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 | ||
| * | CP009273 | 4,177,586 | 0 | T | G | 67.9% | 269.0 / 220.1 | 224 | L770R (CTC→CGC) | rpoC | RNA polymerase, beta prime subunit |
| * | CP009273 | 2,170,734 | 0 | G | T | 41.5% | 47.6 / 78.7 | 142 | intergenic (‑51/+257) | gatY/fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| * | CP009273 | 4,178,500 | 0 | C | T | 37.3% | 220.6 / 246.8 | 209 | R1075C (CGT→TGT) | rpoC | RNA polymerase, beta prime subunit |
| * | CP009273 | 3,313,765 | 0 | A | C | 32.6% | 265.3 / 151.4 | 175 | L403W (TTG→TGG) | yhbX | putative EptAB family phosphoethanolamine transferase, inner membrane protein |
| * | CP009273 | 418,995 | 0 | T | G | 29.9% | 190.1 / 24.5 | 117 | L341R (CTG→CGG) | malZ | maltodextrin glucosidase |
| * | CP009273 | 2,178,908 | 0 | T | G | 27.8% | 207.5 / 16.6 | 108 | intergenic (‑128/+95) | thiM/rcnR | hydoxyethylthiazole kinase/transcriptional repressor of rcnA |
| * | CP009273 | 2,170,724 | 0 | G | T | 25.8% | 150.5 / 17.1 | 136 | intergenic (‑41/+267) | gatY/fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| * | CP009273 | 2,998,305 | 0 | G | T | 25.6% | 182.4 / 23.9 | 121 | Q281K (CAA→AAA) | ygeV | putative sigma‑54‑interacting transcriptional activator |
| * | CP009273 | 2,998,333 | 0 | T | A | 24.1% | 251.5 / 28.0 | 117 | Q271H (CAA→CAT) | ygeV | putative sigma‑54‑interacting transcriptional activator |
| * | CP009273 | 104,042 | 0 | A | T | 24.1% | 211.1 / 16.4 | 86 | intergenic (+81/‑150) | lpxC/secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| * | CP009273 | 838,675 | 0 | C | A | 24.0% | 361.6 / 22.9 | 172 | N296K (AAC→AAA) | rlmF | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| * | CP009273 | 104,033 | 0 | T | G | 23.3% | 177.3 / 10.6 | 86 | intergenic (+72/‑159) | lpxC/secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| * | CP009273 | 2,170,746 | 0 | C | A | 23.1% | 257.7 / 23.7 | 152 | intergenic (‑63/+245) | gatY/fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| * | CP009273 | 3,997,395 | 0 | G | C | 23.1% | 261.7 / 28.8 | 110 | F48L (TTC→TTG) | rarD | putative chloramphenical resistance permease |
| * | CP009273 | 277,680 | 0 | C | A | 22.7% | 248.4 / 19.0 | 154 | M5I (ATG→ATT) | yagA | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| * | CP009273 | 2,810,900 | 0 | G | A | 22.4% | 512.1 / 145.0 | 230 | intergenic (‑38/+243) | yqaB/argQ | fructose‑1‑P and 6‑phosphogluconate phosphatase/tRNA‑Arg |
| * | CP009273 | 838,652 | 0 | T | G | 21.7% | 337.9 / 16.0 | 161 | F289V (TTT→GTT) | rlmF | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| * | CP009273 | 4,402,598 | 0 | C | G | 21.6% | 255.2 / 16.0 | 106 | S132C (TCT→TGT) | yjfM | DUF1190 family protein |
| * | CP009273 | 838,672 | 0 | G | T | 20.9% | 358.6 / 19.5 | 173 | M295I (ATG→ATT) | rlmF | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| * | CP009273 | 838,658 | 0 | G | T | 20.8% | 316.7 / 20.4 | 159 | A291S (GCC→TCC) | rlmF | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| Marginal new junction evidence (lowest skew 10 of 11 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 3399761 = | 245 (1.470) | 8 (0.050) | 6/244 | 7.8 | 3.4% | coding (486/1350 nt) | accC | acetyl‑CoA carboxylase, biotin carboxylase subunit |
| ? | CP009273 | = 3399757 | 235 (1.550) | coding (482/1350 nt) | accC | acetyl‑CoA carboxylase, biotin carboxylase subunit | |||||
| * | ? | CP009273 | = 4532507 | 102 (0.610) | 4 (0.030) | 3/250 | 9.7 | 3.2% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | = 4532803 | 146 (0.940) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | CP009273 | 2886037 = | 214 (1.280) | 3 (0.020) | 3/250 | 9.7 | 1.4% | coding (22/1272 nt) | ygcN | putative oxidoreductase |
| ? | CP009273 | = 2886033 | 211 (1.360) | coding (18/1272 nt) | ygcN | putative oxidoreductase | |||||
| * | ? | CP009273 | = 3584869 | 246 (1.470) | 3 (0.020) | 3/264 | 10.0 | 1.2% | coding (817/1317 nt) | ugpB | glycerol‑3‑phosphate transporter subunit |
| ? | CP009273 | = 4229591 | 253 (1.540) | coding (2030/2097 nt) | yjbH | DUF940 family extracellular polysaccharide protein | |||||
| * | ? | CP009273 | = 2282590 | NA (NA) | 3 (0.020) | 3/264 | 10.0 | 2.1% | noncoding (1003/1195 nt) | IS5 | repeat region |
| ? | CP009273 | = 2616904 | 142 (0.850) | coding (502/2067 nt) | ppk | polyphosphate kinase, component of RNA degradosome | |||||
| * | ? | CP009273 | = 2002623 | 202 (1.210) | 3 (0.020) | 3/262 | 10.0 | 1.6% | coding (866/1206 nt) | yedE | UPF0394 family sulfur transport domain‑containing inner membrane protein |
| ? | CP009273 | = 3372903 | 164 (1.010) | coding (454/1128 nt) | yhcM | putative AFG1‑like family P‑loop ATPase | |||||
| * | ? | CP009273 | = 3923261 | 199 (1.190) | 5 (0.030) | 3/266 | 10.1 | 2.4% | coding (1193/1497 nt) | ravA | hexameric AAA+ MoxR family ATPase, putative molecular chaperone |
| ? | CP009273 | 3923269 = | 201 (1.210) | coding (1185/1497 nt) | ravA | hexameric AAA+ MoxR family ATPase, putative molecular chaperone | |||||
| * | ? | CP009273 | = 2758368 | 159 (0.950) | 3 (0.020) | 3/268 | 10.1 | 1.7% | coding (145/1617 nt) | yfjL | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| ? | CP009273 | 3055585 = | 185 (1.110) | coding (1377/2145 nt) | scpA | methylmalonyl‑CoA mutase | |||||
| * | ? | CP009273 | = 859527 | 212 (1.270) | 3 (0.020) | 3/266 | 10.1 | 1.4% | coding (430/663 nt) | fsaA | fructose‑6‑phosphate aldolase 1 |
| ? | CP009273 | = 3718282 | 207 (1.250) | coding (397/912 nt) | glyQ | glycine tRNA synthetase, alpha subunit | |||||
| * | ? | CP009273 | 221210 = | 130 (0.780) | 5 (0.030) | 3/268 | 10.1 | 2.8% | noncoding (953/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | CP009273 | 267669 = | 221 (1.330) | pseudogene (195/426 nt) | insN | pseudogene, IS911 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related | |||||