mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 36 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 339,986 | 0 | G | A | 73.2% | 62.8 / 25.2 | 41 | R73Q (CGA→CAA) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 339,979 | 0 | G | A | 72.5% | 59.0 / 21.5 | 40 | V71M (GTG→ATG) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 190,843 | 0 | C | A | 40.6% | 128.0 / 11.1 | 96 | intergenic (+244/‑14) | rpsB/tsf | 30S ribosomal subunit protein S2/protein chain elongation factor EF‑Ts |
| * | NC_000913 | 4,136,467 | 0 | A | C | 35.1% | 88.3 / 13.3 | 60 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 1,427,992 | 0 | G | T | 34.2% | 165.2 / 25.3 | 117 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 2,477,265 | 0 | A | C | 33.7% | 184.9 / 32.6 | 104 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 225,579 | 0 | C | A | 32.4% | 118.0 / 15.0 | 105 | intergenic (+4/‑180) | alaV/rrlH | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 2,159,421 | 0 | A | G | 32.2% | 96.6 / 10.8 | 63 | I346V (ATT→GTT) | mdtC | multidrug efflux pump RND permease subunit MdtC |
| * | NC_000913 | 847,955 | 0 | G | A | 32.1% | 160.6 / 52.7 | 132 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 2,159,413 | 0 | C | T | 31.7% | 88.4 / 20.9 | 61 | A343V (GCG→GTG) | mdtC | multidrug efflux pump RND permease subunit MdtC |
| * | NC_000913 | 3,054,886 | 0 | G | T | 31.2% | 191.8 / 29.5 | 112 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,054,894 | 0 | G | T | 31.2% | 180.4 / 31.7 | 113 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,922,815 | 0 | C | A | 29.8% | 173.6 / 16.0 | 114 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 2,767,445 | 0 | C | A | 29.5% | 178.4 / 12.1 | 96 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 3,401,345 | 0 | G | T | 28.6% | 217.9 / 10.1 | 112 | intergenic (‑258/+47) | mreB/csrD | dynamic cytoskeletal protein MreB/regulator of CsrB and CsrC decay |
| * | NC_000913 | 1,334,966 | 0 | A | C | 28.5% | 269.2 / 28.1 | 158 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 3,741,871 | 0 | G | T | 27.8% | 184.4 / 17.5 | 116 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 2,490,240 | 0 | G | T | 27.6% | 294.3 / 14.0 | 152 | intergenic (‑54/+16) | yfdV/oxc | putative transport protein YfdV/oxalyl‑CoA decarboxylase |
| * | NC_000913 | 2,477,282 | 0 | G | A | 27.6% | 221.0 / 11.7 | 107 | C116C (TGC→TGT) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 2,365,840 | 0 | T | G | 27.5% | 274.5 / 24.6 | 178 | intergenic (‑220/‑70) | ais/arnB | putative lipopolysaccharide core heptose(II)‑phosphate phosphatase/UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase |
| Marginal new junction evidence (lowest skew 10 of 63 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4353803 = | 92 (0.870) | 33 (0.310) | 27/598 | 3.3 | 26.4% | coding (915/1518 nt) | lysU | lysine‑‑tRNA ligase/Ap4A synthetase/Ap3A synthetase |
| ? | NC_000913 | 4498181 = | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 38 (0.360) | 27/598 | 3.3 | 37.6% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 3889014 = | 63 (0.600) | coding (285/1416 nt) | tnaA | tryptophanase | |||||
| * | ? | NC_000913 | 3365556 = | NA (NA) | 29 (0.280) | 25/590 | 3.5 | 17.8% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3890222 = | 136 (1.290) | intergenic (+77/‑14) | tnaA/tnaB | tryptophanase/tryptophan:H(+) symporter TnaB | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 26 (0.250) | 23/598 | 4.0 | 22.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 538086 = | 92 (0.870) | coding (454/1455 nt) | ybbW | putative allantoin transporter | |||||
| * | ? | NC_000913 | 2690293 = | 91 (0.860) | 21 (0.200) | 18/598 | 5.1 | 18.8% | coding (806/1428 nt) | glrK | histidine kinase GlrK |
| ? | NC_000913 | 2996361 = | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 2070271 | NA (NA) | 19 (0.180) | 17/598 | 5.3 | 17.4% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 2690297 | 90 (0.850) | coding (802/1428 nt) | glrK | histidine kinase GlrK | |||||
| * | ? | NC_000913 | 3720632 = | NA (NA) | 17 (0.160) | 15/598 | 5.8 | NA | intergenic (‑32/‑48) | hokA/insJ | small toxic polypeptide/insertion element IS150 protein InsA |
| ? | NC_000913 | = 3722077 | NA (NA) | intergenic (+28/+251) | insK/glyS | IS150 family conserved protein InsB/glycine‑‑tRNA ligase subunit beta | |||||
| * | ? | NC_000913 | = 4606166 | 106 (1.000) | 9 (0.120) | 8/420 | 6.1 | 11.4% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 66 (0.890) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 3648146 | 113 (1.070) | 10 (0.120) | 10/482 | 6.1 | 9.8% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 94 (1.100) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 291401 | NA (NA) | 16 (0.150) | 14/598 | 6.1 | 20.2% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 3889014 = | 63 (0.600) | coding (285/1416 nt) | tnaA | tryptophanase | |||||