Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,962,586	G→C	14.4%	V69V (GTG→GTC)	dapF →	diaminopimelate epimerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,962,586	0	G	C	14.4%	60.9 / 5.6	28	V69V (GTG→GTC)	dapF	diaminopimelate epimerase
Reads supporting (aligned to +/- strand):  ref base G (11/13);  new base C (2/2);  total (13/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.58e-01

AACGACTTCATGGTCCTGGACCTGGTCAGCCAGCACGCGCACATCCAGCCCAAGCACGCCAAGCAATGGGGTGACCGCCATACCGGTGTCGGCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAATGCGGCAACGGTGCGCGCTGCTTTGCCCGCTTCGTGCTGGACAAGCGCCTGACCGCGAAAAAGCGCATCCGCGTGGAAACCAAGAGCGGCATCATCGTGC  >  NC_002947/5962449‑5962734                                                                                                                                          |                                                                                                                                                     aaCGACTTCATGGTCCTGGACCTGGTCAGCCAGCACGCGCACATCCAGCCCAAGCACGCCAAGCAATGGGGTGACCGCCATACCGGTGTCGGCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTAc                                                                                                                                          >  2:479814/1‑150 (MQ=255)  aCGACTTCATGGTCCTGGACCTGGTCAGCCAGCACCCGCACATCCAGCCCAAGCACGCCAAGCAATGGGGTGACCGCCATACCGGTGTCGGCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTAcc                                                                                                                                         <  1:41337/150‑1 (MQ=255)       ttCATGGTCCTGGACCTGGTCAGCCAGCACGCGCACATCCAGCCCAAGCACGCCAAGCAATGGGGTGACCGCCATACCGGTGTCGGCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTACCGCATc                                                                                                                                    <  2:445328/150‑1 (MQ=255)            ggTCCTGGACCTGGTCAGCCAGCACGCGCACATCCAGCCCAAGCACGCCAAGCAATGGGGTGACCGCCATACCGGTGTCGGCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTACCGCATCTTCaa                                                                                                                               <  1:564784/150‑1 (MQ=255)                  ggACCTGGTCAGCCAGCACGCGCACATCCAGCCCAAGCACGCCAAGCAATGGGGTGACCGCCATACCGGTGTCGGCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGa                                                                                                                         <  1:479814/150‑1 (MQ=255)                         gTCAGCCAGCACGCGCACATCCAGCCCAAGCACGCCAAGCAATGGGGTGACCGCCATACCGGTGTCGGCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTcc                                                                                                                  >  1:289654/1‑150 (MQ=255)                         gTCAGCCAGCACGCGCACATCCAGCCCAAGCACGCCAAGCAATGGGGTGACCGCCATACCGGTGTCGGCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTcc                                                                                                                  >  1:461599/1‑150 (MQ=255)                          tCAGCCAGCACGCGCCCATCCAGCCCAAGCACGCCAAGGAATGGGGTGACCGCCATACCGGTGTCGGCTTCGACCAGTTGCTGATCGTTGAGGCGCCGAAAATTCCTGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCg                                                                                                                 <  2:150291/150‑1 (MQ=255)                              ccagcACGCGCACATCCAGCCCAAGCACGCCAAGCAATGGGGTGACCGCCATACCGGTGTCGGCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGt                                                                                                             >  2:105392/1‑150 (MQ=255)                                   aCGCGCACATCCAGCCCAAGCACGCCAAGCAATGGGGTGACCGCCATACCGGTGTCGGCTTAGACCAGGTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCGGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGc                                                                                                        >  2:209070/1‑150 (MQ=255)                                        cacaTCCAGCCCAAGCACGCCAAGCAATGGGGTGACCGCCATACCGGTGTCGGCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAATGc                                                                                                   <  1:265219/150‑1 (MQ=255)                                            tCCAGCCCAAGCACGCCAAGCAATGGGGTGACCGCCATACCGGTGTCGGCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAATGCGGCa                                                                                               >  2:150390/1‑150 (MQ=255)                                                            cAAGCAATGGGGTGACCGCCATACCGGTGTCGGCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTCCACTTCCgg                                                                                                                                             <  1:147525/88‑2 (MQ=255)                                                            cAAGCAATGGGGTGACCGCCATACCGGTGTCGGCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTCCACTTCCgg                                                                                                                                             >  2:147525/1‑87 (MQ=255)                                                                   tGGGGTGACCGCCATACCGGTGTCGGCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAATGCGGCAACGGTGCGCGCTGCTTTGCCCGc                                                                        <  1:129499/150‑1 (MQ=255)                                                                                aTACCGGTGTCGGCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAATGCGGCAACGGTGCGCGCTGCTTTGCCCGCTTCGTGCTGGACa                                                           >  1:273310/1‑150 (MQ=255)                                                                                            gCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAAt                                                                                                     <  2:207981/96‑1 (MQ=255)                                                                                            gCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAAt                                                                                                     >  1:207981/1‑96 (MQ=255)                                                                                                   ccAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAATGCGGCAACGGTGCGCGCTGCTTTGCCCGCTTCGTGCTGGACAAGCGCCTGACCGCGaaaaa                                        <  1:105392/150‑1 (MQ=255)                                                                                                     aGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAATGCGGCAACGGTGCGCGCTGCTTTGCCCGCTTCGTGCTGGACAAGCGCCTGACCGCGAAAAAgc                                      <  1:546359/150‑1 (MQ=255)                                                                                                                                  gcGGAAGTCCACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAATGCGGCAACGGTGCGCGCTGCTTTGCCCGCTTCGTGc                                                                 <  1:308517/93‑1 (MQ=255)                                                                                                                                  gcGGAAGTCCACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAATGCGGCAACGGTGCGCGCTGCTTTGCCCGCTTCGTGc                                                                 >  2:308517/2‑94 (MQ=255)                                                                                                                                  ccGGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAATGCGGCAACGGTGCGCGCTGCTTTGCCCGCTTCGTGCTGGACAAGCGCCTGACCGCGAAAAAGCGCATCCGCGTGGAAACCAAGAGCGGcatc         >  1:381286/1‑150 (MQ=255)                                                                                                                                   cGGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAATGCGGCAACGGTGCGCGCTGCTTTGCCCGCTTCGTGCTGGACAAGCGCCTGACCGCGAAAAAGCGCATCCGCGTGGAAACCAAGAGCGGcatca        >  2:490833/1‑150 (MQ=255)                                                                                                                                     gAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAATGCGGCAACGGTGCGCGCTGCTTTGCCCGCTTCGTGCTGGACAAGCGCCTGACCGCGAAAAAGCGCATCCGCGTGGAAACCAAGAGCGGCatcatc      <  2:273310/150‑1 (MQ=255)                                                                                                                                     gAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAATGCGGCAACGGTGCGCGCTGCTTTGCCCGCTTCGTGCTGGACAAGCGCCTGACCGCGAAAAAGCGCATCCGCGTGGAAACCAAGAGCGGCatcatc      <  2:461599/150‑1 (MQ=255)                                                                                                                                       aGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAATGCGGCAACGGTGCGCGCTGCTTTGCCCGCTTCGTGCTGGACAAGCGCCTGACCGCGAAAAAGCGCATCCGCGTGGAAACCAAGAGCGGCATCATCGt    <  2:381286/150‑1 (MQ=255)                                                                                                                                         tGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAATGCGGCAACGGTGCGCGCTGCTTTGCCCGCTTCGTGCTGGACAAGCGCCTGACCGCGAAAAAGCGCATCCGCGTGGAAACCAAGAGCGGCATCATCGTGc  >  1:275744/1‑150 (MQ=255)                                                                                                                                          |                                                                                                                                                     AACGACTTCATGGTCCTGGACCTGGTCAGCCAGCACGCGCACATCCAGCCCAAGCACGCCAAGCAATGGGGTGACCGCCATACCGGTGTCGGCTTCGACCAGTTGCTGATCGTCGAGGCGCCGAACAACCCGGAAGTGGACTTCCGCTACCGCATCTTCAACGCCGACGGCTCCGAGGTCGAGCAATGCGGCAACGGTGCGCGCTGCTTTGCCCGCTTCGTGCTGGACAAGCGCCTGACCGCGAAAAAGCGCATCCGCGTGGAAACCAAGAGCGGCATCATCGTGC  >  NC_002947/5962449‑5962734

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑