breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 10,637 C→A G18G (GGC→GGA mogA → molybdenum cofactor biosynthesis protein MogA
RA 194,161 A→G M42V (ATG→GTG)  LY180_00835 → 1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase
RA 230,529 T→C D275G (GAC→GGC)  LY180_01015 ← LysR family transcripitonal regulator
RA 459,705 Δ1 bp coding (137/276 nt) LY180_02175 ← transcriptional regulator
RA 793,877 T→C C358R (TGT→CGT)  LY180_03720 → rhsA
RA 793,936 T→C S377S (AGT→AGC LY180_03720 → rhsA
RA 793,954 A→G E383E (GAA→GAG LY180_03720 → rhsA
RA 793,985 A→G N394D (AAC→GAC)  LY180_03720 → rhsA
RA 814,037 G→C T139S (ACC→AGC)  gltA ← type II citrate synthase
MC JC 1,011,041 Δ300 bp intergenic (+21/+62) LY180_04735 → / ← pflA hypothetical protein/pyruvate formate lyase‑activating protein
MC JC 1,088,034 Δ103 bp intergenic (+278/+242) helD → / ← LY180_05060 DNA helicase IV/hypothetical protein
RA 1,168,401 C→A S606* (TCG→TAG)  LY180_05445 → glucosyltransferase
JC 1,213,485 Δ7 bp intergenic (+184/‑105) LY180_05705 → / → LY180_05710 DNAse/PTS glucose transporter subunit IIBC
RA 1,324,434 A→C K833T (AAA→ACA)  narZ → nitrate reductase A subunit alpha
RA 1,335,968 A→G intergenic (+281/+21) LY180_06295 → / ← LY180_06300 thymidine kinase/bifunctional acetaldehyde‑CoA/alcohol dehydrogenase
MC JC 1,335,989 2720 bp→18 bp [LY180_06300][LY180_06310] [LY180_06300], LY180_06305, [LY180_06310]
MC JC 1,446,672 Δ2,957 bp [zntB][LY180_06850] [zntB], LY180_06845, [LY180_06850]
RA 1,459,895 C→T T49T (ACC→ACT LY180_06935 → hypothetical protein
RA 1,464,821 A→G intergenic (+486/‑118) LY180_06955 → / → LY180_06960 hypothetical protein/regulatory protein
RA 1,505,743 2 bp→GT intergenic (‑91/+19) LY180_07195 ← / ← LY180_07200 heat‑inducible protein/hypothetical protein
RA 1,505,880 T→C L35L (CTA→CTG LY180_07200 ← hypothetical protein
RA 1,563,485 A→G T256A (ACC→GCC)  LY180_07445 → transposase IS609
RA 1,563,642 G→A R308H (CGC→CAC)  LY180_07445 → transposase IS609
RA 1,563,706 C→T Y329Y (TAC→TAT LY180_07445 → transposase IS609
RA 1,563,726 G→A C336Y (TGC→TAC)  LY180_07445 → transposase IS609
RA 1,563,748 A→G E343E (GAA→GAG LY180_07445 → transposase IS609
RA 1,563,751 T→C N344N (AAT→AAC LY180_07445 → transposase IS609
RA 1,588,241 A→C E403D (GAA→GAC LY180_07560 → type IV secretion protein Rhs
RA 1,645,301 T→G intergenic (+1095/+165) LY180_07765 → / ← LY180_07770 transposase/sulfatase
RA 1,645,397 C→T intergenic (+1191/+69) LY180_07765 → / ← LY180_07770 transposase/sulfatase
RA 1,645,421 C→G intergenic (+1215/+45) LY180_07765 → / ← LY180_07770 transposase/sulfatase
MC JC 1,749,406 Δ777 bp [LY180_08300][LY180_08310] [LY180_08300], LY180_08305, [LY180_08310]
RA 1,964,559 G→A N226N (AAC→AAT LY180_09345 ← transposase IS609
RA 1,964,699 C→T V180I (GTC→ATC)  LY180_09345 ← transposase IS609
RA 1,964,727 G→T S170S (TCC→TCA LY180_09345 ← transposase IS609
RA 1,964,784 A→C T151T (ACT→ACG LY180_09345 ← transposase IS609
RA 2,251,239 G→A P28P (CCC→CCT LY180_10740 ← hypothetical protein
RA 2,251,586 T→C E104E (GAA→GAG LY180_10745 ← major tail tube protein
RA 2,251,616 A→G R94R (CGT→CGC LY180_10745 ← major tail tube protein
RA 2,265,347 G→A intergenic (‑100/‑74) LY180_10855 ← / → LY180_10860 precorrin‑8W decarboxylase/terminase
RA 2,265,396 A→G intergenic (‑149/‑25) LY180_10855 ← / → LY180_10860 precorrin‑8W decarboxylase/terminase
RA 2,265,399 G→T intergenic (‑152/‑22) LY180_10855 ← / → LY180_10860 precorrin‑8W decarboxylase/terminase
RA 2,265,885 C→A A155A (GCC→GCA LY180_10860 → terminase
RA 2,312,761 T→A intergenic (‑71/+448) LY180_11070 ← / ← LY180_11075 hypothetical protein/hypothetical protein
RA 2,312,767 3 bp→GAC intergenic (‑77/+440) LY180_11070 ← / ← LY180_11075 hypothetical protein/hypothetical protein
RA 2,312,771 G→A intergenic (‑81/+438) LY180_11070 ← / ← LY180_11075 hypothetical protein/hypothetical protein
RA 2,312,773 C→G intergenic (‑83/+436) LY180_11070 ← / ← LY180_11075 hypothetical protein/hypothetical protein
RA 2,483,647 G→A P236S (CCG→TCG)  LY180_11800 ← NADH:ubiquinone oxidoreductase subunit M
MC JC 2,505,263 Δ394 bp intergenic (‑620/‑500) LY180_11895 ← / → LY180_11905 hypothetical protein/phosphate acetyltransferase
RA 2,505,816 A→G intergenic (‑1173/‑340) LY180_11895 ← / → LY180_11905 hypothetical protein/phosphate acetyltransferase
RA 2,506,026 T→C intergenic (‑1383/‑130) LY180_11895 ← / → LY180_11905 hypothetical protein/phosphate acetyltransferase
MC JC 2,606,939 Δ122 bp LY180_12380 LY180_12380
RA 3,010,362 G→T E48* (GAA→TAA)  LY180_14330 → type VI secretion protein ImpK
RA 3,278,551 G→A W246* (TGG→TGA LY180_15575 → aldehyde oxidoreductase
MC JC 3,431,620 Δ68 bp coding (288‑355/879 nt) LY180_16320 → protease
RA 3,505,943 C→T G41D (GGT→GAT)  LY180_16680 ← malate dehydrogenase
RA 3,545,689 T→C noncoding (2811/2931 nt) LY180_16870 ← 23S ribosomal RNA
RA 3,545,692 C→T noncoding (2808/2931 nt) LY180_16870 ← 23S ribosomal RNA
RA 3,545,695 G→A noncoding (2805/2931 nt) LY180_16870 ← 23S ribosomal RNA
RA 3,545,697 A→G noncoding (2803/2931 nt) LY180_16870 ← 23S ribosomal RNA
RA 3,772,505 A→G F313F (TTT→TTC LY180_18030 ← glutamate decarboxylase
JC 3,812,239 (AGA)2→4 coding (434/1020 nt) LY180_18170 ← peptide ABC transporter permease
RA 3,943,262 G→A G302D (GGC→GAC)  LY180_18795 → bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA 4,023,563 T→C L4P (CTC→CCC)  rnpA → ribonuclease P
RA 4,178,979 T→C noncoding (1009/1541 nt) LY180_19945 → 16S ribosomal RNA
RA 4,178,988 Δ1 bp noncoding (1018/1541 nt) LY180_19945 → 16S ribosomal RNA
RA 4,178,991 A→T noncoding (1021/1541 nt) LY180_19945 → 16S ribosomal RNA
RA 4,178,993 +G noncoding (1023/1541 nt) LY180_19945 → 16S ribosomal RNA
RA 4,179,007 C→T noncoding (1037/1541 nt) LY180_19945 → 16S ribosomal RNA
RA 4,305,124 G→A G42G (GGG→GGA LY180_20645 → rhsA
RA 4,305,151 G→C P51P (CCG→CCC LY180_20645 → rhsA
RA 4,305,201 C→G A68G (GCC→GGC)  LY180_20645 → rhsA
MC JC 4,394,727 Δ4,605 bp LY180_21020LY180_21030 LY180_21020, adhP, LY180_21030
RA 4,469,025 +A coding (748/1350 nt) LY180_21345 → permase
MC JC 4,815,129 Δ342 bp coding (402‑743/1224 nt) LY180_23005 → phosphopentomutase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP006584 1505920 1510567 4648 32 [30] [31] 32 [LY180_07200]–[LY180_07220] [LY180_07200],LY180_07205,LY180_07210,LY180_07215,[LY180_07220]
* * ÷ CP006584 3028817–3029213 3032142–3032062 2850–3326 32 [30] [31] 32 [LY180_14390]–[LY180_14415] [LY180_14390],LY180_14395,LY180_14400,LY180_14405,LY180_14410,[LY180_14415]
* * ÷ CP006584 3344916–3345689 3377352–3376396 30708–32437 32 [31] [31] 34 ebgC–LY180_16025 ebgC,LY180_15890,LY180_15895,LY180_15900,fadH,LY180_15910,LY180_15915,LY180_15920,LY180_15925,LY180_15930,LY180_15935,LY180_15940,LY180_15945,LY180_15950,LY180_15955,LY180_15960,LY180_15965,LY180_15970,LY180_15975,LY180_15980,LY180_15985,LY180_15990,LY180_15995,LY180_16000,LY180_16005,LY180_16010,LY180_16015,LY180_16020,LY180_16025

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP006584 5598 =NA (NA)102 (1.230) 73/562 0.2 100% intergenic (+69/‑191) LY180_00025/LY180_00030 hypothetical protein/hypothetical protein
?CP006584 3172592 = 0 (0.000)coding (29/273 nt) LY180_15050 hypothetical protein
* ? CP006584 = 225257NA (NA)107 (1.240) 96/584 0.0 NA noncoding (1014/1541 nt) LY180_00980 16S ribosomal RNA
?CP006584 225269 = NA (NA)noncoding (1026/1541 nt) LY180_00980 16S ribosomal RNA
* ? CP006584 = 26913064 (0.740)69 (0.850)
+TCATGTCATTAGTGCGTT
61/550 0.4 69.7% coding (377/414 nt) LY180_01180 hypothetical protein
?CP006584 1594499 = 0 (0.000)coding (168/909 nt) LY180_07575 hypothetical protein
* ? CP006584 294480 =75 (0.870)33 (0.430) 31/518 2.3 31.4% coding (26/996 nt) LY180_01335 hypothetical protein
?CP006584 297564 = 78 (1.020)coding (496/1515 nt) LY180_01350 tail protein
* ? CP006584 346068 =NA (NA)105 (1.210) 90/586 0.0 99.1% intergenic (‑51/‑107) LY180_01675/LY180_01680 CadC family transcriptional regulator/hypothetical protein
?CP006584 = 363812 1 (0.010)intergenic (‑39/‑249) LY180_01770/LY180_01775 outer membrane phosphoporin protein E/gamma‑glutamyl kinase
* ? CP006584 = 34739787 (1.010)130 (1.510) 113/584 0.0 74.6% intergenic (+14/‑444) LY180_01680/LY180_01685 hypothetical protein/flagellin
?CP006584 363805 = 2 (0.020)intergenic (‑32/‑256) LY180_01770/LY180_01775 outer membrane phosphoporin protein E/gamma‑glutamyl kinase
* ? CP006584 794676 =NA (NA)41 (0.480) 38/576 1.9 NA coding (1871/4200 nt) LY180_03720 rhsA
?CP006584 = 794771 NA (NA)coding (1966/4200 nt) LY180_03720 rhsA
* ? CP006584 840689 =43 (0.500)39 (0.500) 36/524 1.8 46.6% intergenic (+68/‑82) LY180_03930/LY180_03935 tRNA‑Lys/tRNA‑Val
?CP006584 = 841381 51 (0.660)intergenic (+125/‑280) LY180_03950/LY180_03955 tRNA‑Lys/quinolinate synthetase
* ? CP006584 917080 =NA (NA)56 (0.650) 51/580 1.0 100% intergenic (+88/‑191) LY180_04320/LY180_04325 heme ABC transporter ATP‑binding protein/hypothetical protein
?CP006584 = 2414713 0 (0.000)coding (1017/1644 nt) LY180_11545 multidrug ABC transporter ATP‑binding protein
* ? CP006584 1643563 =67 (0.770)115 (1.380) 87/566 0.0 78.0% intergenic (‑223/‑80) LY180_07760/LY180_07765 sulfatase/transposase
?CP006584 = 4565632 0 (0.000)intergenic (‑372/+82) LY180_21775/LY180_21780 hypothetical protein/lysine 2,3‑aminomutase
* ? CP006584 1749406 =NA (NA)110 (1.270) 101/586 0.0 96.5% coding (13/864 nt) LY180_08300 transcriptional regulator
?CP006584 = 3920817 4 (0.050)coding (415/984 nt) LY180_18670 beta1,3‑glucosyltransferase
* ? CP006584 = 1750173NA (NA)111 (1.280) 100/586 0.0 96.5% coding (380/384 nt) LY180_08310 gdgsA
?CP006584 3920810 = 4 (0.050)coding (422/984 nt) LY180_18670 beta1,3‑glucosyltransferase
* ? CP006584 1840765 =5 (0.060)68 (0.790) 66/586 0.4 93.2% intergenic (+248/‑63) LY180_08735/LY180_08740 pyruvate kinase/murein lipoprotein
?CP006584 = 1840785 NA (NA)intergenic (+268/‑43) LY180_08735/LY180_08740 pyruvate kinase/murein lipoprotein
* ? CP006584 2030792 =NA (NA)67 (0.780) 62/578 0.5 100% intergenic (+74/+105) znuB/LY180_09680 zinc transporter/hypothetical protein
?CP006584 2414712 = 0 (0.000)coding (1018/1644 nt) LY180_11545 multidrug ABC transporter ATP‑binding protein
* ? CP006584 2253821 =33 (0.380)32 (0.390) 31/556 2.6 47.3% coding (38/414 nt) LY180_10760 hypothetical protein
?CP006584 2255662 = 40 (0.490)coding (826/1284 nt) LY180_10775 tail protein
* ? CP006584 2385043 =4 (0.050)63 (0.730) 56/584 0.7 94.0% coding (718/1026 nt) LY180_11390 microcin C ABC transporter permease
?CP006584 2565085 = NA (NA)intergenic (+71/‑106) LY180_12185/LY180_12190 D‑serine dehydratase/hypothetical protein
* ? CP006584 = 23850525 (0.060)63 (0.730) 56/586 0.7 92.7% coding (727/1026 nt) LY180_11390 microcin C ABC transporter permease
?CP006584 2565084 = NA (NA)intergenic (+70/‑107) LY180_12185/LY180_12190 D‑serine dehydratase/hypothetical protein
* ? CP006584 = 2891935NA (NA)104 (1.210) 90/584 0.0 96.3% intergenic (+12/+249) LY180_13750/LY180_13755 hypothetical protein/transcriptional regulator
?CP006584 = 3268631 4 (0.050)coding (88/1119 nt) LY180_15515 hydrogenase 2 small subunit
* ? CP006584 2896407 =NA (NA)94 (1.100) 80/578 0.1 100% intergenic (+63/+105) LY180_13765/LY180_13770 6‑phospho‑beta‑glucosidase/transposase
?CP006584 3262157 = 0 (0.000)intergenic (+107/+16) LY180_15475/LY180_15480 GSH‑dependent disulfide bond oxidoreductase/hydrogenase 2 accessory protein HypG
* ? CP006584 = 31725930 (0.000)101 (1.180) 93/578 0.0 100% coding (28/273 nt) LY180_15050 hypothetical protein
?CP006584 4311141 = NA (NA)intergenic (‑130/+105) LY180_20655/LY180_20660 hypothetical protein/hypothetical protein
* ? CP006584 = 32621580 (0.000)91 (1.100) 86/562 0.0 100% intergenic (+108/+15) LY180_15475/LY180_15480 GSH‑dependent disulfide bond oxidoreductase/hydrogenase 2 accessory protein HypG
?CP006584 = 4312417 NA (NA)intergenic (‑191/+57) LY180_20660/LY180_20665 hypothetical protein/transcriptional regulator
* ? CP006584 3268622 =2 (0.020)110 (1.270) 93/586 0.0 98.2% coding (97/1119 nt) LY180_15515 hydrogenase 2 small subunit
?CP006584 3344744 = NA (NA)coding (163/330 nt) LY180_15880 hypothetical protein
* ? CP006584 3305035 =3 (0.030)88 (1.020) 74/584 0.2 96.7% intergenic (‑341/‑33) ribB/LY180_15715 3,4‑dihydroxy‑2‑butanone 4‑phosphate synthase/hypothetical protein
?CP006584 = 3672182 NA (NA)coding (475/477 nt) LY180_17575 membrane protein
* ? CP006584 = 33050457 (0.080)119 (1.380) 94/584 0.0 94.5% intergenic (‑351/‑23) ribB/LY180_15715 3,4‑dihydroxy‑2‑butanone 4‑phosphate synthase/hypothetical protein
?CP006584 3344745 = NA (NA)coding (164/330 nt) LY180_15880 hypothetical protein
* ? CP006584 3379202 =2 (0.020)94 (1.090) 83/586 0.1 97.9% intergenic (+70/‑172) LY180_16040/LY180_16045 membrane protein/membrane protein
?CP006584 = 3672183 NA (NA)coding (474/477 nt) LY180_17575 membrane protein
* ? CP006584 = 33792109 (0.100)109 (1.260) 93/586 0.0 92.4% intergenic (+78/‑164) LY180_16040/LY180_16045 membrane protein/membrane protein
?CP006584 = 3672183 NA (NA)coding (474/477 nt) LY180_17575 membrane protein
* ? CP006584 3513901 =43 (0.500)44 (0.540)
+TCGGATAAGGCGTTT
39/556 1.7 52.5% intergenic (‑77/+262) tldD/LY180_16725 protease TldD/membrane protein
?CP006584 = 3514068 41 (0.470)intergenic (‑244/+95) tldD/LY180_16725 protease TldD/membrane protein
* ? CP006584 = 3884875115 (1.330)81 (0.940) 71/584 0.3 40.2% coding (905/1137 nt) LY180_18515 membrane protein
?CP006584 3885089 = 126 (1.460)coding (691/1137 nt) LY180_18515 membrane protein
* ? CP006584 4186759 =NA (NA)128 (1.480) 113/584 0.0 97.7% coding (292/294 nt) LY180_19995 hypothetical protein
?CP006584 4334567 = 3 (0.030)coding (30/1734 nt) LY180_20755 membrane protein
* ? CP006584 = 4188086NA (NA)119 (1.370) 96/586 0.0 98.4% coding (17/1167 nt) LY180_20005 hypothetical protein
?CP006584 = 4334576 2 (0.020)coding (21/1734 nt) LY180_20755 membrane protein
* ? CP006584 4496128 =NA (NA)92 (1.160) 83/538 0.0 97.1% intergenic (‑2037/‑83) LY180_21445/LY180_21450 hypothetical protein/hypothetical protein
?CP006584 4565632 = 3 (0.030)intergenic (‑372/+82) LY180_21775/LY180_21780 hypothetical protein/lysine 2,3‑aminomutase
* ? CP006584 4496731 =NA (NA)391 (4.520) 265/586 0.0 NA coding (521/1209 nt) LY180_21450 hypothetical protein
?CP006584 = 4497432 NA (NA)intergenic (+13/+464) LY180_21450/LY180_21455 hypothetical protein/D‑allose kinase
* ? CP006584 4739807 =65 (0.750)43 (0.510) 41/568 1.6 38.6% intergenic (+48/‑432) LY180_22625/fimA tyrosine recombinase/type‑1 fimbrial protein subunit A
?CP006584 4740121 = 74 (0.880)intergenic (+362/‑118) LY180_22625/fimA tyrosine recombinase/type‑1 fimbrial protein subunit A
* ? CP006584 = 473981565 (0.750)34 (0.410) 34/568 2.3 33.2% intergenic (+56/‑424) LY180_22625/fimA tyrosine recombinase/type‑1 fimbrial protein subunit A
?CP006584 = 4740111 74 (0.880)intergenic (+352/‑128) LY180_22625/fimA tyrosine recombinase/type‑1 fimbrial protein subunit A