt) | PP_5SF | 5S ribosomal RNA |
| ? | JE3692‑4 | 2559453 = | 0 (0.000) | noncoding (72/120 nt) | PP_5SF | 5S ribosomal RNA | |||||
| * | ? | JE3692‑4 | 702925 = | NA (NA) | 25 (0.250) | 14/186 | 8.0 | 100% | noncoding (42/120 nt) | PP_5SD | 5S ribosomal RNA |
| ? | JE3692‑4 | 702955 = | 0 (0.000) | noncoding (72/120 nt) | PP_5SD | 5S ribosomal RNA | |||||
| * | ? | JE3692‑4 | 529825 = | NA (NA) | 25 (0.250) | 14/186 | 8.0 | 89.8% | noncoding (42/120 nt) | PP_5SC | 5S ribosomal RNA |
| ? | JE3692‑4 | 529855 = | 3 (0.030) | noncoding (72/120 nt) | PP_5SC | 5S ribosomal RNA | |||||
| * | ? | JE3692‑4 | = 1298156 | NA (NA) | 17 (0.170) | 13/184 | 8.3 | NA | noncoding (1672/2040 nt) | mobile_element | repeat region |
| ? | JE3692‑4 | = 1298167 | NA (NA) | noncoding (1683/2040 nt) | mobile_element | repeat region | |||||
| * | ? | JE3692‑4 | = 178820 | NA (NA) | 16 (0.160) | 13/186 | 8.4 | NA | noncoding (188/2902 nt) | PP_23SB | 23S ribosomal RNA |
| ? | JE3692‑4 | = 178839 | NA (NA) | noncoding (207/2902 nt) | PP_23SB | 23S ribosomal RNA | |||||
| * | ? | JE3692‑4 | = 173409 | NA (NA) | 16 (0.160) | 13/186 | 8.4 | 100% | noncoding (207/2902 nt) | PP_23SA | 23S ribosomal RNA |
| ? | JE3692‑4 | = 178820 | 0 (0.000) | noncoding (188/2902 nt) | PP_23SB | 23S ribosomal RNA | |||||