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 F3 I0 R1	328	90.1	2317887	85.2%	1974839	62.5

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	558,918	T→C	100%	P55P (CCT→CCC)	cmr →	multidrug efflux system protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	558,918	0	T	C	97.2%	109.4 / ‑4.0	35	P55P (CCT→CCC)	cmr	multidrug efflux system protein
Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (34/0); total (35/0)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.45e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAAT  >  minE/558860‑558961

ttCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGAt                                     >  1:934783/1‑67 (MQ=255)

ttCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGAt                                     >  1:1584624/1‑67 (MQ=255)

                ggCCGTGGTGGATCAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:797626/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCg                                       >  1:700112/1‑49 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGAtc                                    >  1:1946262/1‑51 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:529288/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:2039312/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:1997932/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:606265/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:102807/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:7254/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:1724416/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:870502/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:148215/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:1390621/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:1372257/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:1358524/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:957386/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:1223025/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:1160671/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:1134669/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:967603/1‑67 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggc                      >  1:575972/1‑66 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggc                      >  1:1851278/1‑66 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggc                      >  1:370314/1‑66 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggc                      >  1:216512/1‑66 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggc                      >  1:1883153/1‑66 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggc                      >  1:1825745/1‑66 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggc                      >  1:1807755/1‑66 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggc                      >  1:1545934/1‑66 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggc                      >  1:14913/1‑66 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggc                      >  1:1295635/1‑66 (MQ=255)

                ggCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggc                      >  1:1039996/1‑66 (MQ=255)

                ggCCGTGGTGAAACAATATCAGGCGGGCATTGATTGGGTTCCCACTTCGATGACCGCGTATCTggcg                     >  1:1961503/1‑67 (MQ=255)

                                   cAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAAt  >  1:174327/1‑67 (MQ=255)

TTCAACCCGGTATGTTGGCCGTGGTGGAACAATATCAGGCGGGCATTGATTGGGTTCCTACTTCGATGACCGCGTATCTGGCGGGCGGGATGTTTTTACAAT  >  minE/558860‑558961

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