mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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_3_KO_pgi | 4,294,494 | 0 | C | T | 30.9% | 124.0 / 77.1 | 94 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913_3_KO_pgi | 3,877,558 | 0 | G | C | 24.6% | 129.6 / 48.9 | 66 | intergenic (‑93/+147) | yidB/gyrB | DUF937 family protein/DNA gyrase, subunit B |
| * | NC_000913_3_KO_pgi | 2,814,174 | 0 | T | A | 23.3% | 128.7 / 41.8 | 60 | intergenic (+20/+44) | emrB/luxS | multidrug efflux system protein/S‑ribosylhomocysteine lyase |
| * | NC_000913_3_KO_pgi | 2,814,175 | 0 | T | A | 23.3% | 129.5 / 41.5 | 60 | intergenic (+21/+43) | emrB/luxS | multidrug efflux system protein/S‑ribosylhomocysteine lyase |
| * | NC_000913_3_KO_pgi | 2,596,873 | 0 | C | . | 22.4% | 132.0 / 42.2 | 49 | intergenic (‑136/+32) | ypfJ/purC | putative neutral zinc metallopeptidase/phosphoribosylaminoimidazole‑succinocarboxamide synthetase |
| * | NC_000913_3_KO_pgi | 2,596,878 | 1 | . | G | 21.1% | 143.1 / 50.5 | 52 | intergenic (‑141/+27) | ypfJ/purC | putative neutral zinc metallopeptidase/phosphoribosylaminoimidazole‑succinocarboxamide synthetase |
| * | NC_000913_3_KO_pgi | 1,679,402 | 0 | T | A | 20.7% | 137.9 / 31.4 | 58 | intergenic (+31/‑155) | ydgH/ydgI | DUF1471 family periplasmic protein/putative arginine/ornithine antiporter transporter |
| * | NC_000913_3_KO_pgi | 1,169,382 | 0 | C | G | 20.0% | 126.3 / 32.0 | 56 | intergenic (+52/+30) | bhsA/ldtC | biofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein |
| * | NC_000913_3_KO_pgi | 1,679,400 | 0 | G | C | 20.0% | 153.3 / 32.4 | 60 | intergenic (+29/‑157) | ydgH/ydgI | DUF1471 family periplasmic protein/putative arginine/ornithine antiporter transporter |
| Marginal new junction evidence (lowest skew 10 of 653 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_KO_pgi | = 1920160 | 32 (0.550) | 15 (0.280) | 15/238 | 3.6 | 32.7% | intergenic (+17/‑63) | yebT/rsmF | MCE domain protein/16S rRNA m(5)C1407 methyltransferase, SAM‑dependent |
| ? | NC_000913_3_KO_pgi | = 1920166 | 32 (0.600) | intergenic (+23/‑57) | yebT/rsmF | MCE domain protein/16S rRNA m(5)C1407 methyltransferase, SAM‑dependent | |||||
| * | ? | NC_000913_3_KO_pgi | = 274419 | NA (NA) | 18 (0.320) | 15/246 | 3.8 | NA | coding (699/1017 nt) | insH1 | IS5 transposase and trans‑activator |
| ? | NC_000913_3_KO_pgi | = 274423 | NA (NA) | coding (695/1017 nt) | insH1 | IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913_3_KO_pgi | 225154 = | NA (NA) | 16 (0.290) | 15/246 | 3.8 | NA | noncoding (1384/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_KO_pgi | 225176 = | NA (NA) | noncoding (1406/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913_3_KO_pgi | = 3943643 | NA (NA) | 16 (0.280) | 15/256 | 4.0 | 43.2% | intergenic (+133/‑61) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA of rrnC operon |
| ? | NC_000913_3_KO_pgi | = 4037438 | 21 (0.360) | intergenic (+103/‑81) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA of rrnA operon | |||||
| * | ? | NC_000913_3_KO_pgi | = 2756000 | 52 (0.900) | 17 (0.300) | 14/252 | 4.1 | 23.9% | intergenic (+622/‑159) | smpB/intA | tmRNA‑binding trans‑translation protein/CP4‑57 prophage; integrase |
| ? | NC_000913_3_KO_pgi | = 2756030 | 57 (1.000) | intergenic (+652/‑129) | smpB/intA | tmRNA‑binding trans‑translation protein/CP4‑57 prophage; integrase | |||||
| * | ? | NC_000913_3_KO_pgi | 3426835 = | NA (NA) | 15 (0.260) | 14/256 | 4.2 | NA | intergenic (‑52/+123) | rrlD/alaU | 23S ribosomal RNA of rrnD operon/tRNA‑Ala |
| ? | NC_000913_3_KO_pgi | 3426855 = | NA (NA) | intergenic (‑72/+103) | rrlD/alaU | 23S ribosomal RNA of rrnD operon/tRNA‑Ala | |||||
| * | ? | NC_000913_3_KO_pgi | = 2643100 | 67 (1.160) | 13 (0.250) | 12/228 | 4.2 | 18.9% | intergenic (‑256/+29) | rodZ/rlmN | MreB assembly cytoskeletal protein/dual specificity 23S rRNA m(2)A2503, tRNA m(2)A37 methyltransferase, SAM‑dependent |
| ? | NC_000913_3_KO_pgi | = 2643110 | 52 (1.010) | intergenic (‑266/+19) | rodZ/rlmN | MreB assembly cytoskeletal protein/dual specificity 23S rRNA m(2)A2503, tRNA m(2)A37 methyltransferase, SAM‑dependent | |||||
| * | ? | NC_000913_3_KO_pgi | 987403 = | 76 (1.310) | 13 (0.250) | 12/226 | 4.2 | 16.9% | intergenic (‑421/+182) | ompF/asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| ? | NC_000913_3_KO_pgi | 987440 = | 61 (1.200) | intergenic (‑458/+145) | ompF/asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase | |||||
| * | ? | NC_000913_3_KO_pgi | = 4541124 | 56 (0.970) | 14 (0.260) | 12/238 | 4.4 | 23.1% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913_3_KO_pgi | = 4541420 | 41 (0.760) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913_3_KO_pgi | 4518917 = | 53 (0.920) | 11 (0.220) | 11/222 | 4.4 | 19.8% | intergenic (‑159/+188) | yjhU/yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| ? | NC_000913_3_KO_pgi | 4518956 = | 43 (0.860) | intergenic (‑198/+149) | yjhU/yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter | |||||