mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 536,986 | (G)5→6 | intergenic (+38/‑149) | clpX → / → lon | ATP‑dependent protease ATP‑binding subunit ClpX/endopeptidase La |
| RA | 964,882 | G→A | R74Q (CGG→CAG) | ECW_RS04675 → | DUF2732 family protein |
| RA | 1,160,228 | A→C | L182V (TTG→GTG) | yccM ← | 4Fe‑4S binding protein |
| RA | 1,201,459 | T→A | intergenic (+7/+34) | dgcT → / ← ECW_RS05820 | GGDEF domain‑containing protein/IS3‑like element IS3 family transposase |
| RA | 1,363,044 | G→C | intergenic (‑277/+152) | ECW_RS27505 ← / ← ECW_RS06715 | type I toxin‑antitoxin system toxin Ldr family protein/type I toxin‑antitoxin system toxin Ldr family protein |
| RA | 1,437,357 | C→A | V315F (GTT→TTT) | yciW ← | CMD domain‑containing protein |
| RA | 1,551,980 | (T)8→9 | intergenic (‑337/+29) | ompN ← / ← nifJ | porin OmpN/pyruvate:ferredoxin (flavodoxin) oxidoreductase |
| RA | 1,642,100 | C→T | pseudogene (1017/1137 nt) | ydcC → | ISAs1 family transposase |
| RA | 1,642,952 | T→C | V56V (GTA→GTG) | yddH ← | flavin reductase family protein |
| RA | 1,677,854 | C→A | intergenic (‑110/+21) | digH ← / ← gadC | glycoside hydrolase family 10 protein/acid resistance gamma‑aminobutyrate antiporter GadC |
| RA | 1,679,419 | +C | intergenic (‑9/+146) | gadC ← / ← gadB | acid resistance gamma‑aminobutyrate antiporter GadC/glutamate decarboxylase |
| MC JC | 1,704,950 | (GTTATTT)2→1 | pseudogene (5322‑5328/5428 nt) | ECW_RS08400 ← | ECSE_1600 family autotransporter |
| RA | 1,830,677 | (A)6→7 | pseudogene (137/929 nt) | tus → | DNA replication terminus site‑binding protein |
| RA | 1,867,117 | T→A | intergenic (‑6/‑195) | slyA ← / → ydhI | transcriptional regulator SlyA/DUF1656 domain‑containing protein |
| RA | 2,292,091 | +G | coding (36/39 nt) | ECW_RS27980 ← | hypothetical protein |
| RA | 2,312,962 | T→C | G139G (GGA→GGG) | ECW_RS11560 ← | phage tail sheath protein |
| RA | 2,312,971 | G→A | G136G (GGC→GGT) | ECW_RS11560 ← | phage tail sheath protein |
| RA | 2,312,974 | G→A | L135L (CTC→CTT) | ECW_RS11560 ← | phage tail sheath protein |
| RA | 2,322,282 | A→G | A137A (GCT→GCC) | ECW_RS11650 ← | head completion/stabilization protein |
| RA | 2,322,414 | A→G | V93V (GTT→GTC) | ECW_RS11650 ← | head completion/stabilization protein |
| RA | 2,322,420 | C→A | A91A (GCG→GCT) | ECW_RS11650 ← | head completion/stabilization protein |
| RA | 2,322,732 | T→C | intergenic (‑40/+60) | ECW_RS11650 ← / ← ECW_RS11655 | head completion/stabilization protein/terminase endonuclease subunit |
| RA | 2,322,748 | G→C | intergenic (‑56/+44) | ECW_RS11650 ← / ← ECW_RS11655 | head completion/stabilization protein/terminase endonuclease subunit |
| RA | 2,331,461 | (T)8→7 | intergenic (‑905/+261) | ECW_RS11680 ← / ← ECW_RS11685 | AAA family ATPase/replication endonuclease |
| RA | 2,753,670 | A→G | W20R (TGG→CGG) | ypfG ← | DUF1176 domain‑containing protein |
| RA | 2,860,853 | C→A | R442S (AGG→AGT) | qseE ← | two component system sensor histidine kinase QseE/GlrK |
| RA | 3,020,329 | G→T | intergenic (‑57/+6) | rpoS ← / ← nlpD | RNA polymerase sigma factor RpoS/murein hydrolase activator NlpD |
| RA | 3,053,299 | (A)8→9 | intergenic (‑32/‑286) | ygcW ← / → yqcE | SDR family oxidoreductase/MFS transporter |
| RA | 3,110,650 | C→T | F27F (TTC→TTT) | vgrG → | type VI secretion system tip protein VgrG |
| RA | 3,110,662 | A→G | E31E (GAA→GAG) | vgrG → | type VI secretion system tip protein VgrG |
| RA | 3,114,884 | Δ1 bp | pseudogene (125/2509 nt) | vgrG → | type VI secretion system tip protein VgrG |
| RA | 3,127,359 | C→T | pseudogene (675/1425 nt) | tssA → | type VI secretion system protein TssA |
| RA | 3,127,431 | C→T | pseudogene (747/1425 nt) | tssA → | type VI secretion system protein TssA |
| RA | 3,179,423 | (A)7→8 | intergenic (+11/‑71) | yqeI → / → ECW_RS15855 | transcriptional regulator/hypothetical protein |
| RA | 3,242,636 | +A | intergenic (‑1/+279) | ygfF ← / ← gcvP | SDR family oxidoreductase/aminomethyl‑transferring glycine dehydrogenase |
| RA | 3,375,228 | (T)7→8 | coding (2219/2220 nt) | ygiQ ← | YgiQ family radical SAM protein |
| RA | 3,477,291 | +GC | pseudogene (63/1363 nt) | tdcG ← | L‑serine ammonia‑lyase |
| MC JC | 3,614,356 | Δ11 bp | coding (1926‑1936/1941 nt) | csrD ← | RNase E specificity factor CsrD |
| RA | 3,655,775 | G→A | S431F (TCT→TTT) | secY ← | preprotein translocase subunit SecY |
| RA | 3,750,975 | G→A | intergenic (‑108/‑504) | malP ← / → malT | maltodextrin phosphorylase/HTH‑type transcriptional regulator MalT |
| RA | 3,841,812 | G→A | G12S (GGC→AGC) | gorA → | glutathione‑disulfide reductase |
| RA | 3,904,745 | A→C | intergenic (‑242/+503) | dppA ← / ← ECW_RS25300 | dipeptide ABC transporter substrate‑binding protein DppA/RtT sRNA |
| RA | 3,993,460 | A→T | H16Q (CAT→CAA) | grxC ← | glutaredoxin 3 |
| RA | 4,110,754 | G→T | V8L (GTG→TTG) | tnaC → | tryptophanase leader peptide |
| RA | 4,127,945 | (A)10→9 | intergenic (‑43/+92) | bglF ← / ← bglG | PTS beta‑glucoside transporter subunit IIABC/transcriptional antiterminator BglG |
| RA | 4,172,422 | G→T | intergenic (‑23/‑96) | hdfR ← / → maoP | HTH‑type transcriptional regulator HdfR/macrodomain Ori organization protein MaoP |
| RA | 4,336,992 | C→T | I492I (ATC→ATT) | ECW_RS21660 → | replication endonuclease |
| RA | 4,344,085 | G→A | Y293Y (TAC→TAT) | ECW_RS21690 ← | terminase ATPase subunit family protein |
| RA | 4,345,676 | C→A | pseudogene (540/854 nt) | ECW_RS21695 → | GPO family capsid scaffolding protein |
| RA | 4,350,170 | T→G | L93L (CTT→CTG) | lysB → | Rz‑like lysis system protein LysB |
| RA | 4,667,282 | (T)8→9 | intergenic (+46/‑80) | rlmB → / → yjfI | 23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB/DUF2170 family protein |
| RA | 4,729,669 | C→G | V46L (GTG→CTG) | pyrI ← | aspartate carbamoyltransferase regulatory subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_017635 | 174007 | 174027 | 21 | 2 [1] | [1] 2 | fhuB | Fe(3+)‑hydroxamate ABC transporter permease FhuB |
| * | * | ÷ | NC_017635 | 603100 | 603207–603106 | 7–108 | 2 [0] | [1] 2 | rhsD | rhs element protein RhsD |
| * | * | ÷ | NC_017635 | 799813–800428 | 800547–800435 | 8–735 | 2 [1] | [1] 2 | rhsB | rhs element protein RhsB |
| * | * | ÷ | NC_017635 | 1201511–1201842 | 1202673–1201844 | 3–1163 | 2 [1] | [1] 2 | [ECW_RS05820]–ECW_RS05820 | [ECW_RS05820],ECW_RS05820 |
| * | * | ÷ | NC_017635 | 1609565–1609745 | 1609838–1609750 | 6–274 | 2 [0] | [0] 2 | insQ | RNA‑guided endonuclease TnpB family protein |
| * | * | ÷ | NC_017635 | 1636298 | 1636319 | 22 | 2 [1] | [1] 2 | ECW_RS08125 | RHS element core protein |
| * | * | ÷ | NC_017635 | 3123951 | 3123958 | 8 | 2 [1] | [0] 2 | tssA | type VI secretion system protein TssA |
| * | * | ÷ | NC_017635 | 4474153–4474870 | 4474873 | 4–721 | 2 [0] | [1] 2 | ECW_RS22330 | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_017635 | 254279 = | 3 (0.070) | 43 (1.060) | 32/98 | 0.2 | 93.5% | coding (407/1281 nt) | tagH | type VI secretion system‑associated FHA domain protein TagH |
| ? | NC_017635 | 985471 = | NA (NA) | intergenic (+12/+8) | ECW_RS04805/ECW_RS04810 | phage tail protein/IS3 family transposase | |||||
| * | ? | NC_017635 | = 254282 | 2 (0.050) | 46 (1.160) | 34/96 | 0.1 | 95.9% | coding (404/1281 nt) | tagH | type VI secretion system‑associated FHA domain protein TagH |
| ? | NC_017635 | = 986727 | NA (NA) | coding (12/189 nt) | ECW_RS28140 | hypothetical protein | |||||
| * | ? | NC_017635 | 679483 = | 4 (0.100) | 63 (1.590) | 39/96 | 0.1 | 67.0% | intergenic (‑370/‑72) | ybdK/hokE | YbdK family carboxylate‑amine ligase/type I toxin‑antitoxin system toxin HokE |
| ? | NC_017635 | 3923170 = | 58 (1.460) | intergenic (‑77/+25) | hokA/ECW_RS27255 | type I toxin‑antitoxin system toxin HokA/IS3‑like element IS150 family transposase | |||||
| * | ? | NC_017635 | = 679488 | 3 (0.070) | 53 (1.370) | 42/94 | 0.0 | 65.1% | intergenic (‑375/‑67) | ybdK/hokE | YbdK family carboxylate‑amine ligase/type I toxin‑antitoxin system toxin HokE |
| ? | NC_017635 | = 3924609 | 54 (1.390) | intergenic (‑45/+256) | ECW_RS27255/glyS | IS3‑like element IS150 family transposase/glycine‑‑tRNA ligase subunit beta | |||||
| * | ? | NC_017635 | 985116 = | 46 (1.140) | 9 (0.320) | 8/68 | 1.1 | 23.8% | coding (1049/1392 nt) | ECW_RS04805 | phage tail protein |
| ? | NC_017635 | 987945 = | 26 (0.930) | coding (37/504 nt) | ECW_RS04830 | phage tail protein | |||||
| * | ? | NC_017635 | 2314099 = | 13 (0.320) | 17 (0.610) | 13/68 | 0.6 | 54.0% | coding (38/414 nt) | ECW_RS28245 | hypothetical protein |
| ? | NC_017635 | 2315940 = | 20 (0.720) | pseudogene (1/459 nt) | ECW_RS28250 | phage tail protein | |||||
| * | ? | NC_017635 | = 2314113 | 13 (0.320) | 16 (0.580) | 16/68 | 0.4 | 52.5% | coding (52/414 nt) | ECW_RS28245 | hypothetical protein |
| ? | NC_017635 | = 2315924 | 20 (0.720) | pseudogene (17/459 nt) | ECW_RS28250 | phage tail protein | |||||
| * | ? | NC_017635 | 4805124 = | 39 (0.960) | 31 (0.940) | 21/80 | 0.3 | 56.0% | intergenic (+48/‑432) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NC_017635 | 4805438 = | 17 (0.520) | intergenic (+362/‑118) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||
| * | ? | NC_017635 | = 4805132 | 39 (0.960) | 61 (1.860) | 38/80 | 0.0 | 71.5% | intergenic (+56/‑424) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA |
| ? | NC_017635 | = 4805428 | 17 (0.520) | intergenic (+352/‑128) | fimE/fimA | type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA | |||||