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 |
RA | 49,905 | T→G | L28R (CTC→CGC) | folA → | type 3 dihydrofolate reductase |
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 |
RA | 3,776,510 | A→G | L171P (CTG→CCG) | gpsA ← | NAD(P)H‑dependent glycerol‑3‑phosphate dehydrogenase |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NZ_CP009273 | 234705 | 234762 | 58 | 2 [1] | [1] 2 | [BW25113_RS01095] | [BW25113_RS01095] |
* | * | ÷ | NZ_CP009273 | 356981 | 357569 | 589 | 2 [0] | [0] 2 | lacA | galactoside O‑acetyltransferase |
* | * | ÷ | NZ_CP009273 | 422676 | 422701 | 26 | 4 [1] | [1] 2 | tgt | tRNA guanosine(34) transglycosylase Tgt |
* | * | ÷ | NZ_CP009273 | 508142 | 508150 | 9 | 2 [0] | [1] 2 | ybaT | APC family permease |
* | * | ÷ | NZ_CP009273 | 716393 | 716452 | 60 | 2 [1] | [1] 2 | BW25113_RS26090/kdpE | leader peptide SpeFL/two‑component system response regulator KdpE |
* | * | ÷ | NZ_CP009273 | 764461 | 764507 | 47 | 2 [1] | [1] 2 | mngB | mannosylglycerate hydrolase |
* | * | ÷ | NZ_CP009273 | 804337 | 804346 | 10 | 2 [1] | [1] 2 | bioA | adenosylmethionine‑‑8‑amino‑7‑oxononanoate transaminase |
* | * | ÷ | NZ_CP009273 | 828697 | 828742 | 46 | 2 [1] | [1] 2 | dinG | ATP‑dependent DNA helicase DinG |
* | * | ÷ | NZ_CP009273 | 835559 | 835569 | 11 | 3 [0] | [1] 9 | fiu | catecholate siderophore receptor Fiu |
* | * | ÷ | NZ_CP009273 | 865331 | 865338 | 8 | 2 [0] | [1] 3 | gsiB | glutathione ABC transporter substrate‑binding protein GsiB |
* | * | ÷ | NZ_CP009273 | 868426 | 868438 | 13 | 2 [0] | [0] 2 | [pdeI] | [pdeI] |
* | * | ÷ | NZ_CP009273 | 871190 | 871209 | 20 | 2 [1] | [1] 2 | dgcI | GGDEF domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 877732 | 877774 | 43 | 2 [1] | [1] 2 | deoR | DNA‑binding transcriptional repressor DeoR |
* | * | ÷ | NZ_CP009273 | 913643 | 913653 | 11 | 2 [0] | [0] 2 | ybjX | VirK/YbjX family protein |
* | * | ÷ | NZ_CP009273 | 931355 | 931373 | 19 | 2 [1] | [1] 3 | ftsK | DNA translocase FtsK |
* | * | ÷ | NZ_CP009273 | 950107 | 950176 | 70 | 2 [1] | [0] 2 | focA/ycaO | formate transporter FocA/30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
* | * | ÷ | NZ_CP009273 | 950509 | 950545 | 37 | 2 [1] | [1] 2 | ycaO | 30S ribosomal protein S12 methylthiotransferase accessory factor YcaO |
* | * | ÷ | NZ_CP009273 | 1021685 | 1021705 | 21 | 2 [1] | [0] 2 | helD | DNA helicase IV |
* | * | ÷ | NZ_CP009273 | 1086256 | 1086312 | 57 | 2 [1] | [0] 2 | pgaA | poly‑beta‑1,6 N‑acetyl‑D‑glucosamine export porin PgaA |
* | * | ÷ | NZ_CP009273 | 1099567 | 1099580 | 14 | 2 [1] | [1] 2 | csgB | curli minor subunit CsgB |
* | * | ÷ | NZ_CP009273 | 1099668 | 1099675 | 8 | 2 [1] | [1] 3 | csgB | curli minor subunit CsgB |
* | * | ÷ | NZ_CP009273 | 1101646 | 1101649 | 4 | 4 [0] | [0] 2 | ymdB | O‑acetyl‑ADP‑ribose deacetylase |
* | * | ÷ | NZ_CP009273 | 1116811 | 1116895 | 85 | 2 [1] | [1] 2 | dinI | DNA damage‑inducible protein I |
* | * | ÷ | NZ_CP009273 | 1150097 | 1150105 | 9 | 2 [0] | [1] 2 | yceG | cell division protein YceG |
* | * | ÷ | NZ_CP009273 | 1165747 | 1165754 | 8 | 2 [0] | [0] 2 | ldtC | L,D‑transpeptidase LdtC |
* | * | ÷ | NZ_CP009273 | 1172096 | 1172136 | 41 | 2 [0] | [1] 3 | lolD | lipoprotein‑releasing ABC transporter ATP‑binding protein LolD |
* | * | ÷ | NZ_CP009273 | 1175219 | 1175235 | 17 | 2 [0] | [0] 3 | cobB | NAD‑dependent protein deacylase |
* | * | ÷ | NZ_CP009273 | 1243250 | 1243257 | 8 | 2 [1] | [1] 2 | dhaM | dihydroxyacetone kinase phosphoryl donor subunit DhaM |
* | * | ÷ | NZ_CP009273 | 1251756 | 1251778 | 23 | 2 [1] | [1] 2 | ycgV/ychF | autotransporter outer membrane beta‑barrel domain‑containing protein/redox‑regulated ATPase YchF |
* | * | ÷ | NZ_CP009273 | 1253600 | 1253604 | 5 | 2 [1] | [0] 2 | pth | aminoacyl‑tRNA hydrolase |
* | * | ÷ | NZ_CP009273 | 1276782 | 1276815 | 34 | 2 [1] | [1] 3 | narG | nitrate reductase subunit alpha |
* | * | ÷ | NZ_CP009273 | 1309867 | 1309922 | 56 | 2 [1] | [1] 2 | yciF | ferritin‑like domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1348038 | 1348058 | 21 | 2 [1] | [1] 2 | sapC | peptide ABC transporter permease SapC |
* | * | ÷ | NZ_CP009273 | 1375489 | 1375516 | 28 | 2 [1] | [1] 3 | BW25113_RS06905 | ABC transporter ATP‑binding protein |
* | * | ÷ | NZ_CP009273 | 1384267 | 1384296 | 30 | 2 [1] | [1] 3 | mpaA | murein tripeptide amidase MpaA |
* | * | ÷ | NZ_CP009273 | 1435318 | 1435340 | 23 | 2 [1] | [1] 4 | ydbJ | DUF333 domain‑containing protein |
* | * | ÷ | NZ_CP009273 | 1757736 | 1757738 | 3 | 3 [0] | [1] 2 | sufB | Fe‑S cluster assembly protein SufB |
* | * | ÷ | NZ_CP009273 | 1764424 | 1764456 | 33 | 2 [1] | [1] 3 | [ydiK] | [ydiK] |
* | * | ÷ | NZ_CP009273 | 1881165 | 1881188 | 24 | 2 [1] | [1] 2 | rnd | ribonuclease D |
* | * | ÷ | NZ_CP009273 | 1945241 | 1945251 | 11 | 2 [0] | [1] 2 | yecD | hydrolase |
* | * | ÷ | NZ_CP009273 | 2001035 | 2001109 | 75 | 3 [1] | [1] 2 | amyA | alpha‑amylase |
* | * | ÷ | NZ_CP009273 | 2149175 | 2149195 | 21 | 2 [0] | [1] 2 | mdtB | multidrug efflux RND transporter permease subunit MdtB |
* | * | ÷ | NZ_CP009273 | 2178140 | 2178196 | 57 | 3 [1] | [1] 2 | thiM | hydroxyethylthiazole kinase |
* | * | ÷ | NZ_CP009273 | 2212056 | 2212104 | 49 | 2 [1] | [1] 2 | osmF | glycine betaine ABC transporter substrate‑binding protein OsmF |
* | * | ÷ | NZ_CP009273 | 2462999 | 2463050 | 52 | 3 [1] | [1] 3 | BW25113_RS12270 | hypothetical protein |
* | * | ÷ | NZ_CP009273 | 3628487 | 3646519–3645399 | 16913–18033 | 16 [0] | [1] 3 | [yhiM]–[BW25113_RS18160] | [yhiM],yhiN,pitA,uspB,uspA,BW25113_RS26225,BW25113_RS26230,dtpB,rsmJ,prlC,rlmJ,gorA,dinQ,arsR,arsB,arsC,BW25113_RS18155,[BW25113_RS18160] |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NZ_CP009273 | 360104 = | NA (NA) | 27 (1.550) | 18/168 | 0.1 | 37.5% | intergenic (‑35/+251) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein |
? | NZ_CP009273 | = 360286 | 45 (2.590) | intergenic (‑217/+69) | lacZ/BW25113_RS23320 | beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein | |||||
* | ? | NZ_CP009273 | 1203246 = | 11 (0.630) | 3 (0.210) | 3/136 | 1.2 | 31.7% | coding (290/630 nt) | BW25113_RS05990 | hypothetical protein |
? | NZ_CP009273 | 1205075 = | 4 (0.280) | coding (40/540 nt) | BW25113_RS06005 | phage tail protein | |||||
* | ? | NZ_CP009273 | = 1391494 | NA (NA) | 11 (0.640) | 5/166 | 1.0 | 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 (0.120) | 23 (1.320) | 13/168 | 0.2 | 92.0% | 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 | 2282398 = | NA (NA) | 16 (0.920) | 13/168 | 0.2 | 100% | pseudogene (3/2532 nt) | yejO | autotransporter YejO |
? | NZ_CP009273 | = 3628486 | 0 (0.000) | coding (286/1053 nt) | yhiM | DUF2776 domain‑containing protein | |||||
* | ? | NZ_CP009273 | = 4532507 | 11 (0.630) | 5 (0.320) | 5/150 | 0.9 | 27.9% | intergenic (+57/‑425) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
? | NZ_CP009273 | = 4532803 | 16 (1.030) | intergenic (+353/‑129) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |