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 37 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 442,471 | 0 | C | A | 40.6% | 121.6 / 10.6 | 97 | S308Y (TCC→TAC) | thiI | tRNA uridine 4‑sulfurtransferase |
| * | NC_000913 | 190,843 | 0 | C | A | 40.0% | 109.4 / 10.2 | 95 | intergenic (+244/‑14) | rpsB/tsf | 30S ribosomal subunit protein S2/protein chain elongation factor EF‑Ts |
| * | NC_000913 | 1,351,463 | 0 | C | A | 37.2% | 112.5 / 10.5 | 78 | E100* (GAG→TAG) | ycjD | DUF559 domain‑containing protein YcjD |
| * | NC_000913 | 1,820,763 | 0 | G | T | 36.8% | 112.2 / 20.2 | 87 | S151Y (TCC→TAC) | chbC | N,N'‑diacetylchitobiose‑specific PTS enzyme IIC component |
| * | NC_000913 | 3,911,533 | 0 | C | A | 36.6% | 175.3 / 24.1 | 134 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 2,913,085 | 0 | G | T | 35.9% | 168.2 / 14.4 | 106 | L189L (CTC→CTA) | relA | GDP/GTP pyrophosphokinase |
| * | NC_000913 | 2,288,418 | 0 | G | T | 35.8% | 206.9 / 29.1 | 134 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 58,065 | 0 | C | A | 35.6% | 153.5 / 19.1 | 104 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 1,427,992 | 0 | G | T | 33.6% | 197.7 / 10.0 | 122 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 85,651 | 0 | G | T | 32.8% | 175.0 / 16.2 | 131 | E8* (GAG→TAG) | ilvI | acetolactate synthase/acetohydroxybutanoate synthase, catalytic subunit |
| * | NC_000913 | 332,975 | 0 | C | A | 32.1% | 165.4 / 11.4 | 106 | S202* (TCG→TAG) | pdeL | DNA‑binding transcriptional regulator/c‑di‑GMP phosphodiesterase PdeL |
| * | NC_000913 | 2,117,652 | 0 | G | T | 31.0% | 167.6 / 11.5 | 87 | L251L (CTC→CTA) | wcaK | colanic acid biosynthesis pyruvyl transferase WcaK |
| * | NC_000913 | 847,955 | 0 | G | A | 30.1% | 182.7 / 53.4 | 123 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,217,528 | 0 | C | T | 29.6% | 154.0 / 95.9 | 108 | C67C (TGC→TGT) | pdeG | putative c‑di‑GMP phosphodiesterase PdeG |
| * | NC_000913 | 141,849 | 0 | C | A | 29.4% | 220.5 / 27.3 | 119 | P140Q (CCG→CAG) | hpt | hypoxanthine phosphoribosyltransferase |
| * | NC_000913 | 4,360,965 | 0 | C | A | 29.2% | 306.0 / 22.8 | 147 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 3,741,871 | 0 | G | T | 29.1% | 191.7 / 18.3 | 103 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 3,054,886 | 0 | G | T | 28.0% | 190.7 / 22.8 | 100 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,431,396 | 0 | C | A | 27.6% | 231.7 / 14.5 | 127 | R7I (AGA→ATA) | tsaC | L‑threonylcarbamoyladenylate synthase |
| * | NC_000913 | 1,812,509 | 0 | G | T | 27.2% | 281.4 / 20.6 | 136 | L208L (CTC→CTA) | ydjO | protein YdjO |
| Marginal new junction evidence (lowest skew 10 of 34 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 781222 | 80 (0.820) | 15 (0.210) | 12/438 | 4.0 | 19.3% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781445 = | 66 (0.910) | intergenic (+1/‑132) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys | |||||
| * | ? | NC_000913 | = 696741 | 70 (0.720) | 14 (0.200) | 11/434 | 4.2 | 20.2% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 59 (0.820) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 2653419 | 89 (0.910) | 13 (0.150) | 12/540 | 5.0 | 13.1% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 91 (1.020) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 4606166 | 81 (0.830) | 8 (0.120) | 7/412 | 5.4 | 11.8% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 63 (0.930) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 2518116 | 105 (1.080) | 7 (0.100) | 7/428 | 5.6 | 9.1% | noncoding (1/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2518232 = | 63 (0.890) | intergenic (‑1/‑235) | alaW/yfeC | tRNA‑Ala/DNA‑binding transcriptional dual regulator YfeC | |||||
| * | ? | NC_000913 | = 696506 | 97 (1.000) | 9 (0.110) +45 bp |
8/500 | 6.0 | 10.7% | intergenic (‑2/+36) | glnX/glnV | tRNA‑Gln/tRNA‑Gln |
| ? | NC_000913 | 697057 = | 80 (0.820) | noncoding (77/77 nt) | metT | tRNA‑Met | |||||
| * | ? | NC_000913 | = 2357690 | 98 (1.010) | 9 (0.100) | 7/540 | 6.8 | 9.5% | coding (787/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357874 = | 82 (0.920) | intergenic (+71/+168) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 3269938 | 111 (1.140) | 7 (0.080) | 7/546 | 6.9 | 5.9% | intergenic (+336/+278) | yhaC/rnpB | uncharacterized protein YhaC/RNase P catalytic RNA component |
| ? | NC_000913 | 3270266 = | 120 (1.330) | noncoding (327/377 nt) | rnpB | RNase P catalytic RNA component | |||||
| * | ? | NC_000913 | = 781446 | 89 (0.910) | 4 (0.060) | 4/434 | 7.1 | 6.3% | intergenic (+2/‑131) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781655 = | 54 (0.750) | intergenic (+3/‑430) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 3647886 | 99 (1.020) | 6 (0.070) | 6/540 | 7.3 | 6.3% | intergenic (‑98/‑177) | dinQ/agrA | membrane toxin DinQ/small RNA AgrA |
| ? | NC_000913 | 3648317 = | 88 (0.990) | noncoding (24/82 nt) | agrB | small regulatory RNA AgrB | |||||