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 F8 I0 R1	82	77.9	2158605	86.8%	1873669	62.5

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,147,237	A→T	100%	L87Q (CTG→CAG)	chbA ←	N,N'‑diacetylchitobiose‑specific enzyme IIA component of PTS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,147,237	0	A	T	83.3%	25.2 / 0.4	12	L87Q (CTG→CAG)	chbA	N,N'‑diacetylchitobiose‑specific enzyme IIA component of PTS
Reads supporting (aligned to +/- strand): ref base A (0/2); new base T (0/10); total (0/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATCAGTTCACGCGCAAGCATGGACGTCATTAAATGATCCTGAGCGTGGACCAGCACCAGACTCACTTTCATCTTACCTTCGCCCGCATCGCCTTCAATCAGTTTCGTCTGTAC  >  minE/1147186‑1147298

aTCAGTTCACGCGCAAGCATGGACGTCATTAAATGATCCTGAGCGTGGACCAGCACCAGACTCACtt                                                <  1:1692711/67‑1 (MQ=255)

aTCAGTTCACGCGCAAGCATGGACGTCATTAAATGATCCTGAGCGTGGACCAGCACCAGACTCACtt                                                <  1:1759503/67‑1 (MQ=255)

                                              ggACCTGCACCAGACTCACTTTCATCTTACCTTCGCCCGCATCGCCTTCAATCAGTTTCGTCTGTAc  <  1:1137829/67‑1 (MQ=255)

                                              ggACCTGCACCAGACTCACTTTCATCTTACCTTCGCCCGCATCGCCTTCAATCAGTTTCGTCTGTAc  <  1:1287586/67‑1 (MQ=255)

                                              ggACCTGCACCAGACTCACTTTCATCTTACCTTCGCCCGCATCGCCTTCAATCAGTTTCGTCTGTAc  <  1:1324100/67‑1 (MQ=255)

                                              ggACCTGCACCAGACTCACTTTCATCTTACCTTCGCCCGCATCGCCTTCAATCAGTTTCGTCTGTAc  <  1:1639405/67‑1 (MQ=255)

                                              ggACCTGCACCAGACTCACTTTCATCTTACCTTCGCCCGCATCGCCTTCAATCAGTTTCGTCTGTAc  <  1:1886711/67‑1 (MQ=255)

                                              ggACCTGCACCAGACTCACTTTCATCTTACCTTCGCCCGCATCGCCTTCAATCAGTTTCGTCTGTAc  <  1:256413/67‑1 (MQ=255)

                                              ggACCTGCACCAGACTCACTTTCATCTTACCTTCGCCCGCATCGCCTTCAATCAGTTTCGTCTGTAc  <  1:596294/67‑1 (MQ=255)

                                              ggACCTGCACCAGACTCACTTTCATCTTACCTTCGCCCGCATCGCCTTCAATCAGTTTCGTCTGTAc  <  1:685261/67‑1 (MQ=255)

                                              ggACCTGCACCAGACTCACTTTCATCTTACCTTCGCCCGCATCGCCTTCAATCAGTTTCGTCTGTAc  <  1:75624/67‑1 (MQ=255)

                                               gACCTGCACCAGACTCACTTTCATCTTACCTTCGCCCGCATCGCCTTCAATCAGTTTCGTCTGTAc  <  1:1725866/66‑1 (MQ=255)

ATCAGTTCACGCGCAAGCATGGACGTCATTAAATGATCCTGAGCGTGGACCAGCACCAGACTCACTTTCATCTTACCTTCGCCCGCATCGCCTTCAATCAGTTTCGTCTGTAC  >  minE/1147186‑1147298

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

N/A