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 28 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,620,859 | 0 | C | T | 55.6% | ‑2.5 / 20.2 | 18 | R556R (CGC→CGT) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 3,620,844 | 0 | T | C | 52.9% | ‑1.8 / 23.0 | 18 | R551R (CGT→CGC) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 3,620,862 | 0 | C | T | 50.0% | ‑1.9 / 21.4 | 18 | F557F (TTC→TTT) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 3,620,865 | 0 | G | T | 50.0% | ‑1.6 / 19.2 | 18 | G558G (GGG→GGT) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 4,037,496 | 0 | A | T | 48.1% | 42.6 / 256.9 | 130 | intergenic (+161/‑23) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA |
| * | NC_000913 | 3,620,869 | 0 | A | G | 47.4% | 2.3 / 22.7 | 19 | M560V (ATG→GTG) | rhsB | rhs element protein RhsB |
| * | NC_000913 | 3,911,533 | 0 | C | A | 41.0% | 152.2 / 27.5 | 122 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 2,767,444 | 0 | C | A | 40.6% | 98.8 / 10.9 | 69 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 3,741,871 | 0 | G | T | 39.5% | 143.8 / 23.7 | 109 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 2,767,445 | 0 | C | A | 36.2% | 100.8 / 12.6 | 69 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 4,591,947 | 0 | G | T | 34.9% | 106.3 / 77.1 | 86 | S97S (TCG→TCT) | tsr | methyl‑accepting chemotaxis protein Tsr |
| * | NC_000913 | 1,427,992 | 0 | G | T | 34.4% | 188.2 / 14.7 | 119 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 847,955 | 0 | G | A | 33.3% | 130.3 / 46.0 | 102 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 4,213,310 | 0 | G | T | 30.6% | 178.9 / 11.2 | 111 | G26V (GGA→GTA) | yjaA | stress response protein |
| * | NC_000913 | 1,097,118 | 0 | C | A | 30.4% | 27.9 / 11.3 | 23 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 2,288,418 | 0 | G | T | 30.0% | 190.9 / 20.7 | 111 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 58,065 | 0 | C | A | 29.3% | 136.9 / 11.8 | 82 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 1,502,770 | 0 | T | C | 29.0% | 100.8 / 13.2 | 62 | I105T (ATA→ACA) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 3,401,345 | 0 | G | T | 27.5% | 174.7 / 11.9 | 91 | intergenic (‑258/+47) | mreB/csrD | dynamic cytoskeletal protein MreB/regulator of CsrB and CsrC decay |
| * | NC_000913 | 4,296,191 | 0 | A | C | 26.9% | 37.6 / 12.6 | 26 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Marginal new junction evidence (lowest skew 10 of 22 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4606166 | 80 (0.990) | 10 (0.180) | 8/410 | 3.3 | 15.7% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 52 (0.930) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 2653419 | 60 (0.750) | 12 (0.160) | 11/538 | 3.4 | 15.5% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 76 (1.030) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 2357730 | 95 (1.180) | 7 (0.100) | 7/508 | 4.3 | 8.5% | coding (827/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357926 = | 68 (0.980) | intergenic (+123/+116) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | 4542682 = | 119 (1.480) | 8 (0.100) | 8/570 | 4.5 | 6.8% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 105 (1.350) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 360151 | 1024 (12.720) | 7 (0.090) | 7/566 | 4.7 | 0.69% | coding (160/1155 nt) | cynX | cyanate transporter |
| ? | NC_000913 | 360797 = | 1020 (13.170) | coding (806/1155 nt) | cynX | cyanate transporter | |||||
| * | ? | NC_000913 | = 2904039 | 77 (0.960) | 6 (0.080) | 5/536 | 5.3 | 7.9% | intergenic (+665/+708) | ygcE/queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| ? | NC_000913 | 2904345 = | 70 (0.950) | intergenic (+971/+402) | ygcE/queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE | |||||
| * | ? | NC_000913 | = 781322 | 38 (0.470) | 4 (0.060) | 4/510 | 5.5 | 9.1% | intergenic (+100/‑47) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781811 = | 47 (0.670) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | 2288915 = | NA (NA) | 6 (0.070) | 5/586 | 5.6 | 85.8% | intergenic (‑1/+150) | yejO/insH8 | adhesin‑like autotransporter YejO/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 4044851 = | 1 (0.010) | coding (653/1431 nt) | yihF | DUF945 domain‑containing protein YihF | |||||
| * | ? | NC_000913 | = 3991828 | 58 (0.720) | 4 (0.050) | 4/562 | 5.9 | 5.4% | coding (676/2547 nt) | cyaA | adenylate cyclase |
| ? | NC_000913 | 3992411 = | 85 (1.100) | coding (1259/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | = 3764827 | NA (NA) | 4 (0.050) | 4/564 | 5.9 | 67.6% | coding (2645/4134 nt) | rhsA | rhs element protein RhsA |
| ? | NC_000913 | 3765008 = | 2 (0.020) | coding (2826/4134 nt) | rhsA | rhs element protein RhsA | |||||