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 | 79,893 | C→A | 8.3% | V42L (GTG→TTG) | leuA ← | 2‑isopropylmalate synthase |
| RA | 215,852 | G→T | 5.6% | P77Q (CCA→CAA) | tsaA ← | tRNA‑Thr(GGU) m(6)t(6)A37 methyltransferase, SAM‑dependent |
| RA | 221,338 | A→G | 5.2% | noncoding (1081/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,373:1 | +G | 5.2% | noncoding (1116/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,380 | T→A | 5.3% | noncoding (1123/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,390 | Δ1 bp | 5.5% | noncoding (1133/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,391 | G→A | 5.5% | noncoding (1134/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,393 | C→T | 5.8% | noncoding (1136/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,395 | G→A | 5.8% | noncoding (1138/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,397 | C→T | 5.7% | noncoding (1140/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,398 | C→T | 5.8% | noncoding (1141/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,402 | A→C | 5.8% | noncoding (1145/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,407 | A→T | 5.9% | noncoding (1150/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,412 | A→T | 6.2% | noncoding (1155/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,420 | A→G | 6.6% | noncoding (1163/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,425 | T→C | 8.7% | noncoding (1168/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,430 | T→C | 9.0% | noncoding (1173/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,455 | G→A | 10.5% | noncoding (1198/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,464 | G→C | 7.1% | noncoding (1207/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 263,285 | G→A | 6.8% | D144D (GAC→GAT) | yafZ ← | CP4‑6 prophage; conserved protein |
| RA | 286,409 | T→A | 9.3% | Q152L (CAG→CTG) | insB1 ← | IS1 transposase B |
| JC JC | 370,378 | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences (–) +8 bp :: +ATCTGC | 11.8% | intergenic (+41/‑530) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,422 | A→G | 7.7% | intergenic (+85/‑493) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,428 | T→C | 10.6% | intergenic (+91/‑487) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,442 | T→C | 5.8% | intergenic (+105/‑473) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,576 | Δ1 bp | 7.1% | intergenic (+239/‑339) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,577 | T→G | 7.2% | intergenic (+240/‑338) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,617 | C→T | 6.3% | intergenic (+280/‑298) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 516,583 | G→T | 5.2% | E238* (GAA→TAA) | ybbP → | putative ABC transporter permease |
| RA | 703,110 | Δ1 bp | 5.3% | coding (1562/1665 nt) | glnS → | glutamyl‑tRNA synthetase |
| RA | 727,989 | C→A | 6.4% | A984E (GCA→GAA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 730,138 | A→G | 5.6% | pseudogene (550/1521 nt) | rhsO → | pseudogene, Rhs family protein |
| RA | 732,499 | T→C | 5.5% | pseudogene (219/1137 nt) | ybfL → | pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein |
| RA | 734,222 | T→G | 6.1% | I225M (ATT→ATG) | ybfD → | H repeat‑associated putative transposase |
| RA | 734,251 | C→T | 7.3% | T235I (ACC→ATC) | ybfD → | H repeat‑associated putative transposase |
| RA | 734,285 | G→A | 5.3% | E246E (GAG→GAA) | ybfD → | H repeat‑associated putative transposase |
| RA | 734,308 | A→G | 5.4% | *254W (TAG→TGG) | ybfD → | H repeat‑associated putative transposase |
| RA | 748,699 | G→T | 5.2% | P409Q (CCG→CAG) | gltA ← | citrate synthase |
| RA | 748,701 | A→C | 5.2% | R408R (CGT→CGG) | gltA ← | citrate synthase |
| RA | 748,704 | G→A | 5.1% | A407A (GCC→GCT) ‡ | gltA ← | citrate synthase |
| RA | 748,705 | G→C | 5.1% | A407G (GCC→GGC) ‡ | gltA ← | citrate synthase |
| RA | 748,706 | C→G | 5.1% | A407P (GCC→CCC) ‡ | gltA ← | citrate synthase |
| RA | 748,710 | C→A | 5.1% | K405N (AAG→AAT) | gltA ← | citrate synthase |
| RA | 868,490 | C→A | 10.2% | A19E (GCA→GAA) | yliE → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 957,955 | T→G | 7.5% | S169A (TCT→GCT) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 965,790 | C→A | 5.9% | P316T (CCA→ACA) | ycaQ → | DUF1006 family protein with C‑terminal wHTH domain |
| RA | 1,045,283 | T→G | 7.3% | intergenic (‑83/‑6) | gfcA ← / → insA | O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA |
| RA | 1,108,415 | G→T | 6.2% | V699V (GTG→GTT) | opgH → | membrane glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist |
| RA | 1,160,005 | G→T | 10.7% | G152V (GGT→GTT) | nagZ → | beta N‑acetyl‑glucosaminidase |
| RA | 1,242,915 | A→C | 73.8% | intergenic (‑83/+237) | treA ← / ← dhaM | periplasmic trehalase/putative dihydroxyacetone‑specific PTS enzymes: HPr component/EI component |
| RA | 1,282,249 | A→G | 9.8% | intergenic (+267/+273) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,599 | G→A | 6.7% | noncoding (94/171 nt) P12S (CCA→TCA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,282,608 | T→C | 9.5% | noncoding (85/171 nt) T9A (ACT→GCT) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,282,617 | G→A | 8.3% | noncoding (76/171 nt) Q6* (CAA→TAA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,286,690 | C→A | 7.4% | R331R (CGC→CGA) | rssB → | PcnB‑degradosome interaction factor; response regulator |
| RA | 1,356,077 | G→T | 14.7% | R234L (CGT→CTT) | puuD → | gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,422,060 | G→C | 9.7% | pseudogene (924/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,098 | G→A | 8.8% | pseudogene (886/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,627 | A→G | 6.3% | pseudogene (357/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,460,602 | T→C | 6.0% | pseudogene (954/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,752 | C→T | 7.9% | pseudogene (1104/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,761 | A→G | 7.2% | pseudogene (1113/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,986 | G→A | 7.9% | pseudogene (1338/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,512,745 | A→C | 6.2% | I120S (ATC→AGC) | mnaT ← | methionine N‑acyltransferase; L‑amino acid N‑acyltransferase |
| RA | 1,512,796 | C→A | 6.5% | R103L (CGA→CTA) | mnaT ← | methionine N‑acyltransferase; L‑amino acid N‑acyltransferase |
| RA | 1,681,729 | G→A | 7.6% | R302R (CGC→CGT) | fumA ← | fumarate hydratase (fumarase A), aerobic Class I |
| RA | 1,681,732 | A→G | 7.7% | I301I (ATT→ATC) | fumA ← | fumarate hydratase (fumarase A), aerobic Class I |
| RA | 1,681,735 | C→A | 7.4% | V300V (GTG→GTT) | fumA ← | fumarate hydratase (fumarase A), aerobic Class I |
| RA | 1,681,741 | G→A | 6.7% | I298I (ATC→ATT) | fumA ← | fumarate hydratase (fumarase A), aerobic Class I |
| RA | 1,681,750 | A→C | 7.0% | A295A (GCT→GCG) | fumA ← | fumarate hydratase (fumarase A), aerobic Class I |
| RA | 1,681,765 | A→G | 7.0% | G290G (GGT→GGC) | fumA ← | fumarate hydratase (fumarase A), aerobic Class I |
| RA | 1,702,919 | C→G | 7.0% | Q582E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,714,749 | G→T | 6.4% | R111R (CGC→CGA) | slyA ← | global transcriptional regulator |
| RA | 1,725,727 | C→A | 11.8% | P795Q (CCG→CAG) | lhr → | putative ATP‑dependent helicase |
| RA | 1,812,327 | C→A | 6.2% | W144L (TGG→TTG) | chbF ← | phospho‑chitobiase; general 6‑phospho‑beta‑glucosidase activity |
| RA | 1,851,858 | A→T | 5.5% | S57T (TCA→ACA) | ydjI ← | putative aldolase |
| RA | 1,870,443 | A→G | 5.1% | M172V (ATG→GTG) | yeaN → | putative transporter |
| RA | 1,943,769 | G→A | 6.1% | Y337Y (TAC→TAT) | aspS ← | aspartyl‑tRNA synthetase |
| RA | 2,170,724 | G→T | 16.9% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,264,405 | G→A | 7.4% | R67R (CGG→CGA) | rtn → | resistance protein for phages lambda and N4, putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 2,298,467 | T→C | 6.2% | intergenic (+595/+120) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,422,850 | C→T | 8.6% | E290K (GAA→AAA) | purF ← | amidophosphoribosyltransferase |
| RA | 2,494,884 | G→A | 5.9% | V92V (GTG→GTA) | ypdC → | putative DNA‑binding protein |
| RA | 2,647,656 | C→T | 7.4% | G213S (GGC→AGC) | sseB ← | rhodanase‑like enzyme, sulfur transfer from thiosulfate |
| RA | 2,709,474 | G→T | 5.2% | P112Q (CCG→CAG) | grcA ← | autonomous glycyl radical cofactor |
| RA | 2,709,487 | T→C | 7.0% | N108D (AAC→GAC) | grcA ← | autonomous glycyl radical cofactor |
| RA | 2,709,494 | Δ1 bp | 5.1% | coding (315/384 nt) | grcA ← | autonomous glycyl radical cofactor |
| RA | 2,709,495 | A→T | 5.1% | V105D (GTT→GAT) | grcA ← | autonomous glycyl radical cofactor |
| RA | 2,719,426 | T→C | 92.9% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,993,488 | T→C | 5.3% | intergenic (‑238/‑216) | ygeR ← / → xdhA | LysM domain‑containing M23 family putative peptidase; septation lipoprotein/xanthine dehydrogenase, molybdenum binding subunit |
| RA | 3,096,462 | T→C | 5.8% | Y31H (TAC→CAC) | mutY → | adenine DNA glycosylase |
| RA | 3,176,500 | C→A | 5.9% | P198T (CCG→ACG) | zupT → | zinc transporter |
| RA | 3,263,276 | T→C | 5.0% | intergenic (+315/+299) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,266,510 | G→T | 5.8% | A136E (GCG→GAG) | garL ← | alpha‑dehydro‑beta‑deoxy‑D‑glucarate aldolase |
| RA | 3,287,971 | C→A | 6.6% | L405M (CTG→ATG) | lpoA → | OM lipoprotein stimulator of MrcA transpeptidase |
| RA | 3,337,866 | G→T | 10.0% | L188L (CTG→CTT) | lptB → | lipopolysaccharide export ABC transporter ATP‑binding protein of the LptBFGC export complex |
| RA | 3,337,938 | G→T | 10.4% | Q212H (CAG→CAT) | lptB → | lipopolysaccharide export ABC transporter ATP‑binding protein of the LptBFGC export complex |
| RA | 3,416,890 | T→G | 6.6% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,416,899 | A→G | 12.4% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,547,685 | G→T | 6.0% | L414F (TTG→TTT) | malT → | mal regulon transcriptional activator |
| RA | 3,615,650 | G→C | 6.0% | R1033R (CGG→CGC) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,656,181 | C→A | 5.5% | S803* (TCG→TAG) | mdtF → | anaerobic multidrug efflux transporter, ArcA‑regulated |
| RA | 3,671,569 | G→T | 5.3% | R48S (CGT→AGT) | yhjG ← | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,758,930 | C→A | 6.4% | Q1130K (CAA→AAA) | rhsA → | Rhs family protein, putative polymorphic toxin; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| RA | 3,807,237 | G→T | 5.2% | E383* (GAG→TAG) | dfp → | fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding |
| RA | 3,901,867 | T→G | 7.5% | intergenic (‑141/+42) | pstB ← / ← pstA | phosphate transporter subunit/phosphate transporter subunit |
| RA | 3,909,241 | C→A | 7.0% | G31V (GGT→GTT) | atpC ← | F1 sector of membrane‑bound ATP synthase, epsilon subunit |
| RA | 3,997,389 | C→A | 17.3% | M50I (ATG→ATT) | rarD ← | putative chloramphenical resistance permease |
| RA | 4,002,390 | C→T | 5.5% | L10L (CTG→CTA) | rhtB ← | homoserine, homoserine lactone and S‑methyl‑methionine efflux pump |
| RA | 4,165,449 | C→T | 18.6% | noncoding (50/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,450 | A→C | 18.6% | noncoding (51/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,173,132 | G→T | 9.6% | D654Y (GAC→TAC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,178,209 | C→A | 26.3% | R978S (CGT→AGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,178,500 | C→T | 11.4% | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| JC | 4,178,728 | +AAG | 32.2% | coding (3451/4224 nt) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,202,979 | A→C | 12.3% | noncoding (12/120 nt) | rrfE → | 5S ribosomal RNA of rrnE operon |
| RA | 4,331,451 | G→T | 5.1% | intergenic (‑6/‑277) | melR ← / → melA | melibiose operon transcriptional regulator; autoregulator/alpha‑galactosidase, NAD(P)‑binding |
| RA | 4,361,090 | C→T | 6.9% | D83D (GAC→GAT) | groL → | Cpn60 chaperonin GroEL, large subunit of GroESL |
| RA | 4,460,421 | C→T | 7.1% | A104T (GCA→ACA) | ridA ← | enamine/imine deaminase, reaction intermediate detoxification |
| RA | 4,508,444 | C→A | 5.4% | P34H (CCT→CAT) ‡ | insA → | IS1 repressor TnpA |
| RA | 4,508,445 | T→C | 5.3% | P34P (CCT→CCC) ‡ | insA → | IS1 repressor TnpA |
| RA | 4,530,001 | T→C | 8.3% | intergenic (‑683/‑773) | nanC ← / → fimB | N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 3432079 | 3432495 | 417 | 32 [26] | [15] 30 | [zntR] | [zntR] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 353394 | 51 (0.690) | 4 (0.060) | 4/178 | NT | 7.4% | intergenic (+229/+108) | codA/cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
| ? | CP009273 | 694881 = | NA (NA) | noncoding (1/98 nt) | RIP61 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP61 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | CP009273 | 360104 = | 81 (0.800) | 88 (0.870) | 39/250 | NT | 52.1% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | 1203246 = | 53 (0.520) | 46 (0.520) | 25/218 | NT | 56.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 25 (0.280) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 52 (0.510) | 51 (0.580) | 24/218 | NT | 59.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 25 (0.280) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1972854 = | 4 (0.040) | 91 (0.900) | 39/250 | NT | 95.8% | intergenic (‑400/‑380) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | 3576788 = | NA (NA) | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA | |||||
| * | ? | CP009273 | = 1972861 | 14 (0.140) | 74 (0.730) | 33/250 | NT | 84.1% | intergenic (‑407/‑373) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||