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 74 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,212,959 | 0 | G | C | 79.5% | 90.1 / 20.1 | 40 | intergenic (+13/‑81) | rrlE/rrfE | 23S ribosomal RNA/5S ribosomal RNA |
| * | NC_000913 | 1,336,674 | 0 | G | A | 78.7% | 235.6 / 53.2 | 108 | G282R (GGG→AGG) | acnA | aconitate hydratase 1 |
| * | NC_000913 | 4,449,586 | 0 | G | A | 77.3% | 191.5 / 51.6 | 88 | P23S (CCG→TCG) | ppa | inorganic pyrophosphatase |
| * | NC_000913 | 1,001,251 | 0 | A | C | 76.3% | 170.3 / 35.1 | 76 | Q679P (CAA→CCA) | elfC | putative fimbrial usher protein ElfC |
| * | NC_000913 | 2,042,171 | 0 | G | A | 76.0% | 258.5 / 81.4 | 129 | intergenic (+146/‑197) | zinT/yodB | metal‑binding protein ZinT/putative cytochrome b561 YodB |
| * | NC_000913 | 4,423,337 | 0 | C | T | 75.7% | 140.3 / 41.9 | 70 | S164S (TCC→TCT) | ulaE | L‑ribulose‑5‑phosphate 3‑epimerase UlaE |
| * | NC_000913 | 696,470 | 0 | C | T | 75.3% | 167.7 / 52.8 | 85 | noncoding (35/75 nt) | glnX | tRNA‑Gln |
| * | NC_000913 | 3,152,494 | 0 | G | T | 75.3% | 163.6 / 63.6 | 97 | A87S (GCG→TCG) | metC | cystathionine beta‑lyase/L‑cysteine desulfhydrase/alanine racemase |
| * | NC_000913 | 1,287,040 | 0 | G | A | 73.2% | 95.8 / 28.9 | 58 | intergenic (+56/+26) | ychS/rttR | putative uncharacterized protein YchS/small RNA RttR |
| * | NC_000913 | 2,142,150 | 0 | A | G | 70.1% | 108.0 / 67.6 | 77 | R22R (CGT→CGC) | dcd | dCTP deaminase |
| * | NC_000913 | 58,065 | 0 | C | A | 38.7% | 127.7 / 22.8 | 93 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 1,351,463 | 0 | C | A | 37.8% | 86.9 / 24.6 | 90 | E100* (GAG→TAG) | ycjD | DUF559 domain‑containing protein YcjD |
| * | NC_000913 | 4,213,310 | 0 | G | T | 37.4% | 167.5 / 14.2 | 107 | G26V (GGA→GTA) | yjaA | stress response protein |
| * | NC_000913 | 2,155,880 | 0 | C | T | 33.9% | 60.4 / 58.2 | 59 | L206L (CTC→CTT) | mdtB | multidrug efflux pump RND permease subunit MdtB |
| * | NC_000913 | 3,669,715 | 0 | G | T | 31.1% | 174.5 / 10.0 | 104 | E42* (GAG→TAG) | treF | cytoplasmic trehalase |
| * | NC_000913 | 3,911,533 | 0 | C | A | 30.6% | 276.2 / 17.4 | 144 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 2,990,480 | 0 | C | A | 30.1% | 239.3 / 10.3 | 133 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 1,466,438 | 0 | T | G | 29.6% | 74.2 / 26.3 | 54 | pseudogene (1047/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 1,936,634 | 0 | C | T | 29.6% | 207.4 / 115.7 | 136 | intergenic (‑320/‑18) | zwf/yebK | NADP(+)‑dependent glucose‑6‑phosphate dehydrogenase/DNA‑binding transcriptional repressor YebK |
| * | NC_000913 | 2,472,817 | 0 | C | A | 29.1% | 156.0 / 12.0 | 86 | G22V (GGA→GTA) | yfdN | uncharacterized protein YfdN |
| Marginal new junction evidence (lowest skew 10 of 46 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 696741 | 58 (0.620) | 15 (0.220) | 12/432 | 3.5 | 21.2% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 69 (1.010) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 696469 | 66 (0.710) | 25 (0.270) +T |
18/586 | 3.5 | 27.1% | noncoding (36/75 nt) | glnX | tRNA‑Gln |
| ? | NC_000913 | 696583 = | 69 (0.740) | noncoding (34/75 nt) | glnV | tRNA‑Gln | |||||
| * | ? | NC_000913 | = 4542690 | 163 (1.750) | 22 (0.240) | 17/570 | 3.6 | 13.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 132 (1.460) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 19 (0.200) | 18/588 | 3.6 | 17.0% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 3731420 = | 93 (1.000) | coding (290/993 nt) | xylF | xylose ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 18 (0.190) | 16/588 | 4.0 | 17.3% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 3731428 | 86 (0.920) | coding (298/993 nt) | xylF | xylose ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1978502 | 1 (0.010) | 20 (0.220) | 15/572 | 4.1 | 97.6% | intergenic (‑305/+16) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA5/uspC | IS1 family protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | 2765412 = | 115 (1.230) | 18 (0.230) | 11/500 | 4.5 | 15.6% | intergenic (‑259/+101) | abpA/yfjM | anti‑bacteriophage protein/protein YfjM |
| ? | NC_000913 | = 2765419 | 97 (1.220) | intergenic (‑266/+94) | abpA/yfjM | anti‑bacteriophage protein/protein YfjM | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 17 (0.180) | 13/586 | 4.7 | 14.8% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3349205 | 98 (1.060) | coding (605/729 nt) | mtgA | peptidoglycan glycosyltransferase MtgA | |||||
| * | ? | NC_000913 | = 2237687 | 102 (1.090) | 17 (0.180) | 13/588 | 4.7 | 14.3% | coding (67/1011 nt) | mglC | D‑galactose/methyl‑galactoside ABC transporter membrane subunit |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 4542682 = | 150 (1.610) | 18 (0.200) | 12/570 | 4.8 | 11.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 135 (1.490) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||