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 | seq id | position | mutation | annotation | gene | description |
| RA | CP009273 | 164,770 | +G | coding (800/2244 nt) | fhuA → | ferrichrome outer membrane transporter |
| JC | CP009273 | 189,036 | Δ3 bp | coding (695‑697/726 nt) | pyrH → | uridylate kinase |
| RA | CP009273 | 415,058 | Δ2 bp | coding (12‑13/1320 nt) | brnQ → | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val |
| RA | CP009273 | 420,643 | Δ2 bp | coding (177‑178/1071 nt) | queA → | S‑adenosylmethionine:tRNA ribosyltransferase‑isomerase |
| RA | CP009273 | 485,622 | Δ1 bp | coding (106/162 nt) | ybaM ← | DUF2496 family protein |
| RA | CP009273 | 1,257,049 | C→T | A95T (GCG→ACG) | prs ← | phosphoribosylpyrophosphate synthase |
| RA | CP009273 | 1,293,152 | Δ1 bp | coding (426/2676 nt) | adhE ← | fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase |
| RA | CP009273 | 1,317,625 | Δ1 bp | coding (149/882 nt) | yciV → | PHP domain protein |
| RA | CP009273 | 1,319,060 | Δ2 bp | coding (58‑59/1896 nt) | yciQ → | enhancer of membrane protein expression; putative inner membrane protein |
| RA | CP009273 | 1,325,408 | G→C | R35P (CGC→CCC) | topA → | DNA topoisomerase I, omega subunit |
| JC | CP009273 | 1,436,742 | (GGTGAA)1→2 | coding (359/990 nt) | ldhA ← | fermentative D‑lactate dehydrogenase, NAD‑dependent |
| RA | CP009273 | 1,465,325 | Δ2 bp | pseudogene (552‑553/3497 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | CP009273 | 1,676,131 | Δ1 bp | coding (157/336 nt) | ydgC ← | GlpM family inner membrane protein |
| MC JC | CP009273 | 1,714,758 | Δ3 bp | coding (322‑324/435 nt) | slyA ← | global transcriptional regulator |
| RA | CP009273 | 1,729,616 | Δ1 bp | intergenic (+109/‑19) | mepH → / → sodB | murein DD‑endopeptidase, space‑maker hydrolase/superoxide dismutase, Fe |
| RA | CP009273 | 1,781,885 | Δ1 bp | coding (184/834 nt) | ppsR → | bifunctional regulatory protein: PEP synthase kinase and PEP synthase pyrophosphorylase |
| RA | CP009273 | 1,990,393 | Δ1 bp | intergenic (‑80/+150) | sdiA ← / ← yecC | quorum‑sensing transcriptional activator/putative ABC superfamily transporter ATP‑binding subunit |
| MC JC | CP009273 | 2,024,694 | Δ4 bp | coding (1102‑1105/1419 nt) | dcm ← | DNA cytosine methyltransferase |
| RA | CP009273 | 2,170,739 | (T)5→4 | intergenic (‑56/+252) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| MC JC | CP009273 | 2,400,028 | Δ9 bp | coding (85‑93/939 nt) | lrhA ← | transcriptional repressor of flagellar, motility and chemotaxis genes |
| RA | CP009273 | 2,528,814 | G→A | D464N (GAC→AAC) | ptsI → | PEP‑protein phosphotransferase of PTS system (enzyme I) |
| RA | CP009273 | 2,701,729 | Δ1 bp | coding (385/957 nt) | rseB ← | anti‑sigma E factor, binds RseA |
| RA | CP009273 | 3,305,544 | Δ1 bp | coding (593/945 nt) | truB ← | tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase |
| RA | CP009273 | 3,416,558 | Δ1 bp | intergenic (+5/+224) | yhdZ → / ← rrfF | putative amino‑acid transporter subunit/5S ribosomal RNA of rrnD operon |
| JC | CP009273 | 3,474,602 | Δ3 bp | intergenic (‑82/‑44) | kefG ← / → yheS | potassium‑efflux system ancillary protein for KefB, glutathione‑regulated/putative transporter subunit of ABC superfamily: ATP‑binding component |
| RA | CP009273 | 3,542,161 | Δ1 bp | coding (1269/2085 nt) | malQ ← | 4‑alpha‑glucanotransferase (amylomaltase) |
| RA | CP009273 | 3,658,029 | Δ2 bp | intergenic (‑51/‑194) | gadW ← / → gadY | transcriptional activator of gadA and gadBC; repressor of gadX/sRNA antisense regulator of gadAB transcriptional activator GadX mRNA, Hfq‑dependent |
| RA | CP009273 | 3,724,422 | (A)5→4 | intergenic (‑297/‑69) | xylA ← / → xylF | D‑xylose isomerase/D‑xylose transporter subunit |
| RA | CP009273 | 4,099,055 | Δ1 bp | coding (294/990 nt) | sbp → | sulfate transporter subunit |
| RA | CP009273 | 4,151,176 | T→G | V42G (GTC→GGC) | fabR → | transcriptional repressor of fabA and fabB |
| RA | CP009273 | 4,152,131 | Δ2 bp | coding (1067‑1068/1101 nt) | trmA ← | tRNA m(5)U54 methyltransferase, SAM‑dependent; tmRNA m(5)U341 methyltransferase |
| RA | CP009273 | 4,154,051 | G→C | G162A (GGA→GCA) | btuB → | vitamin B12/cobalamin outer membrane transporter |
| RA | CP009273 | 4,232,046 | Δ1 bp | coding (137/1476 nt) | xylE ← | D‑xylose transporter |
| RA | CP009273 | 4,393,393 | Δ2 bp | coding (277‑278/1005 nt) | hflC → | modulator for HflB protease specific for phage lambda cII repressor |
| JC | CP009273 | 4,478,273 | (ATTGTTAGCAAAGTGTG)1→2 | intergenic (+56/+105) | lptG → / ← yjgR | lipopolysaccharide export ABC permease of the LptBFGC export complex/DUF853 family protein with NTPase fold |
| RA | CP009273 | 4,529,912 | G→T | intergenic (‑594/‑862) | nanC ← / → fimB | N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA |
| JC | CP009273 | 4,581,219 | Δ3 bp | intergenic (‑123/‑253) | yjiY ← / → tsr | putative transporter/methyl‑accepting chemotaxis protein I, serine sensor receptor |
| RA | CP009273 | 4,617,380 | Δ1 bp | coding (249/1233 nt) | nadR → | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 782255 | 783080 | 826 | 69 [66] | [64] 67 | gpmA | gpmA |
| * | * | ÷ | CP009273 | 1800600 | 1801576 | 977 | 69 [66] | [66] 68 | pfkB | pfkB |
| * | * | ÷ | CP009273 | 1929081 | 1930615 | 1535 | 67 [66] | [65] 67 | zwf | zwf |
| * | * | ÷ | CP009273 | 3778575 | 3780189 | 1615 | 69 [66] | [66] 69 | gpmM | gpmM |
| * | * | ÷ | CP009273 | 4097456 | 4098463 | 1008 | 68 [61] | [65] 68 | pfkA | pfkA |
| * | * | ÷ | CP009273 | 4205394 | 4210256 | 4863 | 70 [64] | [63] 67 | aceB–[arpA] | aceB,aceA,[aceK],[arpA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 112 (0.880) | 110 (0.060) +AATTCCCC |
69/184 | 1.0 | 51.7% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | KX077536 | 8127 = | NA (NA) | intergenic (+52/–) | unknown/– | cat/– | |||||
| * | ? | CP009273 | 3877607 = | 12 (0.090) | 133 (1.040) | 101/200 | 0.1 | 91.7% | intergenic (‑518/‑89) | dnaA/rpmH | chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator/50S ribosomal subunit protein L34 |
| ? | CP009273 | = 3877615 | NA (NA) | intergenic (‑526/‑81) | dnaA/rpmH | chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator/50S ribosomal subunit protein L34 | |||||