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 | freq | annotation | gene | description |
| RA | 89,291 | G→A | 5.6% | intergenic (+259/‑343) | cra → / → mraZ | transcriptional repressor‑activator for carbon metabolism/RsmH methytransferase inhibitor |
| RA | 222,958 | Δ1 bp | 100% | coding (126/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| RA | 224,735 | T→A | 6.8% | noncoding (965/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 224,756 | T→A | 5.7% | noncoding (986/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 224,759 | T→C | 5.5% | noncoding (989/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 224,768 | C→G | 5.3% | noncoding (998/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 224,771 | C→G | 5.6% | noncoding (1001/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 226,299 | A→C | 6.2% | noncoding (541/2904 nt) | rrlH → | 23S ribosomal RNA of rrnH operon |
| RA | 226,301 | G→A | 5.9% | noncoding (543/2904 nt) | rrlH → | 23S ribosomal RNA of rrnH operon |
| RA | 226,305 | A→T | 5.8% | noncoding (547/2904 nt) | rrlH → | 23S ribosomal RNA of rrnH operon |
| RA | 226,307 | G→T | 6.3% | noncoding (549/2904 nt) | rrlH → | 23S ribosomal RNA of rrnH operon |
| RA | 226,308 | C→T | 6.0% | noncoding (550/2904 nt) | rrlH → | 23S ribosomal RNA of rrnH operon |
| RA | 226,309 | G→A | 6.1% | noncoding (551/2904 nt) | rrlH → | 23S ribosomal RNA of rrnH operon |
| RA | 226,310 | T→G | 6.2% | noncoding (552/2904 nt) | rrlH → | 23S ribosomal RNA of rrnH operon |
| RA | 226,357 | A→G | 5.1% | noncoding (599/2904 nt) | rrlH → | 23S ribosomal RNA of rrnH operon |
| RA | 226,360 | A→G | 5.3% | noncoding (602/2904 nt) | rrlH → | 23S ribosomal RNA of rrnH operon |
| RA | 226,363 | G→C | 5.3% | noncoding (605/2904 nt) | rrlH → | 23S ribosomal RNA of rrnH operon |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 260,147 | C→A | 5.7% | intergenic (‑47/‑241) | phoE ← / → proB | outer membrane phosphoporin protein E/gamma‑glutamate kinase |
| RA | 281,965 | A→T | 7.4% | W7R (TGG→AGG) | yagA ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| RA | 310,310 | T→C | 6.1% | D121G (GAT→GGT) | ecpA ← | ECP pilin |
| RA | 399,838 | G→T | 6.2% | T362T (ACC→ACA) | ddlA ← | D‑alanine‑D‑alanine ligase A |
| RA | 517,801 | G→A | 5.6% | A160V (GCG→GTG) | ybbN ← | DnaK co‑chaperone, thioredoxin‑like protein |
| RA | 566,173 | C→G | 16.5% | pseudogene (204/279 nt) | exoD ← | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
| RA | 566,205 | T→C | 13.1% | pseudogene (172/279 nt) | exoD ← | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
| RA | 566,245 | G→A | 17.1% | pseudogene (132/279 nt) | exoD ← | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
| RA | 624,598 | A→T | 28.6% | intergenic (‑88/‑287) | fepB ← / → entC | ferrienterobactin ABC transporter periplasmic binding protein/isochorismate synthase 1 |
| RA | 650,244 | C→A | 6.2% | E83* (GAA→TAA) | citE ← | citrate lyase, citryl‑ACP lyase (beta) subunit |
| RA | 666,834 | G→T | 5.7% | P462T (CCA→ACA) | mrdA ← | penicillin‑binding protein 2, transpeptidase involved in peptidoglycan synthesis |
| RA | 705,861 | C→A | 5.6% | Q640K (CAA→AAA) | nagE → | N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components |
| RA | 717,493 | G→A | 5.5% | T258M (ACG→ATG) | potE ← | putrescine/proton symporter: putrescine/ornithine antiporter |
| RA | 738,514 | A→G | 5.6% | G141G (GGA→GGG) | ybfD → | H repeat‑associated putative transposase |
| RA | 786,241 | C→T | 6.4% | A203A (GCC→GCT) | aroG → | 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, phenylalanine repressible |
| RA | 849,546 | C→A | 6.6% | L184F (TTG→TTT) | rhtA ← | threonine and homoserine efflux system |
| RA | 875,787 | T→C | 6.9% | R151R (CGT→CGC) | yliF → | putative membrane‑anchored diguanylate cyclase |
| RA | 984,140 | C→A | 6.1% | P164Q (CCG→CAG) | ycbL → | putative metal‑binding enzyme |
| RA | 1,122,286 | T→G | 55.5% | N108H (AAC→CAC) | pyrC ← | dihydro‑orotase |
| RA | 1,174,994 | G→C | 5.3% | R58G (CGT→GGT) | ycfT ← | inner membrane protein |
| RA | 1,205,446 | C→T | 5.6% | pseudogene (1043/1134 nt) | aaaE → | pseudogene, phage terminase protein A family, e14 prophage;Phage or Prophage Related |
| RA | 1,287,187 | A→T | 7.3% | noncoding (50/171 nt) | rttR ← | rtT sRNA, processed from tyrT transcript |
| RA | 1,287,202 | A→G | 7.1% | noncoding (35/171 nt) | rttR ← | rtT sRNA, processed from tyrT transcript |
| RA | 1,315,945 | C→A | 11.4% | G31C (GGT→TGT) | yciG ← | KGG family protein |
| RA | 1,317,042 | C→T | 5.1% | G61S (GGC→AGC) | trpA ← | tryptophan synthase, alpha subunit |
| RA | 1,318,313 | C→A | 5.1% | A35S (GCG→TCG) | trpB ← | tryptophan synthase, beta subunit |
| RA | 1,355,374 | C→A | 6.2% | A33S (GCG→TCG) | sapB ← | antimicrobial peptide transport ABC transporter permease |
| RA | 1,757,000 | G→T | 5.5% | E435* (GAA→TAA) | pykF → | pyruvate kinase I |
| RA | 1,777,769 | G→T | 6.0% | G192C (GGC→TGC) | ydiO → | putative acyl‑CoA dehydrogenase |
| RA | 1,824,385 | G→T | 6.5% | D291Y (GAC→TAC) H185N (CAT→AAT) |
cho → ves ← |
endonuclease of nucleotide excision repair cold‑ and stress‑inducible protein |
| RA | 1,889,637 | G→A | 5.6% | A37V (GCC→GTC) | fadD ← | acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase) |
| RA | 1,959,898 | C→T | 9.1% | intergenic (‑52/‑164) | yecM ← / → argS | putative metal‑binding enzyme/arginyl‑tRNA synthetase |
| RA | 1,966,050 | C→A | 5.9% | G48C (GGC→TGC) | flhB ← | flagellin export apparatus, substrate specificity protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,019,460 | G→A | 100% | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| RA | 2,059,824 | G→T | 7.6% | intergenic (‑134/‑27) | yeeO ← / → asnU | putative multdrug exporter, MATE family/tRNA‑Asn |
| RA | 2,109,488 | G→T | 8.2% | L33I (CTT→ATT) | wzxB ← | putative polisoprenol‑linked O‑antigen transporter |
| 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 | 2,178,586 | G→T | 5.3% | intergenic (‑22/‑235) | fbaB ← / → yegT | fructose‑bisphosphate aldolase class I/nucleoside transporter, low affinity |
| RA | 2,264,865 | C→A | 6.0% | P335T (CCC→ACC) | setB → | lactose/glucose efflux system |
| RA | 2,364,318 | G→T | 6.6% | intergenic (‑43/‑236) | yfaZ ← / → nudI | outer membrane protein, putative porin/nucleoside triphosphatase |
| JC JC | 2,375,828 | IS186 (+) +4 bp | 100% | coding (132‑135/963 nt) | menC ← | O‑succinylbenzoyl‑CoA synthase |
| RA | 2,590,854 | C→A | 5.9% | E5* (GAA→TAA) | ypfM ← | stress‑induced small enterobacterial protein |
| RA | 2,637,191 | C→A | 6.5% | D56Y (GAT→TAT) | der ← | GTPase; multicopy suppressor of ftsJ |
| RA | 2,650,199 | C→A | 11.8% | E697* (GAA→TAA) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,701,262 | G→T | 7.7% | T156T (ACC→ACA) | pdxJ ← | pyridoxine 5'‑phosphate synthase |
| RA | 2,753,846 | C→A | 5.8% | P81Q (CCA→CAA) | bamE → | lipoprotein component of BamABCDE OM biogenesis complex |
| RA | 2,764,382 | C→A | 6.5% | D258Y (GAC→TAC) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,821,107 | G→A | 5.7% | S302F (TCC→TTC) | alaS ← | alanyl‑tRNA synthetase |
| RA | 2,904,212 | G→A | 100% | intergenic (+838/+535) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| RA | 2,921,444 | G→T | 5.9% | A219A (GCC→GCA) | gudP ← | putative D‑glucarate transporter |
| RA | 2,932,846 | A→G | 8.2% | A56A (GCT→GCC) | fucO ← | L‑1,2‑propanediol oxidoreductase |
| RA | 3,029,648 | C→A | 6.1% | L428L (CTG→CTT) | ygfT ← | putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit |
| RA | 3,037,018 | G→T | 5.3% | P363P (CCC→CCA) | recJ ← | ssDNA exonuclease, 5' ‑‑> 3'‑specific |
| RA | 3,068,728 | C→A | 6.4% | M27I (ATG→ATT) | argO ← | arginine transporter |
| RA | 3,157,433 | G→T | 5.9% | D271Y (GAC→TAC) | dkgA → | 2,5‑diketo‑D‑gluconate reductase A |
| RA | 3,157,442 | G→T | 6.5% | G274C (GGC→TGC) | dkgA → | 2,5‑diketo‑D‑gluconate reductase A |
| JC JC | 3,179,611 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | 8.4% | intergenic (+15/‑128) | tolC → / → ygiB | transport channel/DUF1190 family protein |
| RA | 3,204,386 | A→C | 6.3% | R68R (CGT→CGG) | folB ← | dihydroneopterin aldolase and dihydroneopterin triphosphate 2'‑epimerase |
| RA | 3,244,935 | C→A | 9.9% | intergenic (‑194/‑289) | uxaC ← / → exuT | uronate isomerase/hexuronate transporter |
| RA | 3,244,970 | C→A | 6.8% | intergenic (‑229/‑254) | uxaC ← / → exuT | uronate isomerase/hexuronate transporter |
| RA | 3,265,166 | G→A | 7.0% | A288V (GCA→GTA) | tdcB ← | L‑threonine dehydratase, catabolic |
| RA | 3,423,540 | A→G | 7.2% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,478,768 | C→T | 5.9% | A9T (GCG→ACG) | yheV ← | DUF2387 family putative metal‑binding protein |
| RA | 3,511,719 | C→A | 5.2% | R209L (CGA→CTA) | yhfZ ← | putative DNA‑binding transcriptional regulator |
| RA | 3,546,954 | G→T | 8.1% | A132A (GCG→GCT) | gntT → | gluconate transporter, high‑affinity GNT I system |
| 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 |
| RA | 3,578,495 | A→G | 5.1% | F78L (TTC→CTC) | gntR ← | d‑gluconate inducible gluconate regulon transcriptional repressor |
| RA | 3,815,809 | Δ1 bp | 32.2% | intergenic (‑41/+25) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| JC | 3,815,859 | Δ82 bp | 38.1% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,864,609 | G→T | 5.9% | K237N (AAG→AAT) | yidP → | UTRA domain‑containing GntR family putative transcriptional regulator |
| JC JC | 3,890,075 | IS5 (–) +4 bp | 100% | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,993,981 | C→A | 5.6% | D27Y (GAC→TAC) | cyaY ← | iron‑dependent inhibitor of iron‑sulfur cluster formation; frataxin; iron‑binding and oxidizing protein |
| RA | 4,019,414 | C→A | 7.3% | S187Y (TCC→TAC) | ubiE → | bifunctional 2‑octaprenyl‑6‑methoxy‑1,4‑benzoquinone methylase/ S‑adenosylmethionine:2‑DMK methyltransferase |
| RA | 4,081,426 | C→A | 6.7% | V145V (GTG→GTT) | fdoI ← | formate dehydrogenase‑O, cytochrome b556 subunit |
| RA | 4,181,279 | G→T | 8.2% | R12L (CGT→CTT) | rpoB → | RNA polymerase, beta subunit |
| JC | 4,183,399 | Δ3 bp | 71.4% | coding (2155‑2157/4029 nt) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,187,838 | A→G | 11.6% | D830G (GAC→GGC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,258,317 | G→T | 9.2% | V192V (GTG→GTT) | dinF → | oxidative stress resistance protein; putative MATE family efflux pump; UV and mitomycin C inducible protein |
| RA | 4,258,350 | G→T | 7.9% | M203I (ATG→ATT) | dinF → | oxidative stress resistance protein; putative MATE family efflux pump; UV and mitomycin C inducible protein |
| RA | 4,261,085 | G→A | 7.8% | D163N (GAT→AAT) | yjbM → | uncharacterized protein |
| RA | 4,296,060 | C→T | 26.5% | 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 |
| RA | 4,406,129 | T→C | 100% | intergenic (+144/‑61) | purA → / → nsrR | adenylosuccinate synthetase/nitric oxide‑sensitive repressor for NO regulon |
| RA | 4,528,988 | G→A | 5.2% | A419V (GCG→GTG) | sgcC ← | putative PTS system EIIC permease component |
| RA | 4,613,622 | C→A | 9.5% | R48S (CGT→AGT) | yjjV → | putative DNase |
| RA | 4,633,634 | C→T | 100% | E38K (GAG→AAG) | yjjX ← | non‑canonical purine NTP phosphatase, ITPase/XTPase |
| RA | 4,637,986 | G→T | 5.7% | G431W (GGG→TGG) | creC → | sensory histidine kinase in two‑component regulatory system with CreB or PhoB |
| JC JC | 4,640,551 | IS1 (–) +9 bp | 100% | intergenic (+9/‑383) | yjjY → / → yjtD | uncharacterized protein/putative methyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 773041 | 774175 | 1135 | 23 [20] | [18] 21 | [cydB] | [cydB] |
| * | * | ÷ | NC_000913 | 1037730 | 1039279 | 1550 | 22 [18] | [20] 22 | [cbdA] | [cbdA] |
| * | * | ÷ | NC_000913 | 1166039 | 1167391 | 1353 | 22 [20] | [20] 24 | ndh | ndh |
| * | * | ÷ | NC_000913 | 3423776–3424234 | 3424523–3424238 | 5–748 | 21 [19] | [18] 24 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374922 = | NA (NA) | 7 (0.080) | 4/240 | NT | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | NC_000913 | = 374929 | 79 (1.200) | 14 (0.240) | 6/170 | NT | 16.4% | intergenic (+48/‑530) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| ? | NC_000913 | = 377521 | NA (NA) | noncoding (187/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | NC_000913 | 374930 = | NA (NA) | 17 (0.290) | 5/170 | NT | 22.7% | noncoding (1/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | NC_000913 | 377522 = | 64 (0.970) | intergenic (+211/+13) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | NC_000913 | 375124 = | 98 (1.090) | 7 (0.120) | 4/172 | NT | 9.8% | noncoding (195/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | NC_000913 | 377530 = | 63 (1.050) | intergenic (+219/+5) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | NC_000913 | 566098 = | 93 (1.040) | 12 (0.150) +GAGAGGAGGATTACAAA |
7/222 | NT | 9.4% | pseudogene (279/279 nt) | exoD | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
| ? | NC_000913 | 4397412 = | 175 (1.950) | coding (1/1848 nt) | mutL | methyl‑directed mismatch repair protein | |||||
| * | ? | NC_000913 | 1207790 = | 23 (0.260) | 29 (0.370) | 20/224 | NT | 52.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 32 (0.410) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 24 (0.270) | 37 (0.470) | 24/224 | NT | 58.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 32 (0.410) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 68 (0.780) | 37/248 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3231254 = | NA (NA) | 3 (0.040) | 3/204 | NT | 6.0% | noncoding (3/283 nt) | REP231 (repetitive extragenic palindromic) element; contains 6 REP sequences | REP231 (repetitive extragenic palindromic) element; contains 6 REP sequences |
| ? | NC_000913 | 3234722 = | 47 (0.660) | noncoding (85/86 nt) | REP233 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP233 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||