mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| JC JC | 168,627 | IS2 (+) +5 bp | 7.0% | coding (1144‑1148/2244 nt) | fhuA → | ferrichrome outer membrane transporter |
| RA | 169,078 | C→A | 5.0% | S532* (TCG→TAG) | fhuA → | ferrichrome outer membrane transporter |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 330,848 | G→A | 5.4% | T462T (ACG→ACA) | betT → | choline transporter of high affinity |
| RA | 350,348 | G→T | 5.6% | G113C (GGT→TGT) | prpC → | 2‑methylcitrate synthase |
| RA | 361,901 | T→G | 5.3% | intergenic (‑41/+25) | lacA ← / ← lacY | thiogalactoside acetyltransferase/lactose permease |
| RA | 368,813 | A→T | 6.3% | Q68L (CAG→CTG) | mhpA → | 3‑(3‑hydroxyphenyl)propionate hydroxylase |
| RA | 422,429 | T→G | 23.8% | intergenic (+70/‑89) | proY → / → malZ | proline‑specific permease/maltodextrin glucosidase |
| RA | 553,999 | G→A | 7.8% | H147Y (CAC→TAC) | ppiB ← | peptidyl‑prolyl cis‑trans isomerase B (rotamase B) |
| RA | 675,414 | C→A | 24.3% | H133N (CAT→AAT) | ybeL → | DUF1451 family protein |
| RA | 699,657 | C→T | 5.4% | V224I (GTT→ATT) | umpH ← | UMP phosphatase |
| RA | 710,170 | C→T | 5.3% | intergenic (+54/+30) | chiQ → / ← fur | chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor |
| RA | 710,173 | A→G | 5.3% | intergenic (+57/+27) | chiQ → / ← fur | chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor |
| RA | 751,156 | G→A | 5.2% | R338R (CGC→CGT) | ybgQ ← | putative outer membrane protein |
| RA | 758,983 | T→A | 67.2% | L93Q (CTG→CAG) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 819,973 | T→A | 6.0% | V30V (GTT→GTA) | ybhL → | putative acetate transporter; BAX Inhibitor‑1 family inner membrane protein |
| RA | 848,773 | T→C | 5.5% | T47A (ACC→GCC) | dps ← | Fe‑binding and storage protein; stress‑inducible DNA‑binding protein |
| RA | 1,009,106 | T→C | 5.0% | Y421Y (TAT→TAC) | rlmL → | 23S rRNA m(2)G2445 and m(7)G2069 methyltransferases, SAM‑dependent |
| RA | 1,035,378 | G→A | 5.9% | V105M (GTG→ATG) | hyaC → | hydrogenase 1, b‑type cytochrome subunit |
| RA | 1,066,843 | G→T | 5.1% | intergenic (+17/+21) | agp → / ← yccJ | glucose‑1‑phosphatase/inositol phosphatase/uncharacterized protein |
| RA | 1,066,845 | G→C | 5.0% | intergenic (+19/+19) | agp → / ← yccJ | glucose‑1‑phosphatase/inositol phosphatase/uncharacterized protein |
| RA | 1,066,846 | A→T | 5.0% | intergenic (+20/+18) | agp → / ← yccJ | glucose‑1‑phosphatase/inositol phosphatase/uncharacterized protein |
| RA | 1,066,847 | A→C | 5.0% | intergenic (+21/+17) | agp → / ← yccJ | glucose‑1‑phosphatase/inositol phosphatase/uncharacterized protein |
| RA | 1,071,412 | G→A | 6.4% | N118N (AAC→AAT) | rutD ← | putative reactive intermediate detoxifying aminoacrylate hydrolase |
| RA | 1,077,580 | C→T | 6.7% | G435S (GGC→AGC) | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| RA | 1,087,476 | C→T | 7.4% | R124H (CGC→CAC) | pgaC ← | biofilm PGA synthase PgaCD, catalytic subunit; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine synthase |
| RA | 1,168,106 | A→G | 7.4% | N170D (AAC→GAC) | ycfJ → | uncharacterized protein |
| RA | 1,174,077 | G→A | 6.6% | intergenic (‑113/+15) | mfd ← / ← ycfT | transcription‑repair coupling factor/inner membrane protein |
| RA | 1,174,080 | T→C | 6.7% | intergenic (‑116/+12) | mfd ← / ← ycfT | transcription‑repair coupling factor/inner membrane protein |
| RA | 1,287,009 | A→T | 18.9% | intergenic (+483/+57) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,420,963 | A→G | 5.1% | T94A (ACC→GCC) | ydaT → | Rac prophage; uncharacterized protein |
| RA | 1,452,110 | T→C | 6.8% | K511K (AAA→AAG) | paaZ ← | oxepin‑CoA hydrolase and 3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase |
| RA | 1,501,325 | G→A | 5.1% | Q251Q (CAG→CAA) | tehA → | potassium‑tellurite ethidium and proflavin transporter |
| RA | 1,513,698 | C→T | 7.3% | N294N (AAC→AAT) | ydcT → | putative ABC transporter ATPase |
| RA | 1,533,148 | C→T | 5.7% | L33L (CTG→TTG) | pptA → | 4‑oxalocrotonate tautomerase |
| RA | 1,605,732 | G→A | 6.2% | A228T (GCC→ACC) | lsrB → | autoinducer 2‑binding protein |
| RA | 1,795,227 | A→T | 7.5% | intergenic (‑75/+26) | btuC ← / ← ihfA | vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit |
| RA | 1,795,228 | G→C | 6.4% | intergenic (‑76/+25) | btuC ← / ← ihfA | vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit |
| RA | 1,817,619 | A→G | 5.2% | F294F (TTT→TTC) | chbF ← | phospho‑chitobiase; general 6‑phospho‑beta‑glucosidase activity |
| RA | 1,853,166 | C→T | 6.1% | A272T (GCA→ACA) | ydjE ← | putative MFS sugar transporter, membrane protein |
| RA | 1,857,578 | C→T | 6.2% | M64I (ATG→ATA) | ydjI ← | putative aldolase |
| RA | 1,898,845 | G→A | 5.6% | R140H (CGT→CAT) | yoaD → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase, regulator of cellulose production |
| RA | 1,900,361 | C→T | 7.0% | V409I (GTC→ATC) | yoaE ← | putative membrane protein/conserved protein |
| RA | 1,934,587 | T→C | 62.9% | L6L (TTA→TTG) | edd ← | 6‑phosphogluconate dehydratase |
| JC JC | 1,961,829 | IS5 (–) +4 bp | 68.6% | intergenic (+34/‑140) | argS → / → yecT | arginyl‑tRNA synthetase/uncharacterized protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 1,980,924 | G→T | 6.1% | P230Q (CCG→CAG) | otsA ← | trehalose‑6‑phosphate synthase |
| RA | 2,029,388 | A→G | 7.7% | intergenic (‑22/‑151) | yedI ← / → yedA | DUF808 family inner membrane protein/amino acid exporter for phenylalanine, threonine |
| RA | 2,076,922 | G→T | 6.8% | E36* (GAA→TAA) | yeeT → | CP4‑44 prophage; uncharacterized protein |
| RA | 2,079,004 | G→C | 7.7% | intergenic (+73/+28) | yoeF → / ← yeeX | pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related/UPF0265 family protein |
| RA | 2,096,667 | Δ1 bp | 7.0% | coding (54/612 nt) | hisI → | phosphoribosyl‑AMP cyclohydrolase and phosphoribosyl‑ATP pyrophosphatase |
| RA | 2,096,668 | Δ1 bp | 7.1% | coding (55/612 nt) | hisI → | phosphoribosyl‑AMP cyclohydrolase and phosphoribosyl‑ATP pyrophosphatase |
| JC | 2,100,210 | Δ12 bp | 24.8% | coding (1048‑1059/1407 nt) | gnd ← | 6‑phosphogluconate dehydrogenase, decarboxylating |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,138,988 | G→A | 6.3% | G363S (GGC→AGC) | yegH → | inner membrane protein |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,198,999 | C→T | 5.5% | pseudogene (2526/2847 nt) | yehH → | DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function |
| RA | 2,200,745 | G→T | 7.0% | R156L (CGC→CTC) | yehI → | DUF4132 domain‑containing protein |
| RA | 2,209,135 | A→G | 5.1% | pseudogene (36/2001 nt) | yehQ → | pseudogene |
| RA | 2,248,223 | A→G | 6.0% | Y104H (TAC→CAC) | lysP ← | lysine transporter |
| RA | 2,283,203 | G→T | 5.2% | L249M (CTG→ATG) | yejK ← | spermidine nucleoid‑associated protein |
| RA | 2,293,137 | C→T | 9.7% | A590T (GCC→ACC) | ccmF ← | heme lyase, CcmF subunit |
| RA | 2,305,085 | A→G | 8.6% | intergenic (+692/+23) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,086 | C→G | 8.2% | intergenic (+693/+22) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,087 | C→T | 8.2% | intergenic (+694/+21) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,357,836 | G→A | 7.8% | pseudogene (33/198 nt) | ypaA → | pseudogene, C‑terminal fragment, Transposase_31 family |
| RA | 2,418,506 | C→T | 5.7% | R476C (CGT→TGT) | yfcC → | putative inner membrane transporter; C4‑dicarboxylate anaerobic carrier family protein |
| RA | 2,418,509 | Δ1 bp | 5.6% | coding (1429/1521 nt) | yfcC → | putative inner membrane transporter; C4‑dicarboxylate anaerobic carrier family protein |
| RA | 2,448,244 | G→A | 5.5% | A66V (GCG→GTG) | prmB ← | N5‑glutamine methyltransferase |
| RA | 2,539,991 | A→G | 6.3% | L275P (CTG→CCG) | cysA ← | sulfate/thiosulfate transporter subunit |
| RA | 2,544,953 | A→G | 7.1% | T219T (ACT→ACC) | murR ← | repressor for murPQ, MurNAc 6‑P inducible |
| RA | 2,545,410 | C→T | 5.2% | R67H (CGT→CAT) | murR ← | repressor for murPQ, MurNAc 6‑P inducible |
| RA | 2,560,991 | T→A | 18.1% | intergenic (+93/‑377) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,560,996 | G→T | 14.7% | intergenic (+98/‑372) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,602,905 | T→C | 6.0% | I363T (ATT→ACT) | hyfB → | hydrogenase 4, membrane subunit |
| RA | 2,663,466 | G→T | 6.6% | V9L (GTG→TTG) | suhB → | inositol monophosphatase |
| RA | 2,663,474 | A→T | 7.0% | A11A (GCA→GCT) | suhB → | inositol monophosphatase |
| RA | 2,663,482 | A→C | 6.1% | K14T (AAG→ACG) | suhB → | inositol monophosphatase |
| RA | 2,664,144 | A→G | 5.1% | N235D (AAC→GAC) | suhB → | inositol monophosphatase |
| RA | 2,740,598 | C→T | 5.8% | G185S (GGT→AGT) | aroF ← | 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible |
| RA | 3,424,646 | C→A | 6.9% | noncoding (2138/2904 nt) | rrlD ← | 23S ribosomal RNA of rrnD operon |
| RA | 3,424,661 | C→A | 5.7% | noncoding (2123/2904 nt) | rrlD ← | 23S ribosomal RNA of rrnD operon |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 37.9% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2066296–2066582 | 2066582 | 1–287 | 16 [14] | [13] 17 | [insH1] | [insH1] |
| * | * | ÷ | NC_000913 | 3423785–3424234 | 3424517–3424239 | 6–733 | 15 [13] | [14] 16 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3514390 | 3515068 | 679 | 18 [13] | [11] 17 | [rpe] | [rpe] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 168380 = | 100 (1.150) | 56 (0.640) | 46/262 | NT | 37.3% | coding (897/2244 nt) | fhuA | ferrichrome outer membrane transporter |
| ? | NC_000913 | = 169386 | 88 (1.010) | coding (1903/2244 nt) | fhuA | ferrichrome outer membrane transporter | |||||
| * | ? | NC_000913 | = 228108 | NA (NA) | 5 (0.060) | 3/254 | NT | NA | noncoding (2350/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 228124 | NA (NA) | noncoding (2366/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 381258 = | NA (NA) | 4 (0.050) | 4/260 | NT | NA | pseudogene (3/417 nt) | yaiX | pseudogene, interrupted by IS2A; hexapeptide transferase superfamily; putative transferase |
| ? | NC_000913 | = 382589 | NA (NA) | noncoding (1330/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 17 (0.190) | 35 (0.460) | 32/230 | NT | 66.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 20 (0.260) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 16 (0.180) | 33 (0.430) | 30/230 | NT | 66.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 20 (0.260) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1355762 | 49 (0.560) | 3 (0.040) | 3/246 | NT | 5.9% | coding (1349/1644 nt) | sapA | antimicrobial peptide transport ABC transporter periplasmic binding protein |
| ? | NC_000913 | = 1355783 | 49 (0.600) | coding (1328/1644 nt) | sapA | antimicrobial peptide transport ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1443998 | 51 (0.580) | 3 (0.040) | 3/240 | NT | 5.8% | coding (948/2640 nt) | ydbH | putative membrane‑anchored protein, function unknown |
| ? | NC_000913 | = 1444006 | 51 (0.640) | coding (956/2640 nt) | ydbH | putative membrane‑anchored protein, function unknown | |||||
| * | ? | NC_000913 | = 1795226 | 59 (0.680) | 3 (0.040) | 4/240 | NT | 5.4% | intergenic (‑74/+27) | btuC/ihfA | vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit |
| ? | NC_000913 | = 1795229 | 52 (0.650) | intergenic (‑77/+24) | btuC/ihfA | vitamin B12 ABC transporter permease/integration host factor (IHF), DNA‑binding protein, alpha subunit | |||||
| * | ? | NC_000913 | 1876669 = | 53 (0.610) | 5 (0.060) | 3/246 | NT | 8.8% | coding (997/1182 nt) | yeaN | putative MFS transporter, inner membrane protein |
| ? | NC_000913 | 1876733 = | 54 (0.660) | coding (1061/1182 nt) | yeaN | putative MFS transporter, inner membrane protein | |||||
| * | ? | NC_000913 | 2794028 = | NA (NA) | 4 (0.050) | 4/250 | NT | NA | noncoding (1/136 nt) | REP191 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP191 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | NC_000913 | 2794059 = | NA (NA) | noncoding (32/136 nt) | REP191 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP191 (repetitive extragenic palindromic) element; contains 3 REP sequences | |||||
| * | ? | NC_000913 | = 3427065 | NA (NA) | 3 (0.040) | 3/244 | NT | NA | intergenic (‑32/+11) | alaU/ileU | tRNA‑Ala/tRNA‑Ile |
| ? | NC_000913 | = 3427068 | NA (NA) | intergenic (‑35/+8) | alaU/ileU | tRNA‑Ala/tRNA‑Ile | |||||
| * | ? | NC_000913 | = 4171803 | 115 (1.320) | 18 (0.210) | 3/258 | NT | 12.6% | intergenic (+47/‑254) | rrfB/murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding |
| ? | NC_000913 | = 4213162 | 136 (1.580) | intergenic (+3/‑72) | rrfE/yjaA | 5S ribosomal RNA of rrnE operon/stress‑induced protein | |||||