mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
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 | 3,107,154 | 0 | C | G | 66.7% | 8.7 / 17.7 | 18 | A668P (GCG→CCG) | speC | ornithine decarboxylase, constitutive |
| * | NC_000913 | 4,606,094 | 0 | G | C | 53.8% | 2.8 / 16.6 | 13 | noncoding (72/87 nt) | leuV | tRNA‑Leu |
| * | NC_000913 | 1,991,442 | 0 | C | G | 50.0% | 2.8 / 14.1 | 18 | A60P (GCT→CCT) | yecA | UPF0149 family protein |
| * | NC_000913 | 3,770,229 | 0 | C | G | 46.2% | 6.2 / 10.1 | 13 | intergenic (+83/+14) | yibU/yibH | pseudogene, H repeat‑associated protein/putative membrane fusion protein (MFP) component of efflux pump |
| * | NC_000913 | 2,879,536 | 0 | C | G | 44.0% | 10.5 / 22.5 | 25 | G79G (GGG→GGC) | ygbT | multifunctional endonuclease Cas1, CRISPR adaptation protein; DNA repair enzyme |
| * | NC_000913 | 4,296,060 | 0 | C | T | 43.2% | 15.4 / 46.6 | 37 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 1,984,188 | 0 | C | G | 42.9% | 18.5 / 19.6 | 21 | G294G (GGG→GGC) | araG | L‑arabinose ABC transporter ATPase |
| * | NC_000913 | 1,563,398 | 0 | G | C | 41.7% | 24.9 / 11.8 | 24 | S779C (TCC→TGC) | dosP | oxygen sensor, c‑di‑GMP phosphodiesterase, heme‑regulated; cold‑ and stationary phase‑induced bioflim regulator |
| * | NC_000913 | 1,041,386 | 0 | G | C | 37.9% | 27.4 / 17.9 | 29 | G257A (GGA→GCA) | appA | phosphoanhydride phosphorylase |
| * | NC_000913 | 1,618,075 | 0 | G | C | 37.5% | 37.4 / 11.0 | 25 | A350P (GCG→CCG) | ydeA | arabinose efflux transporter, arabinose‑inducible |
| * | NC_000913 | 1,135,975 | 0 | G | C | 32.1% | 39.3 / 21.9 | 28 | A138P (GCC→CCC) | flgH | flagellar protein of basal‑body outer‑membrane L ring |
| * | NC_000913 | 269,735 | 0 | G | C | 29.7% | 63.5 / 17.8 | 38 | P150A (CCC→GCC) | perR | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| * | NC_000913 | 34,508 | 0 | G | C | 29.6% | 58.5 / 11.8 | 28 | G70A (GGA→GCA) | caiF | cai operon transcriptional activator |
| * | NC_000913 | 1,527,602 | 0 | G | C | 28.6% | 88.4 / 20.4 | 42 | intergenic (+450/‑300) | yncH/rhsE | IPR020099 family protein/pseudogene, Rhs family |
| * | NC_000913 | 2,779,939 | 0 | C | G | 26.5% | 67.8 / 17.8 | 34 | A930P (GCA→CCA) | ypjA | adhesin‑like autotransporter |
| Marginal new junction evidence (lowest skew 10 of 90 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 3798342 | 34 (1.310) | 6 (0.260) | 5/120 | 1.6 | 19.1% | coding (971/1074 nt) | waaU | lipopolysaccharide core biosynthesis |
| ? | NC_000913 | = 3798496 | 20 (0.850) | coding (817/1074 nt) | waaU | lipopolysaccharide core biosynthesis | |||||
| * | ? | NC_000913 | = 2941507 | 27 (1.040) | 5 (0.230) | 4/112 | 1.8 | 17.3% | coding (125/396 nt) | ygdD | UPF0382 family inner membrane protein |
| ? | NC_000913 | = 2941815 | 25 (1.140) | coding (753/918 nt) | gcvA | glycine cleavage system transcriptional activator; autorepressor | |||||
| * | ? | NC_000913 | = 2482514 | 39 (1.510) | 5 (0.230) | 4/112 | 1.8 | 14.7% | coding (826/1164 nt) | emrK | multidrug resistance efflux pump membrane fusion protein |
| ? | NC_000913 | = 2482573 | 25 (1.140) | coding (767/1164 nt) | emrK | multidrug resistance efflux pump membrane fusion protein | |||||
| * | ? | NC_000913 | = 1995482 | 18 (0.700) | 4 (0.180) | 4/114 | 1.8 | 14.7% | intergenic (‑123/‑336) | uvrY/yecF | response regulator in two‑component regulatory system with BarA/DUF2594 family protein |
| ? | NC_000913 | = 1995562 | 31 (1.390) | intergenic (‑203/‑256) | uvrY/yecF | response regulator in two‑component regulatory system with BarA/DUF2594 family protein | |||||
| * | ? | NC_000913 | 340840 = | 30 (1.160) | 4 (0.180) | 4/112 | 1.8 | 13.7% | coding (676/951 nt) | yahI | carbamate kinase‑like protein |
| ? | NC_000913 | 341156 = | 25 (1.140) | coding (32/1383 nt) | yahJ | putative metallo‑dependent hydrolase domain deaminase | |||||
| * | ? | NC_000913 | = 2943600 | 40 (1.550) | 4 (0.180) | 4/116 | 1.9 | 10.7% | coding (264/1206 nt) | csdA | cysteine sulfinate desulfinase |
| ? | NC_000913 | = 2943639 | 32 (1.410) | coding (303/1206 nt) | csdA | cysteine sulfinate desulfinase | |||||
| * | ? | NC_000913 | = 243009 | 17 (0.660) | 4 (0.170) | 4/118 | 1.9 | 16.6% | coding (295/2445 nt) | fadE | acyl coenzyme A dehydrogenase |
| ? | NC_000913 | = 243192 | 25 (1.080) | coding (112/2445 nt) | fadE | acyl coenzyme A dehydrogenase | |||||
| * | ? | NC_000913 | 3858193 = | 29 (1.120) | 4 (0.190) | 3/106 | 2.0 | 19.0% | coding (212/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein |
| ? | NC_000913 | 3858242 = | 11 (0.530) | coding (163/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein | |||||
| * | ? | NC_000913 | 3275581 = | 13 (0.500) | 3 (0.140) | 3/112 | 2.1 | 16.7% | coding (300/1572 nt) | garD | D‑galactarate dehydrogenase |
| ? | NC_000913 | 3275672 = | 19 (0.870) | coding (391/1572 nt) | garD | D‑galactarate dehydrogenase | |||||
| * | ? | NC_000913 | 3079260 = | 35 (1.350) | 3 (0.140) | 3/112 | 2.1 | 10.4% | coding (71/444 nt) | cmtB | putative mannitol‑specific enzyme IIA component of PTS |
| ? | NC_000913 | 3080360 = | 22 (1.000) | coding (1276/1992 nt) | tktA | transketolase 1, thiamine triphosphate‑binding | |||||