Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,814,267	A→G	A368A (GCT→GCC)	alaS ←	alanine‑‑tRNA ligase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,814,267	0	A	G	90.3%	77.3 / 2.2	31	A368A (GCT→GCC)	alaS	alanine‑‑tRNA ligase
Reads supporting (aligned to +/- strand):  ref base A (2/1);  new base G (11/17);  total (13/18)
Fisher's exact test for biased strand distribution p-value = 5.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

CGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACG  >  NZ_CP009273/2814181‑2814351                                                                                       |                                                                                     cGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCa                                                                                   >  1:468191/1‑90 (MQ=255)     aaGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACt                                                                               <  2:471091/90‑1 (MQ=255)          gTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGctct                                                                          <  1:570251/90‑1 (MQ=255)             tCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCtcttct                                                                       >  2:678592/1‑90 (MQ=255)               aCCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCGGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCttcttc                                                                     <  2:17301/90‑1 (MQ=255)               aCCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCttcttc                                                                     <  1:779518/90‑1 (MQ=255)                  aTCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTtcttcagt                                                                  >  1:234298/1‑90 (MQ=255)                  aTCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTtcttcagt                                                                  >  1:763101/1‑90 (MQ=255)                          tATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCa                                                          >  1:242577/1‑90 (MQ=255)                            tCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCAcc                                                        >  2:678257/1‑90 (MQ=255)                            tCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCAcc                                                        >  1:299532/1‑90 (MQ=255)                                 aGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTc                                                   <  1:312145/90‑1 (MQ=255)                                 aGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTc                                                   <  1:423831/90‑1 (MQ=255)                                 aGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTc                                                   <  1:678257/90‑1 (MQ=255)                                                ctctTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGctc                                                                           <  2:269336/51‑1 (MQ=255)                                                ctctTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGctc                                                                           >  1:269336/1‑51 (MQ=255)                                                ctctTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCctgctg                                    >  2:783778/1‑90 (MQ=255)                                                             aaCGCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCt                       <  2:609146/90‑1 (MQ=255)                                                                gCCAGACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCa                    >  1:815699/1‑90 (MQ=255)                                                                    gACCGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTTAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCg                >  1:26114/1‑90 (MQ=255)                                                                      ccGCGCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTCCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCa              <  1:34818/90‑1 (MQ=255)                                                                       cgcgCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCag             <  1:803693/90‑1 (MQ=255)                                                                       cgcgCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCag             <  1:835478/90‑1 (MQ=255)                                                                       cgcgCTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCag             <  1:326480/90‑1 (MQ=255)                                                                         cgcTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCagag           <  1:598870/90‑1 (MQ=255)                                                                         cgcTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCagag           >  1:285559/1‑90 (MQ=255)                                                                         cgcTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCagag           <  1:480333/90‑1 (MQ=255)                                                                         cgcTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCagag           <  2:351937/90‑1 (MQ=255)                                                                         cgcTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCagag           <  1:407956/90‑1 (MQ=255)                                                                         cgcTCCAGAGTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCagag           <  1:114998/90‑1 (MQ=255)                                                                                  gTACGGGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACg  >  1:413956/1‑90 (MQ=255)                                                                                       |                                                                                     CGGAAAGCAGTTTCACCATCCAGCGTATCACCAGAAAGTTTTGCCAGCTCTTCATCCAGCAACGCCAGACCGCGCTCCAGAGTACGAGCAAACTGCTCTTCTTCAGTCTTCAGCACCTGCTCAACCTGCGCCTGCTGGCGTTTCAGGTCTTCACCCGCAGAGCCCATAACG  >  NZ_CP009273/2814181‑2814351

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑