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 26 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | AP012306 | 1,091,992 | 0 | T | G | 39.8% | 546.7 / 94.0 | 319 | intergenic (+38/‑145) | narI/ychS | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/predicted protein |
| * | AP012306 | 341,377 | 0 | T | G | 32.9% | 264.8 / 44.2 | 164 | G60G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidin e deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | AP012306 | 1,944,288 | 0 | A | C | 32.2% | 485.1 / 53.3 | 237 | G361G (GGT→GGG) | menE | o‑succinylbenzoate‑CoA ligase |
| * | AP012306 | 3,527,368 | 0 | A | C | 31.9% | 592.8 / 67.2 | 276 | L140F (TTA→TTC) | rhaS | DNA‑binding transcriptional activator, L‑rhamnose‑binding |
| * | AP012306 | 3,182,861 | 0 | A | C | 30.9% | 295.6 / 28.0 | 136 | L198F (TTA→TTC) | yiaN | predicted transporter |
| * | AP012306 | 644,417 | 0 | G | A | 30.0% | 996.8 / inf | 617 | intergenic (+32/‑401) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A |
| * | AP012306 | 3,938,887 | 0 | C | T | 29.7% | 478.4 / 175.7 | 259 | S44F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator |
| * | AP012306 | 3,020,670 | 0 | T | G | 28.4% | 427.3 / 14.3 | 216 | K195N (AAA→AAC) | glgC | glucose‑1‑phosphate adenylyltransferase |
| * | AP012306 | 800,675 | 0 | A | C | 27.3% | 741.7 / 52.8 | 319 | T192P (ACC→CCC) | lolA | chaperone for lipoproteins |
| * | AP012306 | 2,212,753 | 0 | A | C | 25.9% | 430.5 / 51.8 | 170 | Y241D (TAT→GAT) | hcaT | predicted 3‑phenylpropionic transporter |
| * | AP012306 | 1,226,557 | 0 | A | G | 25.0% | 458.2 / 85.6 | 200 | G55G (GGA→GGG) | ydcU | predicted spermidine/putrescine transporter subunit |
| * | AP012306 | 1,421,147 | 0 | T | G | 24.4% | 597.9 / 15.7 | 270 | T79P (ACC→CCC) | ydhB | predicted DNA‑binding transcriptional regulator |
| * | AP012306 | 472,868 | 0 | T | G | 24.2% | 602.7 / 19.3 | 227 | D435A (GAC→GCC) | cusS | sensory histidine kinase in two‑component regulatory system with CusR, senses copper ions |
| * | AP012306 | 406,677 | 0 | A | G | 23.1% | 672.7 / 24.3 | 256 | K294E (AAA→GAA) | hemH | ferrochelatase |
| * | AP012306 | 2,758,909 | 0 | T | G | 22.8% | 709.9 / 22.1 | 263 | G33G (GGT→GGG) | agaD | N‑acetylgalactosamine‑specific enzyme IID component of PTS |
| * | AP012306 | 1,066,323 | 0 | A | C | 22.0% | 784.1 / 12.6 | 277 | intergenic (‑92/+33) | ychM/prsA | predicted transporter/phosphoribosylpyrophosphate synthase |
| * | AP012306 | 1,393,379 | 0 | A | C | 21.8% | 711.1 / 37.8 | 266 | T92P (ACC→CCC) | nth | DNA glycosylase and apyrimidinic (AP) lyase |
| * | AP012306 | 202,417 | 0 | T | G | 21.2% | 829.7 / 26.8 | 317 | V409G (GTA→GGA) | tilS | tRNA(Ile)‑lysidine synthetase |
| * | AP012306 | 2,326,979 | 0 | A | C | 21.1% | 686.7 / 15.3 | 273 | intergenic (‑5/+68) | gshA/yqaA | gamma‑glutamate‑cysteine ligase/conserved inner membrane protein |
| * | AP012306 | 1,854,851 | 0 | A | C | 21.0% | 887.7 / 79.1 | 329 | T25P (ACC→CCC) | yejH | predicted ATP‑dependet helicase |
| Marginal new junction evidence (lowest skew 10 of 128 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | AP012306 | = 1092512 | 447 (1.210) | 12 (0.040) | 11/258 | 19.6 | 3.4% | intergenic (+100/+3) | ychS/tpr | predicted protein/predicted protamine‑like protein |
| ? | AP012306 | 1092985 = | 303 (0.950) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | AP012306 | = 1092334 | 383 (1.040) | 9 (0.030) | 9/258 | 20.6 | 2.8% | coding (198/276 nt) | ychS | predicted protein |
| ? | AP012306 | 1092985 = | 303 (0.950) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | AP012306 | = 997497 | 354 (0.960) | 9 (0.030) | 9/268 | 21.0 | 2.7% | coding (41/1305 nt) | ndh | respiratory NADH dehydrogenase 2/cupric reductase |
| ? | AP012306 | 997993 = | 326 (0.990) | coding (537/1305 nt) | ndh | respiratory NADH dehydrogenase 2/cupric reductase | |||||
| * | ? | AP012306 | 1392778 = | 327 (0.890) | 8 (0.020) | 8/290 | 22.2 | 2.4% | coding (368/696 nt) | rsxE | predicted inner membrane NADH‑quinone reductase |
| ? | AP012306 | 1392801 = | 323 (0.900) | coding (391/696 nt) | rsxE | predicted inner membrane NADH‑quinone reductase | |||||
| * | ? | AP012306 | 2718234 = | 447 (1.210) | 7 (0.020) | 7/274 | 22.3 | 1.7% | intergenic (‑160/‑203) | uxaC/exuT | uronate isomerase/hexuronate transporter |
| ? | AP012306 | 2718246 = | 420 (1.240) | intergenic (‑172/‑191) | uxaC/exuT | uronate isomerase/hexuronate transporter | |||||
| * | ? | AP012306 | 2651964 = | 364 (0.990) | 7 (0.020) | 7/288 | 22.7 | 2.0% | coding (1232/1350 nt) | qseC | sensory histidine kinase in two‑component regulatory system with QseB |
| ? | AP012306 | 2651980 = | 343 (0.960) | coding (1248/1350 nt) | qseC | sensory histidine kinase in two‑component regulatory system with QseB | |||||
| * | ? | AP012306 | 3045989 = | 484 (1.310) | 8 (0.020) | 7/294 | 22.9 | 1.7% | intergenic (‑412/‑12) | livK/yhhK | leucine transporter subunit/conserved protein |
| ? | AP012306 | 3046004 = | 461 (1.270) | coding (4/384 nt) | yhhK | conserved protein | |||||
| * | ? | AP012306 | = 2049432 | 409 (1.110) | 7 (0.020) | 6/274 | 22.9 | 1.8% | coding (470/1146 nt) | yfdE | predicted CoA‑transferase, NAD(P)‑binding |
| ? | AP012306 | = 2049420 | 388 (1.150) | coding (482/1146 nt) | yfdE | predicted CoA‑transferase, NAD(P)‑binding | |||||
| * | ? | AP012306 | = 215364 | NA (NA) | 7 (0.020) | 6/288 | 23.3 | NA | noncoding (745/2905 nt) | rrlH | 23S ribosomal RNA (rrlH) |
| ? | AP012306 | = 215372 | NA (NA) | noncoding (753/2905 nt) | rrlH | 23S ribosomal RNA (rrlH) | |||||
| * | ? | AP012306 | 2664736 = | 517 (1.400) | 6 (0.020) | 6/292 | 23.4 | 1.2% | intergenic (‑21/+336) | ribB/glgS | 3,4 dihydroxy‑2‑butanone‑4‑phosphate synthase/predicted glycogen synthesis protein |
| ? | AP012306 | 2664753 = | 490 (1.360) | intergenic (‑38/+319) | ribB/glgS | 3,4 dihydroxy‑2‑butanone‑4‑phosphate synthase/predicted glycogen synthesis protein | |||||