mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 52 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,269,747 | 0 | C | . | 76.8% | 228.5 / 96.2 | 99 | intergenic (+145/+469) | yhaC/rnpB | uncharacterized protein YhaC/RNase P catalytic RNA component |
| * | NC_000913 | 339,986 | 0 | G | A | 75.7% | 58.3 / 12.8 | 37 | R73Q (CGA→CAA) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 339,979 | 0 | G | A | 75.0% | 49.2 / 17.0 | 37 | V71M (GTG→ATG) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 2,724,821 | 0 | C | . | 72.2% | 304.7 / 181.2 | 152 | coding (926/1299 nt) | kgtP | alpha‑ketoglutarate:H(+) symporter |
| * | NC_000913 | 1,259,977 | 0 | C | T | 70.5% | 134.2 / 67.4 | 90 | R276H (CGC→CAC) | dauA | aerobic C4‑dicarboxylate transporter DauA |
| * | NC_000913 | 3,875,298 | 0 | C | T | 63.0% | 110.4 / 103.9 | 108 | intergenic (‑138/‑140) | dgoR/yidX | DNA‑binding transcriptional regulator DgoR/putative lipoprotein YidX |
| * | NC_000913 | 2,171,384 | 0 | A | C | 52.4% | 14.8 / 24.8 | 21 | K285Q (AAG→CAG) | insF5 | IS3 element protein InsF |
| * | NC_000913 | 3,319,766 | 0 | C | A | 40.0% | 100.3 / 18.2 | 100 | S377* (TCA→TAA) | argG | argininosuccinate synthetase |
| * | NC_000913 | 3,911,533 | 0 | C | A | 39.2% | 155.3 / 19.1 | 121 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 1,611,507 | 0 | G | T | 34.6% | 130.9 / 15.4 | 101 | L116L (CTC→CTA) | dgcF | putative diguanylate cyclase DgcF |
| * | NC_000913 | 3,054,886 | 0 | G | T | 34.3% | 173.3 / 32.1 | 108 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,351,463 | 0 | C | A | 32.6% | 157.6 / 13.0 | 95 | E100* (GAG→TAG) | ycjD | DUF559 domain‑containing protein YcjD |
| * | NC_000913 | 1,502,772 | 0 | G | A | 32.1% | 150.0 / 35.2 | 107 | A106T (GCG→ACG) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 3,054,894 | 0 | G | T | 32.0% | 165.4 / 23.8 | 100 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,631,903 | 0 | G | T | 31.5% | 178.8 / 13.2 | 108 | S128Y (TCC→TAC) | ydfJ | putative transporter YdfJ |
| * | NC_000913 | 2,662,442 | 0 | T | A | 30.9% | 61.2 / 43.0 | 42 | intergenic (‑311/+141) | iscR/trmJ | DNA‑binding transcriptional dual regulator IscR/tRNA Cm32/Um32 methyltransferase |
| * | NC_000913 | 58,065 | 0 | C | A | 30.4% | 184.3 / 13.1 | 102 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 1,557,428 | 0 | G | T | 30.3% | 146.3 / 11.1 | 99 | S204* (TCG→TAG) | ddpF | putative D,D‑dipeptide ABC transporter ATP‑binding subunit DdpF |
| * | NC_000913 | 2,722,838 | 0 | G | T | 29.6% | 198.7 / 10.4 | 108 | E38* (GAG→TAG) | pssA | phosphatidylserine synthase |
| * | NC_000913 | 314,594 | 0 | G | T | 29.0% | 199.5 / 12.0 | 107 | intergenic (‑1352/‑697) | ykgR/insE1 | putative membrane protein YkgR/IS3 element protein InsE |
| Marginal new junction evidence (lowest skew 10 of 48 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 20 (0.200) | 16/586 | 4.4 | 15.2% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4002526 = | 112 (1.150) | coding (274/381 nt) | yigF | DUF2628 domain‑containing protein YigF | |||||
| * | ? | NC_000913 | = 4606166 | 86 (0.880) | 11 (0.160) | 9/408 | 4.6 | 16.0% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 56 (0.820) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 781446 | 65 (0.670) | 10 (0.140) | 9/430 | 4.8 | 18.4% | intergenic (+2/‑131) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781655 = | 41 (0.570) | intergenic (+3/‑430) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 2653419 | 105 (1.080) | 15 (0.170) | 12/536 | 5.0 | 14.0% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 88 (0.990) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | 2170171 = | NA (NA) | 30 (0.310) | 13/582 | 5.1 | 19.9% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 2700291 = | 121 (1.250) | intergenic (‑94/‑229) | shoB/ohsC | toxic peptide ShoB/small regulatory RNA OhsC | |||||
| * | ? | NC_000913 | 315229 = | NA (NA) | 30 (0.310) +T |
13/584 | 5.2 | 19.9% | noncoding (1/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 2700289 = | 121 (1.240) | intergenic (‑92/‑231) | shoB/ohsC | toxic peptide ShoB/small regulatory RNA OhsC | |||||
| * | ? | NC_000913 | = 696741 | 64 (0.660) | 8 (0.110) | 7/430 | 5.6 | 15.1% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 43 (0.600) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 3648146 | 138 (1.410) | 10 (0.130) | 8/470 | 5.7 | 8.2% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 114 (1.460) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 2947467 | 73 (0.750) | 6 (0.090) | 6/420 | 5.9 | 10.1% | intergenic (+4/‑30) | metZ/metW | tRNA‑Met/tRNA‑Met |
| ? | NC_000913 | 2947688 = | 54 (0.770) | intergenic (+5/+69) | metV/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C | |||||
| * | ? | NC_000913 | = 2518116 | 72 (0.740) | 6 (0.080) | 6/424 | 6.0 | 11.3% | noncoding (1/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2518232 = | 42 (0.590) | intergenic (‑1/‑235) | alaW/yfeC | tRNA‑Ala/DNA‑binding transcriptional dual regulator YfeC | |||||