mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 125,085 | T→A | 100% | I690N (ATC→AAC) | aceE → | pyruvate dehydrogenase E1 component |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| JC JC | 568,268 | IS1 (–) +9 bp | 100% | intergenic (+21/‑39) | renD → / → emrE | DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE |
| RA | 639,694 | G→T | 21.1% | intergenic (+186/‑59) | ahpC → / → ahpF | alkyl hydroperoxide reductase, AhpC component/alkyl hydroperoxide reductase, AhpF component |
| RA | 705,916 | T→C | 12.7% | intergenic (+26/‑177) | nagE → / → glnS | N‑acetylglucosamine specific PTS enzyme IIABC component/glutamine‑‑tRNA ligase |
| RA | 1,147,548 | T→G | 10.7% | intergenic (+8/‑73) | rpmF → / → plsX | 50S ribosomal subunit protein L32/putative phosphate acyltransferase |
| RA | 1,196,220 | C→T | 100% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | 100% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,260,901 | C→T | 13.8% | intergenic (‑98/+27) | dauA ← / ← prs | aerobic C4‑dicarboxylate transporter DauA/ribose‑phosphate diphosphokinase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,311,830 | A→G | 11.0% | intergenic (+22/+18) | tonB → / ← yciA | Ton complex subunit TonB/acyl‑CoA thioesterase |
| RA | 1,311,831 | C→T | 11.5% | intergenic (+23/+17) | tonB → / ← yciA | Ton complex subunit TonB/acyl‑CoA thioesterase |
| RA | 1,426,178 | A→T | 6.3% | intergenic (+198/‑276) | ydaY → / → ynaA | Rac prophage; putative uncharacterized protein YdaY/Rac prophage; putative prophage tail length tape measure domain‑containing protein YnaA |
| RA | 1,466,336 | C→G | 8.4% | pseudogene (945/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,701,108 | A→T | 9.9% | N51I (AAT→ATT) | malY → | negative regulator of MalT activity/cystathionine beta‑lyase |
| RA | 1,712,338 | A→T | 9.6% | intergenic (+180/‑431) | nth → / → dtpA | endonuclease III/dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,884,303 | G→T | 20.4% | M372I (ATG→ATT) | yeaV → | putative transporter YeaV |
| RA | 1,934,900 | C→T | 50.1% | G472E (GGA→GAA) | zwf ← | NADP(+)‑dependent glucose‑6‑phosphate dehydrogenase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,041,159 | G→A | 8.7% | intergenic (+41/‑216) | msrQ → / → zinT | periplasmic protein‑L‑methionine sulfoxide reductase heme binding subunit/metal‑binding protein ZinT |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,314,800 | A→C | 11.2% | Q438P (CAG→CCG) ‡ | rcsD → | RcsD phosphotransferase |
| RA | 2,314,801 | G→T | 9.4% | Q438H (CAG→CAT) ‡ | rcsD → | RcsD phosphotransferase |
| RA | 2,323,330 | C→T | 53.0% | intergenic (+79/‑117) | atoC → / → atoD | DNA‑binding transcriptional activator/ornithine decarboxylase inhibitor AtoC/acetyl‑CoA:acetoacetyl‑CoA transferase subunit alpha |
| JC | 2,392,615 | Δ3 bp | 33.9% | coding (425‑427/1530 nt) | nuoM ← | NADH:quinone oxidoreductase subunit M |
| JC | 2,399,785 | Δ40 bp | 51.4% | coding (342‑381/2727 nt) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| RA | 2,447,483 | G→T | 67.4% | intergenic (‑10/+25) | aroC ← / ← prmB | chorismate synthase/50S ribosomal subunit protein L3 N(5)‑glutamine methyltransferase |
| JC JC | 2,449,199 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | 18.5% | intergenic (+42/+24) | smrB → / ← yfcO | putative endonuclease SmrB/DUF2544 domain‑containing protein YfcO |
| RA | 2,518,272 | Δ1 bp | 8.3% | intergenic (‑41/‑195) | alaW ← / → yfeC | tRNA‑Ala/putative DNA‑binding transcriptional regulator YfeC |
| RA | 2,518,275 | T→G | 8.9% | intergenic (‑44/‑192) | alaW ← / → yfeC | tRNA‑Ala/putative DNA‑binding transcriptional regulator YfeC |
| RA | 2,661,816 | T→G | 64.1% | T106P (ACC→CCC) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,662,029 | G→C | 35.8% | Q35E (CAG→GAG) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,785,436 | A→G | 9.1% | intergenic (‑425/+326) | ypjC ← / ← ileY | DUF5507 domain‑containing protein YpjC/tRNA‑Ile |
| RA | 3,041,398 | T→G | 100% | L29R (CTT→CGT) | ygfZ → | folate‑binding protein |
| JC JC | 3,190,486 | IS5 (+) +4 bp | 24.1% | coding (606‑609/750 nt) | yqiH → | putative fimbrial chaperone YqiH |
| RA | 3,210,839 | A→T | 17.2% | K20M (AAG→ATG) | rpsU → | 30S ribosomal subunit protein S21 |
| RA | 3,351,007 | Δ1 bp | 55.2% | coding (2019/2337 nt) | arcB ← | sensory histidine kinase ArcB |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,578,609 | T→G | 11.2% | I40L (ATT→CTT) | gntR ← | DNA‑binding transcriptional repressor GntR |
| RA | 3,578,610 | C→A | 9.1% | K39N (AAG→AAT) | gntR ← | DNA‑binding transcriptional repressor GntR |
| RA | 3,602,498 | T→C | 16.0% | I84V (ATT→GTT) | ftsE ← | cell division protein FtsE |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,832,797 | T→G | 6.4% | N581H (AAC→CAC) | yicI ← | alpha‑D‑xyloside xylohydrolase |
| RA | 3,832,800 | C→A | 5.7% | A580S (GCG→TCG) | yicI ← | alpha‑D‑xyloside xylohydrolase |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,060,261 | G→T | 6.3% | intergenic (+31/‑186) | bipA → / → yihL | ribosome‑dependent GTPase, ribosome assembly factor/putative transcriptional regulator YihL |
| RA | 4,060,264 | A→C | 6.0% | intergenic (+34/‑183) | bipA → / → yihL | ribosome‑dependent GTPase, ribosome assembly factor/putative transcriptional regulator YihL |
| RA | 4,174,083 | C→T | 51.1% | R315H (CGC→CAC) | coaA ← | pantothenate kinase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,196,235 | C→A | 29.3% | intergenic (‑136/+97) | thiC ← / ← rsd | phosphomethylpyrimidine synthase/regulator of sigma D |
| RA | 4,296,060 | C→T | 25.3% | 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 | 4,314,227 | A→T | 7.7% | intergenic (+30/+117) | yjdP → / ← phnP | protein YjdP/5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase |
| RA | 4,314,233 | A→T | 9.8% | intergenic (+36/+111) | yjdP → / ← phnP | protein YjdP/5‑phospho‑alpha‑D‑ribosyl 1,2‑cyclic phosphate phosphodiesterase |
| RA | 4,356,445 | A→T | 6.6% | intergenic (‑34/+25) | dtpC ← / ← cadA | dipeptide/tripeptide:H(+) symporter DtpC/lysine decarboxylase 1 |
| RA | 4,376,280 | G→A | 6.9% | intergenic (+15/‑37) | efp → / → ecnA | protein chain elongation factor EF‑P/entericidin A lipoprotein, antidote to entericidin B |
| RA | 4,376,291 | T→C | 7.7% | intergenic (+26/‑26) | efp → / → ecnA | protein chain elongation factor EF‑P/entericidin A lipoprotein, antidote to entericidin B |
| RA | 4,472,434 | G→A | 7.3% | R34* (CGA→TGA) | pyrL ← | pyrBI operon leader peptide |
| RA | 4,472,437 | T→C | 7.4% | N33D (AAT→GAT) | pyrL ← | pyrBI operon leader peptide |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196243 | 1211467 | 15225 | 13 [11] | [12] 13 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 3621168–3622311 | 3653113–3652031 | 29721–31946 | 13 [12] | [12] 13 | [rhsB]–[insH‑11] | [rhsB],yhhH,yhhI,yhhJ,rbbA,yhiI,yhiJ,yhiL,yhiM,yhiN,pitA,uspB,uspA,dtpB,rsmJ,prlC,rlmJ,gor,dinQ,agrA,agrB,arsR,arsB,arsC,yhiS,[insH‑11] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 42783 = | 24 (0.570) | 3 (0.080) | 3/250 | NT | 12.1% | coding (381/771 nt) | fixA | putative electron transfer flavoprotein FixA |
| ? | NC_000913 | 42803 = | 21 (0.530) | coding (401/771 nt) | fixA | putative electron transfer flavoprotein FixA | |||||
| * | ? | NC_000913 | 225078 = | NA (NA) | 5 (0.130) | 5/250 | NT | NA | noncoding (1308/1542 nt) | rrsH | 16S ribosomal RNA |
| ? | NC_000913 | 225100 = | NA (NA) | noncoding (1330/1542 nt) | rrsH | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | = 228744 | 19 (0.450) | 5 (0.120) | 4/252 | NT | 21.6% | intergenic (+82/‑12) | rrlH/rrfH | 23S ribosomal RNA/5S ribosomal RNA |
| ? | NC_000913 | = 4040481 | NA (NA) | intergenic (+58/‑36) | rrlA/rrfA | 23S ribosomal RNA/5S ribosomal RNA | |||||
| * | ? | NC_000913 | = 1097101 | 18 (0.430) | 5 (0.130) | 5/248 | NT | 22.8% | intergenic (+272/+464) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| ? | NC_000913 | = 1097105 | NA (NA) | intergenic (+276/+460) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser | |||||
| * | ? | NC_000913 | 1579554 = | 34 (0.810) | 3 (0.080) | 3/246 | NT | 9.0% | coding (10/123 nt) | yneP | protein YneP |
| ? | NC_000913 | 1579580 = | 29 (0.740) | coding (36/123 nt) | yneP | protein YneP | |||||
| * | ? | NC_000913 | = 2411407 | 36 (0.850) | 3 (0.080) | 3/250 | NT | 8.0% | intergenic (‑55/+32) | yfbS/hxpA | putative transporter YfbS/hexitol phosphatase A |
| ? | NC_000913 | = 2411413 | 35 (0.880) | intergenic (‑61/+26) | yfbS/hxpA | putative transporter YfbS/hexitol phosphatase A | |||||
| * | ? | NC_000913 | = 2630411 | 29 (0.690) | 3 (0.070) | 3/252 | NT | 9.1% | coding (86/540 nt) | yfgI | nalidixic acid resistance protein YfgI |
| ? | NC_000913 | = 2630423 | 32 (0.790) | coding (98/540 nt) | yfgI | nalidixic acid resistance protein YfgI | |||||
| * | ? | NC_000913 | 2726200 = | NA (NA) | 6 (0.150) | 5/252 | NT | NA | intergenic (‑12/+81) | rrfG/rrlG | 5S ribosomal RNA/23S ribosomal RNA |
| ? | NC_000913 | 2726224 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA/23S ribosomal RNA | |||||
| * | ? | NC_000913 | 2729630 = | NA (NA) | 4 (0.100) | 4/254 | NT | NA | noncoding (1528/1542 nt) | rrsG | 16S ribosomal RNA |
| ? | NC_000913 | 2729652 = | NA (NA) | noncoding (1506/1542 nt) | rrsG | 16S ribosomal RNA | |||||
| * | ? | NC_000913 | = 2879381 | 42 (0.990) | 3 (0.070) | 3/254 | NT | 6.7% | coding (392/918 nt) | cas1 | multifunctional nuclease Cas1 |
| ? | NC_000913 | = 2879386 | 43 (1.060) | coding (387/918 nt) | cas1 | multifunctional nuclease Cas1 | |||||
| * | ? | NC_000913 | 4165491 = | 62 (1.470) | 3 (0.080) | 3/250 | NT | 5.1% | coding (64/858 nt) | murI | glutamate racemase |
| ? | NC_000913 | 4165527 = | 52 (1.300) | coding (100/858 nt) | murI | glutamate racemase | |||||