Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,892,019:1	+GC	100%	intergenic (‑437/+54)	gudP ← / ← ygdL	predicted D‑glucarate transporter/conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,892,019	1	.	G	100.0%	76.9 / NA	32	intergenic (‑437/+54)	gudP/ygdL	predicted D‑glucarate transporter/conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (30/2); total (30/2)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
*	minE	1,892,019	2	.	C	100.0%	77.2 / NA	32	intergenic (‑437/+54)	gudP/ygdL	predicted D‑glucarate transporter/conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (30/2); total (30/2)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCA‑‑TAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTG  >  minE/1891977‑1892071

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tcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCTGGTCGGATaa                              >  1:2286802/1‑69 (MQ=255)

tcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATaa                              >  1:1325221/1‑69 (MQ=255)

 cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAAcc                                         >  1:3199404/1‑57 (MQ=255)

 cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATa                               >  1:1695118/1‑67 (MQ=255)

 cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAg                             >  1:2500991/1‑69 (MQ=255)

 cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAg                             >  1:993833/1‑69 (MQ=255)

 cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAg                             >  1:3433178/1‑69 (MQ=255)

 cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAg                             >  1:3100838/1‑69 (MQ=255)

 cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAg                             >  1:2944151/1‑69 (MQ=255)

 cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAg                             >  1:1134343/1‑69 (MQ=255)

 cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAg                             >  1:2296134/1‑69 (MQ=255)

 cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAg                             >  1:1948472/1‑69 (MQ=255)

 cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAg                             >  1:1221545/1‑69 (MQ=255)

 cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAg                             >  1:1345327/1‑69 (MQ=255)

 cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAg                             >  1:1559375/1‑69 (MQ=255)

 cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAg                             >  1:1735222/1‑69 (MQ=255)

 cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAg                             >  1:178171/1‑69 (MQ=255)

                      tACCGCTCGCTGAACATATCAGCTAAGCACAGAAcc                                         >  1:2624284/1‑36 (MQ=25)

                      tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGt                                     >  1:1560920/1‑40 (MQ=255)

                      tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGa                                 >  1:2478175/1‑44 (MQ=255)

                      tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGCTAacacc                          >  1:2397569/1‑50 (MQ=255)

                      tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGATGTTCGCGTCTCATCCGAc         >  1:2387601/1‑68 (MQ=255)

                      tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcg                      >  1:559370/1‑55 (MQ=255)

                      tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTc                       >  1:545734/1‑54 (MQ=255)

                      tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGt                   >  1:258228/1‑58 (MQ=255)

                      tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGAc         >  1:877146/1‑68 (MQ=255)

                         cgctcgctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTg      <  1:376897/68‑1 (MQ=255)

                         cgctcgctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTg      <  1:896446/68‑1 (MQ=255)

                             cgctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGAc                           >  1:710809/1‑43 (MQ=37)

                             cgctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcgcg                    >  1:3316611/1‑50 (MQ=255)

                             cgctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTc                       >  1:3117455/1‑47 (MQ=37)

                             cgctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTg  >  1:1963500/1‑68 (MQ=38)

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TCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCA‑‑TAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTG  >  minE/1891977‑1892071

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

N/A