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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,296,060 | 0 | C | T | 37.1% | 32.7 / 32.3 | 35 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 1,788,336 | 0 | A | T | 28.0% | 33.5 / 12.7 | 25 | intergenic (+58/‑99) | ppsR/aroH | PEP synthase kinase and PEP synthase pyrophosphorylase/3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible |
| * | NC_000913 | 3,313,207 | 0 | G | A | 27.5% | 61.5 / 24.7 | 40 | intergenic (‑29/+135) | rbfA/infB | 30s ribosome binding factor/translation initiation factor IF‑2 |
| * | NC_000913 | 3,313,208 | 0 | T | A | 27.5% | 58.7 / 23.6 | 40 | intergenic (‑30/+134) | rbfA/infB | 30s ribosome binding factor/translation initiation factor IF‑2 |
| * | NC_000913 | 3,313,209 | 0 | T | C | 27.5% | 58.9 / 24.0 | 40 | intergenic (‑31/+133) | rbfA/infB | 30s ribosome binding factor/translation initiation factor IF‑2 |
| * | NC_000913 | 2,305,086 | 0 | C | G | 22.6% | 62.8 / 17.7 | 31 | intergenic (+693/+22) | eco/mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| * | NC_000913 | 2,305,087 | 0 | C | T | 22.6% | 54.3 / 13.3 | 31 | intergenic (+694/+21) | eco/mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| * | NC_000913 | 59,625 | 0 | G | A | 22.2% | 83.7 / 20.9 | 45 | intergenic (+346/+62) | yabP/rluA | pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent |
| * | NC_000913 | 2,305,085 | 0 | A | G | 21.9% | 59.9 / 13.2 | 32 | intergenic (+692/+23) | eco/mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| * | NC_000913 | 59,627 | 0 | C | T | 21.7% | 88.7 / 20.4 | 46 | intergenic (+348/+60) | yabP/rluA | pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent |
| * | NC_000913 | 59,628 | 0 | T | C | 21.7% | 83.6 / 21.4 | 46 | intergenic (+349/+59) | yabP/rluA | pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent |
| * | NC_000913 | 59,626 | 0 | A | G | 21.3% | 92.8 / 20.9 | 47 | intergenic (+347/+61) | yabP/rluA | pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent |
| * | NC_000913 | 2,462,677 | 0 | A | T | 21.1% | 75.7 / 17.3 | 38 | intergenic (+31/‑335) | fadL/yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| * | NC_000913 | 2,462,678 | 0 | T | A | 21.1% | 78.4 / 17.3 | 38 | intergenic (+32/‑334) | fadL/yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| * | NC_000913 | 2,462,679 | 0 | A | T | 21.1% | 78.9 / 17.3 | 38 | intergenic (+33/‑333) | fadL/yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| * | NC_000913 | 1,357,224 | 0 | G | A | 20.7% | 57.8 / 10.3 | 30 | intergenic (‑114/+199) | sapA/ymjA | antimicrobial peptide transport ABC transporter periplasmic binding protein/DUF2543 family protein |
| * | NC_000913 | 2,247,030 | 0 | G | A | 20.4% | 89.5 / 16.8 | 44 | intergenic (‑261/+33) | cirA/lysP | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter/lysine transporter |
| * | NC_000913 | 2,247,031 | 0 | G | A | 20.4% | 89.7 / 15.7 | 44 | intergenic (‑262/+32) | cirA/lysP | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter/lysine transporter |
| * | NC_000913 | 2,247,032 | 0 | T | C | 20.4% | 85.3 / 18.0 | 44 | intergenic (‑263/+31) | cirA/lysP | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter/lysine transporter |
| * | NC_000913 | 2,247,033 | 0 | T | C | 20.4% | 85.2 / 17.9 | 44 | intergenic (‑264/+30) | cirA/lysP | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter/lysine transporter |
| Marginal new junction evidence (lowest skew 10 of 35 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4555361 = | 42 (1.150) | 7 (0.210) | 7/246 | 3.1 | 15.6% | intergenic (+12/+129) | uxuR/yjiC | fructuronate‑inducible hexuronate regulon transcriptional repressor; autorepressor/uncharacterized protein |
| ? | NC_000913 | 4555390 = | 37 (1.100) | intergenic (+41/+100) | uxuR/yjiC | fructuronate‑inducible hexuronate regulon transcriptional repressor; autorepressor/uncharacterized protein | |||||
| * | ? | NC_000913 | = 3795026 | 52 (1.420) | 6 (0.170) | 6/250 | 3.5 | 11.1% | coding (98/1047 nt) | waaF | ADP‑heptose:LPS heptosyltransferase II |
| ? | NC_000913 | = 3795059 | 47 (1.370) | coding (131/1047 nt) | waaF | ADP‑heptose:LPS heptosyltransferase II | |||||
| * | ? | NC_000913 | 895626 = | 26 (0.710) | 6 (0.170) | 6/252 | 3.5 | 19.8% | coding (636/1134 nt) | potG | putrescine ABC transporter ATPase |
| ? | NC_000913 | 895654 = | 24 (0.690) | coding (664/1134 nt) | potG | putrescine ABC transporter ATPase | |||||
| * | ? | NC_000913 | 2731065 = | 29 (0.790) | 6 (0.170) | 6/260 | 3.6 | 17.5% | noncoding (93/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | 3428688 = | NA (NA) | noncoding (75/1542 nt) | rrsD | 16S ribosomal RNA of rrnD operon | |||||
| * | ? | NC_000913 | = 1428264 | NA (NA) | 12 (0.340) | 5/254 | 3.9 | 86.3% | noncoding (531/1196 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2066866 | 2 (0.050) | noncoding (488/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1396531 = | NA (NA) | 12 (0.340) | 5/254 | 3.9 | NA | noncoding (488/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1428264 | NA (NA) | noncoding (531/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 3649868 | 41 (1.120) | 6 (0.170) | 5/258 | 4.0 | 12.9% | coding (934/1290 nt) | arsB | arsenite/antimonite transporter |
| ? | NC_000913 | = 3649901 | 41 (1.160) | coding (967/1290 nt) | arsB | arsenite/antimonite transporter | |||||
| * | ? | NC_000913 | 3488740 = | 34 (0.930) | 5 (0.140) | 5/256 | 4.0 | 13.2% | coding (1950/2103 nt) | yhfK | putative transporter, FUSC superfamily inner membrane protein |
| ? | NC_000913 | 3488758 = | 33 (0.940) | coding (1968/2103 nt) | yhfK | putative transporter, FUSC superfamily inner membrane protein | |||||
| * | ? | NC_000913 | = 1670967 | 28 (0.770) | 4 (0.120) | 4/240 | 4.1 | 13.7% | intergenic (+15/‑409) | ynfM/asr | putative arabinose efflux transporter/acid shock‑inducible periplasmic protein |
| ? | NC_000913 | = 1670981 | 25 (0.760) | intergenic (+29/‑395) | ynfM/asr | putative arabinose efflux transporter/acid shock‑inducible periplasmic protein | |||||
| * | ? | NC_000913 | = 3895233 | 50 (1.370) | 4 (0.120) | 4/242 | 4.2 | 7.6% | intergenic (+15/+39) | chrR/adeP | chromate reductase, Class I, flavoprotein/adenine permease, high affinity; adenine:H+ symporter |
| ? | NC_000913 | = 3895244 | 52 (1.570) | intergenic (+26/+28) | chrR/adeP | chromate reductase, Class I, flavoprotein/adenine permease, high affinity; adenine:H+ symporter | |||||