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 |
| RA | 82,046 | A→G | V495A (GTT→GCT) | leuA ← | 2‑isopropylmalate synthase |
| RA | 251,586 | A→G | D230G (GAC→GGC) | dinB → | DNA polymerase IV |
| MC | 361,238 | Δ680 bp | between other | lacA | lacA |
| RA | 393,516 | A→G | pseudogene (547/1449 nt) | yaiT → | putative autotransporter YaiT |
| RA | 418,132 | A→G | M82V (ATG→GTG) | phoR → | sensory histidine kinase PhoR |
| RA | 500,945 | C→T | A274V (GCG→GTG) | gsk → | inosine/guanosine kinase |
| RA | 570,683 | T→C | intergenic (+255/‑210) | ybcK → / → ybcL | DLP12 prophage; putative recombinase/DLP12 prophage; periplasmic protein YbcL |
| RA | 646,808 | (C)6→7 | coding (702/879 nt) | citG ← | triphosphoribosyl‑dephospho‑CoA synthase |
| RA | 651,821 | A→G | R12R (CGT→CGC) | citC ← | citrate lyase synthetase |
| RA | 684,567 | T→C | D230G (GAC→GGC) | gltL ← | glutamate/aspartate ABC transporter ATP binding subunit |
| RA | 696,576 | C→T | noncoding (41/75 nt) | glnV ← | tRNA‑Gln |
| RA | 741,848 | C→T | V237I (GTA→ATA) | dtpD ← | dipeptide:H(+) symporter DtpD |
| RA | 749,643 | A→G | V22A (GTG→GCG) | ybgP ← | putative fimbrial chaperone YbgP |
| RA | 962,281 | T→A | I96N (ATC→AAC) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 967,101 | T→C | F161L (TTC→CTC) | msbA → | ATP‑binding lipopolysaccharide transport protein |
| RA | 1,005,099 | A→G | N111S (AAC→AGC) | pyrD → | dihydroorotate dehydrogenase, type 2 |
| RA | 1,010,934 | A→G | D324G (GAC→GGC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,125,402 | A→G | intergenic (‑76/‑160) | mdtH ← / → rimJ | multidrug efflux pump MdtH/ribosomal‑protein‑S5‑alanine N‑acetyltransferase |
| RA | 1,149,770 | A→G | T15A (ACC→GCC) | fabD → | [acyl‑carrier‑protein] S‑malonyltransferase |
| RA | 1,199,473 | T→C | V260A (GTG→GCG) | lit → | e14 prophage; cell death peptidase Lit |
| RA | 1,239,471 | A→G | H198R (CAC→CGC) | dadX → | alanine racemase 2 |
| RA | 1,287,315 | T→C | noncoding (14/85 nt) | tyrV ← | tRNA‑Tyr |
| RA | 1,320,256 | C→T | G377R (GGG→AGG) | trpD ← | anthranilate synthase subunit TrpD |
| RA | 1,336,213 | A→G | D128G (GAC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,449,126 | T→C | N742D (AAC→GAC) | tynA ← | copper‑containing amine oxidase |
| RA | 1,462,320 | A→G | T66A (ACC→GCC) | paaK → | phenylacetate‑CoA ligase |
| RA | 1,534,885 | C→T | intergenic (+16/+80) | nhoA → / ← yddE | arylamine N‑acetyltransferase/PF02567 family protein YddE |
| RA | 1,658,173 | T→C | F35F (TTT→TTC) | ynfE → | putative selenate reductase YnfE |
| RA | 1,665,258 | T→C | intergenic (+138/‑57) | dmsD → / → clcB | redox enzyme maturation protein DmsD/putative chloride:H(+) antiporter ClcB |
| RA | 1,736,325 | C→T | A322A (GCG→GCA) | ydhP ← | putative transporter YdhP |
| RA | 1,745,998 | T→C | T44A (ACC→GCC) | ydhQ ← | adhesin‑like autotransporter YdhQ |
| JC JC | 1,873,031 | IS1 (–) +9 bp | coding (991‑999/1491 nt) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,915,493 | G→A | I14I (ATC→ATT) | proQ ← | RNA chaperone ProQ |
| RA | 1,927,241 | (C)6→7 | coding (1599/2061 nt) | ptrB ← | oligopeptidase B |
| RA | 1,990,786 | G→A | R369Q (CGG→CAG) | tyrP → | tyrosine:H(+) symporter |
| RA | 2,021,787 | (C)5→6 | coding (284/366 nt) | fliO → | flagellar biosynthesis protein FliO |
| RA | 2,030,457 | T→C | *307Q (TAA→CAA) L154L (TTA→TTG) |
yedA → vsr ← |
putative transporter YedA DNA mismatch endonuclease of the very short patch (VSP) mismatch repair pathway |
| RA | 2,115,377 | T→C | N174D (AAC→GAC) | wcaM ← | putative colanic acid biosynthesis protein WcaM |
| RA | 2,153,388 | T→C | noncoding (78/144 nt) I7M (ATA→ATG) |
sibA → ibsA ← |
small RNA SibA toxic peptide IbsA |
| RA | 2,199,090 | A→G | intergenic (+1792/‑1189) | yehF → / → yehI | putative protein YehF/DUF4132 domain‑containing protein YehI |
| RA | 2,292,186 | A→G | S75S (AGT→AGC) | ccmH ← | holocytochrome c synthetase ‑ thiol:disulfide oxidoreductase CcmH |
| RA | 2,462,889 | (C)9→8 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,500,163 | A→G | H498R (CAC→CGC) | ypdA → | sensory histidine kinase YpdA |
| RA | 2,597,326 | G→A | A98V (GCT→GTT) | purC ← | phosphoribosylaminoimidazole‑succinocarboxamide synthase |
| RA | 2,601,899 | G→A | D28N (GAC→AAC) | hyfB → | hydrogenase 4 component B |
| RA | 2,656,435 | G→T | intergenic (‑77/+101) | pepB ← / ← iscX | aminopeptidase B/accessory iron‑sulfur cluster assembly protein IscX |
| RA | 2,656,566 | A→G | I57I (ATT→ATC) | iscX ← | accessory iron‑sulfur cluster assembly protein IscX |
| RA | 2,674,003 | G→A | A229V (GCA→GTA) | yphB ← | putative aldose 1‑epimerase YphB |
| RA | 2,698,170 | T→C | E127E (GAA→GAG) | pgpC ← | phosphatidylglycerophosphatase C |
| RA | 2,737,290 | A→G | Q46R (CAA→CGA) | raiA → | stationary phase translation inhibitor and ribosome stability factor |
| RA | 2,755,139 | T→C | C82R (TGC→CGC) | smpB → | SsrA‑binding protein |
| RA | 2,758,577 | G→T | N8K (AAC→AAA) | yfjH ← | CP4‑57 prophage; protein YfjH |
| RA | 2,777,301 | C→T | L63L (CTG→TTG) | yfjZ → | CP4‑57 prophage; putative antitoxin of the YpjF‑YfjZ toxin‑antitoxin system |
| RA | 2,908,897 | T→C | D257G (GAC→GGC) | pyrG ← | CTP synthetase |
| RA | 3,041,234 | T→C | intergenic (‑164/‑79) | sdhE ← / → ygfZ | FAD assembly factor/folate‑binding protein |
| RA | 3,075,081 | G→A | P39S (CCG→TCG) | fumE ← | fumarase E |
| RA | 3,092,563 | G→A | G229E (GGG→GAG) | gshB → | glutathione synthetase |
| RA | 3,101,039 | (C)7→8 | coding (585/720 nt) | yggN ← | putative EcfF |
| RA | 3,140,586 | G→A | Q72* (CAA→TAA) | hybE ← | hydrogenase 2‑specific chaperone |
| RA | 3,210,463 | G→A | N27N (AAC→AAT) | tsaD ← | N(6)‑L‑threonylcarbamoyladenine synthase, TsaD subunit |
| RA | 3,241,289 | A→T | N152K (AAT→AAA) | ygjV ← | inner membrane protein |
| RA | 3,267,060 | G→A | S2S (AGC→AGT) | tdcA ← | DNA‑binding transcriptional activator TdcA |
| RA | 3,385,572 | T→C | V12A (GTA→GCA) | yhcN → | DUF1471 domain‑containing stress‑induced protein YhcN |
| RA | 3,413,548 | A→G | intergenic (‑83/‑316) | envR ← / → acrE | DNA‑binding transcriptional repressor EnvR/multidrug efflux pump membrane fusion lipoprotein AcrE |
| RA | 3,440,129 | T→C | T301A (ACT→GCT) | rpoA ← | RNA polymerase subunit alpha |
| RA | 3,584,362 | A→G | intergenic (+53/‑42) | yrhA → / → yrhD | putative uncharacterized protein YrhA/uncharacterized protein YrhD |
| RA | 3,648,610 | T→C | L28P (CTG→CCG) | arsR → | DNA‑binding transcriptional repressor ArsR |
| RA | 3,825,418 | A→G | N70S (AAC→AGC) | recG → | ATP‑dependent DNA helicase RecG |
| RA | 3,878,537 | T→C | Y528C (TAC→TGC) | gyrB ← | DNA gyrase subunit B |
| RA | 3,891,768 | G→A | A52T (GCA→ACA) | mdtL → | efflux pump MdtL |
| RA | 4,293,106 | (G)7→8 | coding (1595/1659 nt) | nrfE → | putative cytochrome c‑type biogenesis protein NrfE |
| RA | 4,294,366 | A→T | intergenic (+227/‑115) | nrfG → / → gltP | putative formate‑dependent nitrite reductase complex subunit NrfG/glutamate/aspartate : H(+) symporter GltP |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,395,008 | A→G | T315A (ACC→GCC) | nnr → | NAD(P)HX epimerase/NAD(P)HX dehydratase |
| RA | 4,424,909 | (A)7→6 | intergenic (‑118/‑209) | yjfY ← / → rpsF | DUF1471 domain‑containing protein YjfY/30S ribosomal subunit protein S6 |
| RA | 4,487,240 | A→G | L341L (TTA→TTG) | lptF → | lipopolysaccharide transport system protein LptF |
| RA | 4,521,565 | (A)6→7 | coding (456/1350 nt) | yjhF ← | KpLE2 phage‑like element; putative transporter YjhF |
| RA | 4,524,976 | G→A | S12F (TCC→TTC) | yjhH ← | KpLE2 phage‑like element; putative 2‑dehydro‑3‑deoxy‑D‑pentonate aldolase |
| RA | 4,537,770 | C→T | L332L (TTG→TTA) | nanM ← | N‑acetylneuraminate mutarotase |
| RA | 4,612,684 | T→C | F92L (TTC→CTC) | yjjU → | putative patatin‑like phospholipase YjjU |
| RA | 4,634,141 | T→C | R115R (CGT→CGC) | ytjC → | putative phosphatase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2857006 | 2857095 | 90 | 186 [181] | [0] 400 | [mutS] | [mutS] |
| * | * | ÷ | NC_000913 | 3423696–3424234 | 3424599–3424238 | 5–904 | 185 [180] | [182] 188 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 70046 = | 393 (1.040) | 379 (1.030) | 159/188 | 0.2 | 66.6% | coding (3/1701 nt) | araB | ribulokinase |
| ? | NC_000913 | 2857096 = | 0 (0.000) | coding (4/2562 nt) | mutS | DNA mismatch repair protein MutS | |||||
| * | ? | NC_000913 | 1207790 = | 93 (0.250) | 193 (0.610) | 112/162 | 1.6 | 69.1% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 95 (0.300) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 91 (0.240) | 175 (0.550) | 100/162 | 2.8 | 67.2% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 95 (0.300) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||