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 |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| MC JC | 2,399,465 | Δ7 bp | coding (650‑656/939 nt) | lrhA ← | transcriptional regulator LrhA |
| RA | 3,754,231 | G→T | R127S (CGC→AGC) | selA ← | L‑seryl‑tRNA(Sec) selenium transferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_CP009273 | 356981 | 357577 | 597 | 7 [0] | [1] 2 | [lacA] | [lacA] |
| * | * | ÷ | NZ_CP009273 | 772409 | 772442 | 34 | 3 [1] | [0] 2 | tolA | cell envelope integrity protein TolA |
| * | * | ÷ | NZ_CP009273 | 772567 | 772593 | 27 | 2 [0] | [1] 2 | tolA | cell envelope integrity protein TolA |
| * | * | ÷ | NZ_CP009273 | 903017 | 903039 | 23 | 2 [1] | [1] 2 | ybjT | SDR family oxidoreductase |
| * | * | ÷ | NZ_CP009273 | 990849 | 990865 | 17 | 2 [1] | [1] 2 | ssuD | FMNH2‑dependent alkanesulfonate monooxygenase |
| * | * | ÷ | NZ_CP009273 | 1137941 | 1138002 | 62 | 2 [1] | [1] 2 | rne | ribonuclease E |
| * | * | ÷ | NZ_CP009273 | 1168124 | 1168172 | 49 | 3 [1] | [1] 3 | mfd | transcription‑repair coupling factor |
| * | * | ÷ | NZ_CP009273 | 1314832 | 1314896 | 65 | 2 [1] | [1] 2 | trpD | bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD |
| * | * | ÷ | NZ_CP009273 | 1314987 | 1315027 | 41 | 2 [1] | [1] 2 | trpD | bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD |
| * | * | ÷ | NZ_CP009273 | 1316655 | 1316677 | 23 | 2 [0] | [1] 2 | trpE | anthranilate synthase component I |
| * | * | ÷ | NZ_CP009273 | 1374873 | 1374883 | 11 | 3 [1] | [0] 2 | pgmB | beta‑phosphoglucomutase |
| * | * | ÷ | NZ_CP009273 | 1424082 | 1424123 | 42 | 2 [1] | [1] 2 | stfR | prophage tail fiber N‑terminal domain‑containing protein |
| * | * | ÷ | NZ_CP009273 | 1424214 | 1424249 | 36 | 3 [0] | [1] 2 | stfR | prophage tail fiber N‑terminal domain‑containing protein |
| * | * | ÷ | NZ_CP009273 | 2000989 | 2000998 | 10 | 2 [1] | [0] 4 | amyA | alpha‑amylase |
| * | * | ÷ | NZ_CP009273 | 2370627 | 2370682 | 56 | 2 [1] | [1] 2 | menH | 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase |
| * | * | ÷ | NZ_CP009273 | 2669867 | 2669867 | 1 | 2 [0] | [0] 2 | yphD | ABC transporter permease |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP009273 | 224503 = | NA (NA) | 4 (0.210) | 4/156 | 1.4 | NA | noncoding (2258/2904 nt) | BW25113_RS01025 | 23S ribosomal RNA |
| ? | NZ_CP009273 | 224528 = | NA (NA) | noncoding (2283/2904 nt) | BW25113_RS01025 | 23S ribosomal RNA | |||||
| * | ? | NZ_CP009273 | 360104 = | NA (NA) | 32 (1.560) | 21/170 | 0.1 | NA | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
| ? | NZ_CP009273 | = 360286 | NA (NA) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
| * | ? | NZ_CP009273 | = 729706 | NA (NA) | 3 (0.160) | 3/154 | 1.6 | NA | pseudogene (103/1506 nt) | BW25113_RS03635 | RHS repeat protein |
| ? | NZ_CP009273 | = 729729 | NA (NA) | pseudogene (126/1506 nt) | BW25113_RS03635 | RHS repeat protein | |||||
| * | ? | NZ_CP009273 | = 1203261 | 7 (0.340) | 5 (0.300) | 5/138 | 1.0 | 44.1% | coding (305/630 nt) | BW25113_RS05990 | hypothetical protein |
| ? | NZ_CP009273 | = 1205058 | 7 (0.420) | coding (57/540 nt) | BW25113_RS06005 | phage tail protein | |||||
| * | ? | NZ_CP009273 | = 1391494 | NA (NA) | 14 (0.690) | 12/168 | 0.4 | 100% | intergenic (+145/‑128) | BW25113_RS06980/ynaJ | IS5‑like element IS5 family transposase/DUF2534 family protein |
| ? | NZ_CP009273 | 1972747 = | 0 (0.000) | intergenic (‑293/‑487) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC | |||||
| * | ? | NZ_CP009273 | = 1972751 | 2 (0.100) | 28 (1.360) | 20/170 | 0.1 | 93.3% | intergenic (‑297/‑483) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
| ? | NZ_CP009273 | = 2283592 | NA (NA) | intergenic (‑68/‑387) | BW25113_RS11435/narP | IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP | |||||
| * | ? | NZ_CP009273 | 2279605 = | 18 (0.870) | 4 (0.230) | 3/144 | 1.5 | 24.8% | coding (1751/1761 nt) | yejM | LPS biosynthesis‑modulating metalloenzyme YejM |
| ? | NZ_CP009273 | 2279638 = | 9 (0.520) | intergenic (+23/‑52) | yejM/BW25113_RS11425 | LPS biosynthesis‑modulating metalloenzyme YejM/tRNA‑Pro | |||||
| * | ? | NZ_CP009273 | = 4532507 | 13 (0.630) | 10 (0.540) | 7/152 | 0.8 | 38.0% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NZ_CP009273 | = 4532803 | 21 (1.140) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||