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 | 8,702 | G→A | 8.5% | L155L (CTG→CTA) | talB → | transaldolase B |
| RA | 58,764 | A→C | 5.9% | K97N (AAA→AAC) | yabP → | putative uncharacterized protein YabP |
| RA | 68,349 | T→A | 7.7% | *567L (TAA→TTA) | araB ← | ribulokinase |
| RA | 93,526 | A→T | 10.3% | T121S (ACC→TCC) | murE → | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase |
| RA | 124,752 | Δ1 bp | 12.8% | coding (1736/2664 nt) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 221,232 | C→T | 8.9% | P130P (CCG→CCA) | metI ← | L‑methionine/D‑methionine ABC transporter membrane subunit |
| RA | 238,497 | G→T | 23.6% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,503 | G→T | 19.9% | F78L (TTC→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,523 | G→T | 29.2% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,532 | C→A | 16.4% | V69L (GTA→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 29.5% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| RA | 242,015 | G→A | 9.5% | A430V (GCG→GTG) | fadE ← | acyl‑CoA dehydrogenase |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 298,557 | A→C | 43.2% | L57R (CTC→CGC) | paoD ← | molybdenum cofactor insertion chaperone for PaoABC |
| RA | 429,626 | T→C | 7.3% | M41T (ATG→ACG) | secF → | Sec translocon accessory complex subunit SecF |
| RA | 590,421 | A→G | 5.8% | F178F (TTT→TTC) | nfrA ← | bacteriophage N4 receptor, outer membrane protein |
| RA | 638,257 | C→T | 6.5% | W106* (TGG→TAG) | dsbG ← | protein sulfenic acid reductase DsbG |
| RA | 727,949:1 | +C | 8.9% | coding (784/1674 nt) | kdpA ← | K(+) transporting P‑type ATPase subunit KdpA |
| RA | 727,949:2 | +A | 8.9% | coding (784/1674 nt) | kdpA ← | K(+) transporting P‑type ATPase subunit KdpA |
| RA | 727,949:3 | +G | 8.9% | coding (784/1674 nt) | kdpA ← | K(+) transporting P‑type ATPase subunit KdpA |
| RA | 729,372 | A→C | 41.1% | intergenic (+32/‑211) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 774,718 | A→G | 7.4% | intergenic (+116/‑34) | ybgE → / → ybgC | cyd operon protein YbgE/esterase/thioesterase |
| RA | 842,522 | A→G | 6.9% | Y64C (TAC→TGC) | rlmF → | 23S rRNA m(6)A1618 methyltransferase |
| RA | 899,196 | G→A | 9.3% | D227N (GAC→AAC) | rlmC → | 23S rRNA m(5)U747 methyltransferase |
| MC JC | 932,613 | Δ459 bp | 100% | coding (19‑477/495 nt) | lrp → | DNA‑binding transcriptional dual regulator Lrp |
| RA | 955,328 | A→G | 8.7% | D435D (GAT→GAC) | ycaO ← | ribosomal protein S12 methylthiotransferase accessory factor YcaO |
| RA | 965,379 | G→A | 8.0% | V354I (GTA→ATA) | ycaI → | conserved inner membrane protein YcaI |
| RA | 1,022,239 | C→T | 6.9% | A549T (GCC→ACC) | yccS ← | putative transporter YccS |
| RA | 1,236,826 | C→A | 7.7% | S139I (AGC→ATC) | ycgB ← | PF04293 family protein YcgB |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,319,269 | C→T | 11.4% | A174T (GCC→ACC) | trpC ← | fused indole‑3‑glycerol phosphate synthase/phosphoribosylanthranilate isomerase |
| RA | 1,331,265 | T→G | 15.3% | V73G (GTT→GGT) | topA → | DNA topoisomerase 1 |
| RA | 1,331,325 | T→A | 72.6% | V93D (GTC→GAC) | topA → | DNA topoisomerase 1 |
| RA | 1,431,131 | C→G | 8.5% | H695D (CAT→GAT) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,434,496 | T→C | 5.8% | intergenic (‑90/+462) | ynaM ← / ← ttcC | Rac prophage; protein YnaM/putative tRNA 2‑thiocytidine (s(2)C32) synthase |
| RA | 1,438,185 | C→T | 6.3% | R867H (CGT→CAT) | ydbK ← | putative pyruvate‑flavodoxin oxidoreductase |
| RA | 1,558,504 | A→G | 10.8% | S172P (TCC→CCC) | ddpD ← | putative D,D‑dipeptide ABC transporter ATP‑binding subunit DdpD |
| RA | 1,712,731 | C→T | 7.3% | intergenic (+573/‑38) | nth → / → dtpA | endonuclease III/dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,834,081 | C→T | 7.1% | S227S (AGC→AGT) | ydjX → | DedA family protein YdjX |
| RA | 1,857,430 | G→T | 6.2% | R114S (CGT→AGT) | ydjI ← | putative aldolase YdjI |
| RA | 1,915,050 | Δ1 bp | 19.4% | coding (485/699 nt) | proQ ← | RNA chaperone ProQ |
| RA | 1,915,051 | Δ1 bp | 19.4% | coding (484/699 nt) | proQ ← | RNA chaperone ProQ |
| RA | 1,915,250 | Δ1 bp | 29.4% | coding (285/699 nt) | proQ ← | RNA chaperone ProQ |
| RA | 1,955,956 | G→A | 8.5% | A351V (GCA→GTA) | torZ ← | trimethylamine N‑oxide reductase 2 |
| RA | 1,975,543 | A→T | 8.2% | V238D (GTC→GAC) | motB ← | motility protein B |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,001,297 | G→T | 11.2% | Q165K (CAG→AAG) | fliA ← | RNA polymerase, sigma 28 (sigma F) factor |
| JC | 2,109,888 | Δ3 bp | 9.0% | coding (249‑251/558 nt) | rfbC ← | dTDP‑4‑dehydrorhamnose 3,5‑epimerase |
| RA | 2,113,659 | C→T | 8.9% | P223P (CCG→CCA) | galF ← | UTP:glucose‑1‑phosphate uridylyltransferase, low activity |
| RA | 2,139,598 | T→G | 32.3% | intergenic (+113/+161) | yegH → / ← asmA | inner membrane protein YegH/putative assembly protein AsmA |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,177,245 | G→T | 60.3% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,272 | T→A | 24.2% | intergenic (‑68/+240) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,472,968 | G→C | 8.4% | S93R (AGC→AGG) | yfdO ← | CPS‑53 (KpLE1) prophage; putative defective phage replication protein O |
| RA | 2,473,023 | G→A | 5.4% | S75L (TCG→TTG) | yfdO ← | CPS‑53 (KpLE1) prophage; putative defective phage replication protein O |
| RA | 2,661,021 | G→A | 7.3% | R171C (CGT→TGT) | iscS ← | cysteine desulfurase |
| RA | 2,764,488 | G→T | 10.8% | H222Q (CAC→CAA) | abpA ← | CP4‑57 prophage; anti‑bacteriophage protein |
| JC JC | 2,809,537 | IS1 (+) +9 bp | 78.7% | intergenic (+44/‑72) | ygaY → / → ygaZ | putative transporter YgaY, N‑terminal fragment/L‑valine exporter subunit YgaZ |
| RA | 2,920,075 | T→C | 7.3% | K224K (AAA→AAG) | gudX ← | glucarate dehydratase‑related protein |
| RA | 2,943,815 | G→C | 6.6% | R160P (CGT→CCT) | csdA → | cysteine sulfinate desulfinase |
| RA | 2,960,434 | C→T | 6.8% | M665I (ATG→ATA) | recC ← | exodeoxyribonuclease V subunit RecC |
| RA | 3,072,981 | C→A | 5.2% | V237V (GTG→GTT) | epd ← | D‑erythrose‑4‑phosphate dehydrogenase |
| RA | 3,191,688 | T→C | 5.1% | Y353H (TAT→CAT) | yqiI → | putative fimbrial protein YqiI |
| RA | 3,366,996 | T→A | 5.6% | V24E (GTA→GAA) | yhcF → | DUF1120 domain‑containing protein YhcF |
| RA | 3,418,500 | T→A | 27.7% | N37K (AAT→AAA) | yhdV → | lipoprotein YhdV |
| RA | 3,452,080 | A→C | 22.2% | R69R (CGT→CGG) | rplD ← | 50S ribosomal subunit protein L4 |
| RA | 3,468,306 | G→A | 8.1% | S516S (AGC→AGT) | chiA ← | endochitinase |
| RA | 3,484,509 | T→A | 7.1% | V7D (GTC→GAC) | prkB → | putative phosphoribulokinase |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,593,166 | A→C | 30.6% | V91G (GTC→GGC) | livF ← | branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivF |
| RA | 3,633,506 | G→A | 5.8% | pseudogene (953/1607 nt) | yhiL ← | putative uncharacterized protein YhiL |
| RA | 3,670,551 | G→T | 8.2% | G320G (GGG→GGT) | treF → | cytoplasmic trehalase |
| RA | 3,774,119 | T→C | 9.3% | D613D (GAT→GAC) | mtlA → | mannitol‑specific PTS enzyme IICBA component |
| JC | 3,815,859 | Δ82 bp | 70.3% | [rph] | [rph] | |
| JC | 3,816,605 | Δ103 bp | 15.9% | [yicC] | [yicC] | |
| RA | 3,817,916 | A→T | 7.1% | S53C (AGT→TGT) | dinD → | DNA damage‑inducible protein D |
| RA | 4,022,704 | C→T | 6.6% | P163S (CCT→TCT) | tatB → | twin arginine protein translocation system ‑ TatB protein |
| RA | 4,139,087 | C→G | 19.3% | E208Q (GAA→CAA) | fsaB ← | fructose‑6‑phosphate aldolase 2 |
| RA | 4,186,541 | A→G | 5.9% | K398E (AAG→GAG) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,220,007 | T→G | 32.5% | V471G (GTG→GGG) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,245,123 | G→A | 9.1% | intergenic (‑48/+106) | malF ← / ← malE | maltose ABC transporter membrane subunit MalF/maltose ABC transporter periplasmic binding protein |
| RA | 4,283,228 | T→G | 45.8% | intergenic (‑153/+25) | yjcF ← / ← actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| RA | 4,296,060 | C→T | 38.1% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,436,214 | C→T | 8.2% | E118K (GAG→AAG) | cpdB ← | 2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase |
| RA | 4,451,160 | G→T | 7.7% | G35C (GGC→TGC) | ytfR → | galactofuranose ABC transporter putative ATP binding subunit |
| RA | 4,595,560 | T→C | 8.0% | M98V (ATG→GTG) | lgoR ← | putative DNA‑binding transcriptional regulator LgoR |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 291401 | NA (NA) | 7 (0.150) | 6/232 | NT | 13.7% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1907525 = | 44 (0.970) | coding (67/144 nt) | yobF | DUF2527 domain‑containing protein YobF | |||||
| * | ? | NC_000913 | 1207790 = | 31 (0.680) | 34 (0.870) | 25/200 | NT | 64.9% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 10 (0.260) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 29 (0.640) | 13 (0.330) | 10/200 | NT | 42.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 10 (0.260) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1755755 = | 55 (1.210) | 4 (0.090) | 3/232 | NT | 6.8% | coding (58/1413 nt) | pykF | pyruvate kinase I |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2068944 = | NA (NA) | 5 (0.110) | 5/226 | NT | NA | noncoding (1328/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 2070275 | NA (NA) | intergenic (‑95/‑2) | insC‑3/yoeA | CP4‑44 prophage; IS2 insertion element repressor InsA/CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA | |||||
| * | ? | NC_000913 | 2996361 = | NA (NA) | 12 (0.260) | 11/232 | NT | 23.1% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 3228002 | 40 (0.880) | coding (202/1071 nt) | ygjJ | protein YgjJ | |||||