BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_pae_tpiA	1,362,060	Δ228,509 bp		[puuR]–yneL	223 genes [puuR], puuC, puuB, puuE, pspF, pspA, pspB, pspC, pspD, pspE, ycjM, ycjN, ycjO, ycjP, ycjQ, ycjR, ycjS, ycjT, ycjU, ycjV, ycjV, ompG, ycjW, ycjX, ycjF, tyrR, tpx, ycjG, mpaA, ymjC, ymjD, ycjY, pgrR, mppA, ynaI, insH1, ynaJ, uspE, fnr, ogt, abgT, abgB, abgA, abgR, mcaS, smrA, ydaM, ydaN, fnrS, dbpA, ttcA, intR, ydaQ, ydaC, ralR, recT, recE, racC, ydaE, kilR, sieB, ydaF, ydaG, racR, ydaS, ydaT, ydaU, ydaV, ydaW, rzpR, rzoR, trkG, ynaK, ydaY, tmpR, lomR, insH1, lomR, stfR, tfaR, pinR, ynaE, ttcC, uspF, ompN, micC, pfo, ydbJ, hslJ, ldhA, ydbH, ynbE, ydbL, feaR, feaB, tynA, paaZ, paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK, paaX, paaY, ynbG, ydbA, insD1, insC1, ydbA, insI1, ydbA, ydbC, ydbD, ynbA, ynbB, ynbC, ynbD, azoR, hrpA, ydcF, aldA, gapC, gapC, cybB, rydC, ydcA, hokB, mokB, sokB, trg, ydcI, ydcJ, opgD, ydcH, rimL, ydcK, tehA, tehB, ydcL, insP, insQ, ydcO, ydcN, ydcP, yncJ, hicA, hicB, ydcR, ydcS, ydcT, ydcU, ydcV, patD, yncL, ydcX, ydcY, ydcZ, mnaT, curA, mcbR, yncD, yncE, ansP, yncG, yncH, rhsE, ydcD, yncI, yncI, ydcC, pptA, yddH, nhoA, yddE, narV, narW, narY, narZ, narU, yddK, yddK, yddL, yddG, fdnG, fdnH, fdnI, yddM, adhP, maeA, sra, bdm, osmC, ddpF, ddpD, ddpC, ddpB, ddpA, ddpX, dosP, dosC, yddW, gadC, gadB, pqqL, yddB, yddA, ydeM, ydeN, ydeO, safA, ydeP, ydeQ, ydeR, ydeS, ydeT, yneL, yneL

Predicted mutation

evidence

seq id

position

mutation

annotation

gene

description

MC JC

NC_000913_3_pae_tpiA

1,362,060

Δ228,509 bp

[puuR]–yneL

223 genes

[puuR]puuCpuuBpuuEpspFpspApspBpspCpspDpspEycjMycjNycjOycjPycjQycjRycjSycjTycjUycjVycjVompGycjWycjXycjFtyrRtpxycjGmpaAymjCymjDycjYpgrRmppAynaIinsH1ynaJuspEfnrogtabgTabgBabgAabgRmcaSsmrAydaMydaNfnrSdbpAttcAintRydaQydaCralRrecTrecEracCydaEkilRsieBydaFydaGracRydaSydaTydaUydaVydaWrzpRrzoRtrkGynaKydaYtmpRlomRinsH1lomRstfRtfaRpinRynaEttcCuspFompNmicCpfoydbJhslJldhAydbHynbEydbLfeaRfeaBtynApaaZpaaApaaBpaaCpaaDpaaEpaaFpaaGpaaHpaaIpaaJpaaKpaaXpaaYynbGydbAinsD1insC1ydbAinsI1ydbAydbCydbDynbAynbBynbCynbDazoRhrpAydcFaldAgapCgapCcybBrydCydcAhokBmokBsokBtrgydcIydcJopgDydcHrimLydcKtehAtehBydcLinsPinsQydcOydcNydcPyncJhicAhicBydcRydcSydcTydcUydcVpatDyncLydcXydcYydcZmnaTcurAmcbRyncDyncEansPyncGyncHrhsEydcDyncIyncIydcCpptAyddHnhoAyddEnarVnarWnarYnarZnarUyddKyddKyddLyddGfdnGfdnHfdnIyddMadhPmaeAsrabdmosmCddpFddpDddpCddpBddpAddpXdosPdosCyddWgadCgadBpqqLyddByddAydeMydeNydeOsafAydePydeQydeRydeSydeTyneLyneL

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913_3_pae_tpiA	1362060	1590568	228509	61 [0]	[0] 61	[puuR]–yneL	[puuR],puuC,puuB,puuE,pspF,pspA,pspB,pspC,pspD,pspE,ycjM,ycjN,ycjO,ycjP,ycjQ,ycjR,ycjS,ycjT,ycjU,ycjV,ycjV,ompG,ycjW,ycjX,ycjF,tyrR,tpx,ycjG,mpaA,ymjC,ymjD,ycjY,pgrR,mppA,ynaI,insH1,ynaJ,uspE,fnr,ogt,abgT,abgB,abgA,abgR,mcaS,smrA,ydaM,ydaN,fnrS,dbpA,ttcA,intR,ydaQ,ydaC,ralR,recT,recE,racC,ydaE,kilR,sieB,ydaF,ydaG,racR,ydaS,ydaT,ydaU,ydaV,ydaW,rzpR,rzoR,trkG,ynaK,ydaY,tmpR,lomR,insH1,lomR,stfR,tfaR,pinR,ynaE,ttcC,uspF,ompN,micC,pfo,ydbJ,hslJ,ldhA,ydbH,ynbE,ydbL,feaR,feaB,tynA,paaZ,paaA,paaB,paaC,paaD,paaE,paaF,paaG,paaH,paaI,paaJ,paaK,paaX,paaY,ynbG,ydbA,insD1,insC1,ydbA,insI1,ydbA,ydbC,ydbD,ynbA,ynbB,ynbC,ynbD,azoR,hrpA,ydcF,aldA,gapC,gapC,cybB,rydC,ydcA,hokB,mokB,sokB,trg,ydcI,ydcJ,opgD,ydcH,rimL,ydcK,tehA,tehB,ydcL,insP,insQ,ydcO,ydcN,ydcP,yncJ,hicA,hicB,ydcR,ydcS,ydcT,ydcU,ydcV,patD,yncL,ydcX,ydcY,ydcZ,mnaT,curA,mcbR,yncD,yncE,ansP,yncG,yncH,rhsE,ydcD,yncI,yncI,ydcC,pptA,yddH,nhoA,yddE,narV,narW,narY,narZ,narU,yddK,yddK,yddL,yddG,fdnG,fdnH,fdnI,yddM,adhP,maeA,sra,bdm,osmC,ddpF,ddpD,ddpC,ddpB,ddpA,ddpX,dosP,dosC,yddW,gadC,gadB,pqqL,yddB,yddA,ydeM,ydeN,ydeO,safA,ydeP,ydeQ,ydeR,ydeS,ydeT,yneL,yneL

Missing coverage evidence...

seq id

start

end

size

←reads

reads→

gene

description

NC_000913_3_pae_tpiA

1362060

1590568

228509

61 [0]

[0] 61

[puuR]–yneL

[puuR],puuC,puuB,puuE,pspF,pspA,pspB,pspC,pspD,pspE,ycjM,ycjN,ycjO,ycjP,ycjQ,ycjR,ycjS,ycjT,ycjU,ycjV,ycjV,ompG,ycjW,ycjX,ycjF,tyrR,tpx,ycjG,mpaA,ymjC,ymjD,ycjY,pgrR,mppA,ynaI,insH1,ynaJ,uspE,fnr,ogt,abgT,abgB,abgA,abgR,mcaS,smrA,ydaM,ydaN,fnrS,dbpA,ttcA,intR,ydaQ,ydaC,ralR,recT,recE,racC,ydaE,kilR,sieB,ydaF,ydaG,racR,ydaS,ydaT,ydaU,ydaV,ydaW,rzpR,rzoR,trkG,ynaK,ydaY,tmpR,lomR,insH1,lomR,stfR,tfaR,pinR,ynaE,ttcC,uspF,ompN,micC,pfo,ydbJ,hslJ,ldhA,ydbH,ynbE,ydbL,feaR,feaB,tynA,paaZ,paaA,paaB,paaC,paaD,paaE,paaF,paaG,paaH,paaI,paaJ,paaK,paaX,paaY,ynbG,ydbA,insD1,insC1,ydbA,insI1,ydbA,ydbC,ydbD,ynbA,ynbB,ynbC,ynbD,azoR,hrpA,ydcF,aldA,gapC,gapC,cybB,rydC,ydcA,hokB,mokB,sokB,trg,ydcI,ydcJ,opgD,ydcH,rimL,ydcK,tehA,tehB,ydcL,insP,insQ,ydcO,ydcN,ydcP,yncJ,hicA,hicB,ydcR,ydcS,ydcT,ydcU,ydcV,patD,yncL,ydcX,ydcY,ydcZ,mnaT,curA,mcbR,yncD,yncE,ansP,yncG,yncH,rhsE,ydcD,yncI,yncI,ydcC,pptA,yddH,nhoA,yddE,narV,narW,narY,narZ,narU,yddK,yddK,yddL,yddG,fdnG,fdnH,fdnI,yddM,adhP,maeA,sra,bdm,osmC,ddpF,ddpD,ddpC,ddpB,ddpA,ddpX,dosP,dosC,yddW,gadC,gadB,pqqL,yddB,yddA,ydeM,ydeN,ydeO,safA,ydeP,ydeQ,ydeR,ydeS,ydeT,yneL,yneL

New junction evidence
	seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 1362059	0 (0.000)	61 (0.950)	47/276	0.3	100%	coding (149/558 nt)	puuR	repressor for the divergent puu operons, putrescine inducible
?	NC_000913_3_pae_tpiA	1590569 =	0 (0.000)	intergenic (‑33/+285)	yneL/hipA	pseudogene, AraC family/inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase

New junction evidence

seq id

position

reads (cov)

score

skew

freq

annotation

gene

product

NC_000913_3_pae_tpiA

= 1362059

0 (0.000)

61 (0.950)

47/276

0.3

100%

coding (149/558 nt)

puuR

repressor for the divergent puu operons, putrescine inducible

NC_000913_3_pae_tpiA

1590569 =

0 (0.000)

intergenic (‑33/+285)

yneL/hipA

pseudogene, AraC family/inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.

Alignment Legend

Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG

Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑

Reads not counted as support for junction

read_name Not counted due to insufficient overlap past the breakpoint.

read_name Not counted due to not crossing MOB target site duplication.