BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,902,968	Δ1 bp	coding (56/144 nt)	mgrB ←	PhoP/PhoQ regulator MgrB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,902,966	0	A	.	91.7%	81.8 / 4.0	24	coding (58/144 nt)	mgrB	PhoP/PhoQ regulator MgrB
Reads supporting (aligned to +/- strand): ref base A (0/2); new base . (13/9); total (13/11)
Fisher's exact test for biased strand distribution p-value = 1.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.41e-01

ACGGGATAAACTGGTTAATGGCACAAATTCCGCTGAAAAATTGTACATCCTGATCGCACATCATGTTGAATACCTGCGCCCAAAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTAT  >  NZ_CP009273/1902885‑1903049

acGGGATAAACTGGTTAATGGCACAAATTCCGCTGAAAAATTGTACATCCTGATCGCACATCATGTTGAATACCTGCGCCC‑AAGCagcaa                                                                            >  2:419467/1‑90 (MQ=255)

  gggATAAACTGGTTAATGGCACAAATTCCGCTGAAAAATTGTACATCCTGATCGCACATCATGTTGAATACCTGCGCCC‑AAGCagcaagc                                                                          <  1:553114/90‑1 (MQ=255)

        aaCTGGTTAATGGCACAAATTCCGCTGAAAAATTGTACATCCTGATCGCACATCATGTTGAATACCTGCGCCC‑AAGCAGCAAGCAAGCCa                                                                    <  1:44936/90‑1 (MQ=255)

            ggTTAATGGCACAAATTCCGCTGAAAAATTGTACATCCTGATCGCACATCATGTTGAATACCTGCGCCC‑AAGCAGCAAGCAAGCCAacac                                                                >  2:229883/1‑90 (MQ=255)

            ggTTAATGGCACAAATTCCGCTGAAAAATTGTACATCCTGATCGCACATCATGTTGAATACCTGCGCCC‑AAGCAGCAAGCAAGCCAacac                                                                >  2:146508/1‑90 (MQ=255)

                 aTGGCACAAATTCCGCTGAAAAATTGTACATCCTGATCGCACATCATGTTGAATACCTGCGCCCAAAGCAGCAAGCAAGCCAACACCACg                                                            <  2:98776/90‑1 (MQ=255)

                   ggCACAAATTCCGCTGAAAAATTGTACATCCTGATCGCACATCATGTTGAATACCTGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACa                                                         <  2:34404/90‑1 (MQ=255)

                           ttCCGCTGAAAAATTGTACATCCTGATCGCACATCATGTTGAATACCTGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACAACCAGAAc                                                 <  2:345219/90‑1 (MQ=255)

                               gCTGAAAAATTGTACATCCTGATCGCACATCATGTTGAATACCTGCGCCCAAAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGAc                                              <  1:499067/90‑1 (MQ=255)

                                                 cTGATCGCACATCATGTTGAATACCTGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACt                           >  2:267259/1‑90 (MQ=255)

                                                    aTCGCACATCATGTTGAATACCTGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCa                        >  2:40393/1‑90 (MQ=255)

                                                         acaTCATGTTGAATACCTGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAAtctc                   >  1:477846/1‑90 (MQ=255)

                                                             catGTTGAATACCTGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGtt               <  2:477846/90‑1 (MQ=255)

                                                               tGTTGAATACCTGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTc             >  1:486433/1‑90 (MQ=255)

                                                                  tGAATACCTGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCTAAACTTTTTCACTCCAATCTCCGTTTCacc          <  1:419467/90‑1 (MQ=255)

                                                                  tGAATACCTGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCacc          >  1:181600/1‑90 (MQ=255)

                                                                  tGAATACCTGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCacc          <  2:486433/90‑1 (MQ=255)

                                                                   gAATACCTGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCacct         <  2:49108/90‑1 (MQ=255)

                                                                   gAATACCTGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCacct         <  2:60188/90‑1 (MQ=255)

                                                                      tACCTGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCacctacc      >  1:73050/1‑90 (MQ=255)

                                                                          tGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTAt  >  2:302468/1‑90 (MQ=255)

                                                                          tGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTAt  >  1:19809/1‑90 (MQ=255)

                                                                          tGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTAt  >  1:715647/1‑90 (MQ=255)

                                                                          tGCGCCC‑AAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTAt  >  1:521422/1‑90 (MQ=255)

ACGGGATAAACTGGTTAATGGCACAAATTCCGCTGAAAAATTGTACATCCTGATCGCACATCATGTTGAATACCTGCGCCCAAAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTAT  >  NZ_CP009273/1902885‑1903049

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`