mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 96,085 | C→T | V28V (GTC→GTT) | mraY → | phospho‑N‑acetylmuramoyl‑pentapeptide transferase |
| RA | 111,683 | T→C | E55G (GAA→GGA) | yacG ← | DNA gyrase inhibitor |
| RA | 218,942 | A→G | V218A (GTT→GCT) | tsaA ← | tRNA‑Thr(GGU) m(6)t(6)A37 methyltransferase, SAM‑dependent |
| RA | 219,435 | A→G | F54L (TTC→CTC) | tsaA ← | tRNA‑Thr(GGU) m(6)t(6)A37 methyltransferase, SAM‑dependent |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 323,006 | T→C | G223G (GGT→GGC) | ykgF → | ferridoxin‑like LutB family protein; putative electron transport chain YkgEFG component |
| RA | 348,596 | C→A | intergenic (‑153/‑86) | prpR ← / → prpB | propionate catabolism operon regulatory protein/2‑methylisocitrate lyase |
| RA | 350,070 | T→C | V20A (GTG→GCG) | prpC → | 2‑methylcitrate synthase |
| RA | 452,681 | A→G | F289L (TTC→CTC) | ampG ← | muropeptide transporter |
| RA | 473,179 | G→A | V72M (GTG→ATG) | amtB → | ammonium transporter |
| RA | 488,628 | T→C | V698A (GTG→GCG) | mscK → | mechanosensitive channel protein, intermediate conductance, K+ regulated |
| RA | 577,085 | G→A | intergenic (‑260/‑313) | nmpC ← / → essD | DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage/DLP12 prophage; putative phage lysis protein |
| RA | 613,255 | A→G | E173E (GAA→GAG) | fes → | enterobactin/ferrienterobactin esterase |
| RA | 621,409 | A→G | F261L (TTT→CTT) | fepD ← | ferrienterobactin ABC transporter permease |
| RA | 741,429 | A→G | S376S (TCT→TCC) | dtpD ← | dipeptide and tripeptide permease D |
| RA | 755,804 | A→G | D82G (GAC→GGC) | sdhD → | succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| RA | 781,084 | T→C | noncoding (17/76 nt) | valZ → | tRNA‑Val |
| RA | 807,115 | T→C | Q56R (CAA→CGA) | ybhC ← | acyl‑CoA thioesterase, lipoprotein |
| RA | 900,315 | A→G | G87G (GGT→GGC) | artJ ← | arginine ABC transporter periplasmic binding protein |
| RA | 910,972 | G→A | G26G (GGC→GGT) | poxB ← | pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding |
| JC JC | 944,912 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | intergenic (+16/+14) | dmsC → / ← ycaC | dimethyl sulfoxide reductase, anaerobic, subunit C/putative isochorismatase family hydrolase |
| RA | 960,557 | T→C | Y98Y (TAT→TAC) | ycaL → | putative peptidase‑related chaperone |
| RA | 1,000,789 | A→G | Y525C (TAC→TGC) | elfC → | putative outer membrane fimbrial subunit export usher protein |
| RA | 1,013,234 | T→C | S412P (TCA→CCA) | pqiA → | paraquat‑inducible, SoxRS‑regulated inner membrane protein |
| RA | 1,154,782 | A→G | E224G (GAA→GGA) | yceG → | septation protein, ampicillin sensitivity |
| RA | 1,246,015 | T→C | A454A (GCA→GCG) | treA ← | periplasmic trehalase |
| RA | 1,249,386 | T→C | E124E (GAA→GAG) | dhaL ← | dihydroxyacetone kinase, C‑terminal domain |
| RA | 1,314,744 | T→C | T161A (ACT→GCT) | yciE ← | putative rubrerythrin/ferritin‑like metal‑binding protein |
| RA | 1,350,111 | C→T | intergenic (‑4/+140) | yciW ← / ← fabI | putative oxidoreductase/enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent |
| RA | 1,435,242 | A→G | G126G (GGT→GGC) | uspF ← | stress‑induced protein, ATP‑binding protein |
| RA | 1,442,318 | A→G | Y176H (TAT→CAT) | ldhA ← | fermentative D‑lactate dehydrogenase, NAD‑dependent |
| RA | 1,474,735 | C→T | A172V (GCG→GTG) | ydbC → | putative NAD(P)‑binding oxidoreductase |
| JC JC | 1,518,887 | IS5 (+) +4 bp | intergenic (‑41/‑137) | mnaT ← / → curA | methionine N‑acyltransferase; L‑amino acid N‑acyltransferase/curcumin/dihydrocurcumin reductase, NADPH‑dependent |
| RA | 1,559,306 | A→C | I202S (ATC→AGC) | ddpC ← | D,D‑dipeptide ABC transporter permease |
| RA | 1,588,435 | C→T | Q135Q (CAG→CAA) | ydeS ← | putative fimbrial‑like adhesin protein |
| RA | 1,592,933 | T→C | pseudogene (1193/1461 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,798,559 | T→C | A128A (GCA→GCG) | pheS ← | phenylalanine tRNA synthetase, alpha subunit |
| RA | 1,863,313 | T→C | A181A (GCT→GCC) | gapA → | glyceraldehyde‑3‑phosphate dehydrogenase A |
| RA | 1,931,721 | T→C | S281P (TCC→CCC) | purT → | phosphoribosylglycinamide formyltransferase 2 |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,000,046 | G→A | R114C (CGC→TGC) | fliY ← | cystine transporter subunit |
| RA | 2,058,079 | T→C | noncoding (24/76 nt) | asnW ← | tRNA‑Asn |
| RA | 2,088,009 | C→T | A84T (GCG→ACG) | yeeY ← | LysR family putative transcriptional regulator |
| RA | 2,101,014 | A→G | D85D (GAT→GAC) | gnd ← | 6‑phosphogluconate dehydrogenase, decarboxylating |
| RA | 2,117,002 | T→C | T42T (ACA→ACG) | wcaL ← | putative glycosyl transferase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,174,510 | C→T | A19A (GCG→GCA) | gatB ← | galactitol‑specific enzyme IIB component of PTS |
| RA | 2,178,910 | T→C | S30S (AGT→AGC) | yegT → | nucleoside transporter, low affinity |
| RA | 2,224,908 | C→T | intergenic (‑38/+136) | pbpG ← / ← yohC | D‑alanyl‑D‑alanine endopeptidase/Yip1 family inner membrane protein |
| RA | 2,230,378 | A→G | V3A (GTG→GCG) | dusC ← | tRNA‑dihydrouridine synthase C |
| RA | 2,241,409 | T→C | Q87R (CAG→CGG) | galS ← | galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor; mgl operon transcriptional repressor; autorepressor |
| RA | 2,246,756 | T→C | N5S (AAC→AGC) | cirA ← | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter |
| RA | 2,325,154 | T→C | G133G (GGT→GGC) | atoE → | short chain fatty acid transporter |
| RA | 2,331,551 | T→C | pseudogene (2852/4605 nt) | yfaS ← | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| RA | 2,406,631 | G→A | A4V (GCA→GTA) | lrhA ← | transcriptional repressor of flagellar, motility and chemotaxis genes |
| RA | 2,467,446 | A→G | K301R (AAG→AGG) | intS → | CPS‑53 (KpLE1) prophage; putative prophage CPS‑53 integrase |
| RA | 2,473,880 | C→T | R93C (CGC→TGC) | yfdP → | CPS‑53 (KpLE1) prophage; uncharacterized protein |
| RA | 2,476,804 | T→C | T276A (ACG→GCG) | dsdC ← | dsd operon activator; autorepressor |
| RA | 2,501,851 | T→C | I241T (ATT→ACT) | ypdC → | putative DNA‑binding protein |
| RA | 2,527,897 | A→G | T318A (ACC→GCC) | yfeH → | putative inorganic ion transporter |
| RA | 2,566,929 | T→C | P393P (CCA→CCG) | eutH ← | ethanolamine transporter |
| RA | 2,603,573 | C→T | P586S (CCG→TCG) | hyfB → | hydrogenase 4, membrane subunit |
| RA | 2,609,458 | T→C | R324R (CGT→CGC) | hyfG → | hydrogenase 4, subunit |
| RA | 2,631,911 | T→C | T209A (ACG→GCG) | guaA ← | GMP synthetase (glutamine aminotransferase) |
| JC | 2,636,790 | (TTC)3→2 | coding (565‑567/1473 nt) | der ← | GTPase; multicopy suppressor of ftsJ |
| RA | 2,647,150 | G→A | A59V (GCT→GTT) | pbpC ← | penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain protein |
| RA | 2,651,365 | T→C | Q308R (CAA→CGA) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,662,523 | A→G | intergenic (‑392/+60) | iscR ← / ← trmJ | isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress‑ and iron starvation‑inducible; autorepressor/tRNA mC32,mU32 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 2,694,036 | A→G | V503A (GTT→GCT) | purL ← | phosphoribosylformyl‑glycineamide synthetase |
| RA | 2,695,585 | (G)7→8 | intergenic (‑42/‑216) | purL ← / → mltF | phosphoribosylformyl‑glycineamide synthetase/membrane‑bound lytic transglycosylase F, murein hydrolase |
| RA | 2,704,781 | A→G | C177R (TGT→CGT) | lepB ← | leader peptidase (signal peptidase I) |
| RA | 2,767,140 | T→C | L53L (TTG→CTG) | rnlB → | CP4‑57 prophage; uncharacterized protein |
| RA | 2,780,330 | G→A | G799G (GGC→GGT) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,808,515 | T→C | pseudogene (200/261 nt) | ygaY → | pseudogene, major facilitator transporter superfamily;putative transport; Not classified; putative transport protein |
| RA | 2,816,485 | A→G | intergenic (‑46/+27) | gshA ← / ← yqaA | glutamate‑cysteine ligase/COG1238 family inner membrane protein |
| RA | 2,872,857 | T→C | intergenic (‑37/+157) | ftsB ← / ← ygbE | cell division protein/DUF3561 family inner membrane protein |
| RA | 2,903,235 | C→T | A447V (GCC→GTC) | ygcE → | putative kinase |
| RA | 2,912,885 | A→G | I256T (ATC→ACC) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,946,466 | T→C | H238R (CAC→CGC) | mltA ← | membrane‑bound lytic murein transglycosylase A |
| RA | 3,012,527 | T→C | intergenic (+134/+87) | yqeA → / ← yqeB | putative amino acid kinase/XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold |
| RA | 3,079,093 | A→G | S80P (TCT→CCT) | cmtB ← | putative mannitol‑specific enzyme IIA component of PTS |
| RA | 3,086,618 | A→G | intergenic (+216/‑88) | yqgC → / → metK | uncharacterized protein/S‑adenosylmethionine synthetase |
| RA | 3,096,477 | A→G | D32G (GAC→GGC) | yggU → | UPF0235 family protein |
| RA | 3,147,279 | T→A | pseudogene (413/420 nt) | yghX ← | pseudogene, dienlactone hydrolase family |
| RA | 3,195,078 | (G)6→7 | intergenic (+253/‑63) | ibsD → / → ibsE | toxic membrane protein/toxic membrane protein |
| RA | 3,242,272 | T→C | K348R (AAA→AGA) | uxaA ← | altronate hydrolase |
| RA | 3,249,662 | T→C | V96V (GTT→GTC) | yqjD → | membrane‑anchored ribosome‑binding protein |
| RA | 3,272,271 | Δ1 bp | coding (481/885 nt) | garR ← | tartronate semialdehyde reductase |
| RA | 3,335,787 | A→G | G236G (GGT→GGC) | murA ← | UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase |
| JC JC | 3,368,136 | IS2 (–) +5 bp | coding (310‑314/1128 nt) | yhcG → | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| RA | 3,376,403 | T→C | D125G (GAC→GGC) | sspB ← | ClpXP protease specificity enhancing factor |
| RA | 3,377,215 | A→G | L69P (CTG→CCG) | sspA ← | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog |
| RA | 3,430,410 | A→G | C143C (TGT→TGC) | aroE ← | dehydroshikimate reductase, NAD(P)‑binding |
| RA | 3,440,116 | T→C | D305G (GAC→GGC) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,449,100 | T→C | T24A (ACG→GCG) | rplP ← | 50S ribosomal subunit protein L16 |
| RA | 3,515,565 | A→G | Y117H (TAC→CAC) | dam ← | DNA adenine methyltransferase |
| RA | 3,544,910 | T→C | L10P (CTA→CCA) | gntX → | DNA catabolic protein |
| RA | 3,560,455 | +G | 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 | 3,602,080 | T→C | K3E (AAG→GAG) | ftsX ← | putative ABC transporter permease |
| RA | 3,612,540 | T→C | W226R (TGG→CGG) | yhhT → | UPF0118 family putative transporter |
| RA | 3,784,753 | T→C | E88G (GAG→GGG) | yibN ← | putative rhodanese‑related sulfurtransferase |
| RA | 3,815,808 | (A)8→7 | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,930,868 | A→G | F76L (TTC→CTC) | ravA ← | hexameric AAA+ MoxR family ATPase, putative molecular chaperone |
| RA | 3,964,868 | A→G | W255R (TGG→CGG) | rhlB ← | ATP‑dependent RNA helicase |
| RA | 4,001,381 | T→C | intergenic (‑325/‑45) | yigE ← / → corA | DUF2233 family protein/magnesium/nickel/cobalt transporter |
| RA | 4,003,303 | A→G | R292R (CGT→CGC) | rarD ← | putative chloramphenical resistance permease |
| RA | 4,091,611 | A→G | L252L (CTT→CTC) | frvB ← | putative PTS enzyme, IIB component/IIC component |
| RA | 4,096,230 | T→C | T407A (ACG→GCG) | rhaB ← | rhamnulokinase |
| RA | 4,128,316 | A→G | V27A (GTT→GCT) | metJ ← | transcriptional repressor, S‑adenosylmethionine‑binding |
| RA | 4,185,098 | A→G | Y1285C (TAC→TGC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,215,624 | A→G | A49A (GCA→GCG) | aceB → | malate synthase A |
| RA | 4,254,557 | A→G | V637A (GTA→GCA) | plsB ← | glycerol‑3‑phosphate O‑acyltransferase |
| RA | 4,285,704 | A→G | G556G (GGT→GGC) | acs ← | acetyl‑CoA synthetase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,307,018 | G→A | A261V (GCC→GTC) | alsK ← | D‑allose kinase |
| RA | 4,366,223 | A→G | F184S (TTC→TCC) | dcuA ← | C4‑dicarboxylate antiporter |
| RA | 4,389,337 | A→G | C12R (TGC→CGC) | mscM ← | mechanosensitive channel protein, miniconductance |
| RA | 4,399,151 | Δ1 bp | coding (1740/1848 nt) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,578,549 | A→G | C263C (TGT→TGC) | mcrB ← | 5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrB |
| RA | 4,622,655 | T→C | V296A (GTG→GCG) | yjjJ → | putative protein kinase |
| RA | 4,632,187 | A→G | K485K (AAA→AAG) | slt → | lytic murein transglycosylase, soluble |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1633044–1633222 | 1633540–1633226 | 5–497 | 45 [43] | [43] 44 | ydfK | ydfK |
| * | * | ÷ | NC_000913 | 3423700–3424234 | 3424586–3424239 | 6–887 | 44 [43] | [43] 44 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 83 (1.050) | 70/290 | 0.2 | 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 | |||||