Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,458,940:1	+A	17.2%	intergenic (+17/‑45)	leuS → / → PP_4795	leucine‑‑tRNA ligase/lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,458,940	1	.	A	17.2%	77.3 / 15.2	29	intergenic (+17/‑45)	leuS/PP_4795	leucine‑‑tRNA ligase/lipoprotein
Reads supporting (aligned to +/- strand):  ref base . (12/12);  new base A (2/3);  total (14/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.63e-01

CGCTGCCAGCCGCGAAGAAGTCGAAGCCGCTGCCCGCAGCAACGAGAATGTCCTGCGCTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCGGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGC‑ATCGATTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAAACGCAATTTGCTGGTAATCGGCCTGGCGGTCATGCTCAGCGCCTGCGGTTTCCAGCTGCGCGGCACCGGCGCCACCGAGCTGAGCGTGAAGGAAATG  >  NC_002947/5458794‑5459089                                                                                                                                                    |                                                                                                                                                      cGCTGCCAGCCGCGAAGAAGTCGAAGCCGCTGCCCGCAGCAACGAGAATGTCCTGCGCTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCGGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGC‑ATc                                                                                                                                                    <  2:177985/150‑1 (MQ=255)            gcgAAGAAGTCGAAGCCGCTGCCCGCAGCAACGAGAATGTCCTGCGCTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCGGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGCAATCGA‑TGCGGGTg                                                                                                                                         <  1:597578/150‑1 (MQ=255)             cgAAGAAGTCGAAGCCGCTGCCCGCAGCAACGAGAATGTCCTGCGCTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCGGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGCAATCGA‑TGCGGGTgg                                                                                                                                        <  1:239035/150‑1 (MQ=255)               aagaagTCGAAGCCGCTGCCCGCAGCAACGAGAATGTCCTGCGCTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCGGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGC‑ATCGATTGCGGGTGGGc                                                                                                                                      <  2:183757/150‑1 (MQ=255)                     tCGAAGCCGCTGCCCGCAGCAACGAGAATGTCCTGCGCTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCGGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGC‑ATCGATTGCGGGTGGGCGGAACa                                                                                                                                >  2:1543/1‑150 (MQ=255)                       gAAGCCGCTGCCCGCAGCAACGAGAATGTCCTGCGCTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCTGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGC‑ATCGATTGCGGGTGGGCGGAACAgg                                                                                                                              >  1:74777/1‑150 (MQ=255)                                 cccGCAGCAACGAGAATGTCCTGCGCTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCGGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGC‑ATCGATTGCGGGTggg                                                                                                                                       >  1:177113/1‑131 (MQ=255)                                 cccGCAGCAACGAGAATGTCCTGCGCTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCGGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGC‑ATCGATTGCGGGTggg                                                                                                                                       <  2:177113/131‑1 (MQ=255)                                          aCGAGAATGTCCTGCGCTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCGGGCAAGCTGGTCAACATCGTCGACAACTGATGAAAACGCCAAACCGC‑ATCGATTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCaacaac                                                                                                           <  2:258168/150‑1 (MQ=255)                                               aaTGTCCTGCGCTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCGGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCGCACCCGC‑ATCGATTGCGGGTGGGCGGAACAGGCCCAGAACGGAGCAACAACATGAt                                                                                                      >  1:401681/1‑150 (MQ=255)                                                aTGTCCTGCGCTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCGGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGC‑ATCGATTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATc                                                                                                     <  2:102732/150‑1 (MQ=255)                                                    ccTGCGCTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCGGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGC‑ATCGATTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAAAc                                                                                                 >  2:515161/1‑150 (MQ=255)                                                      tGCGCTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCGGGCACGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGC‑ATCGATTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAACCGc                                                                                               >  2:208088/1‑150 (MQ=255)                                                          cTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCGGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGC‑ATCGATTGCGGGTGGGCGGAACAGGcc                                                                                                                            <  2:345535/117‑1 (MQ=255)                                                          cTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCGGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGC‑ATCGATTGCGGGTGGGCGGAACAGGcc                                                                                                                            >  1:345535/1‑117 (MQ=255)                                                                             aTCCGCAAGGTCATCGTGGTACCGGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGC‑ATCGATTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAAACGCAATTTGCTGGTAATCGGCCTGGc                                                                        <  1:1543/150‑1 (MQ=255)                                                                                                   cGGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGC‑ATCGCTTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAAACGCAATTTGCTGGTAATCGGCCTGGCGGTCATGCTCAGCGCCTGCGGt                                                  >  2:151516/1‑150 (MQ=255)                                                                                                      gCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGC‑ATCGATTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAAACGCAATTTGCTGGTAATCGGCCTGGCGGTCATGCTCAGCGCCTGCGGTTTc                                               <  1:151516/150‑1 (MQ=255)                                                                                                                             aaCTGATGAAAACGCCCACCCGC‑ATCGATTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAAACGCAATTTGCTGGTAATCGGCCTGGCGGTCATGCTCAGCGCCTGCGGTTTCCAGCTGCGCGGCACCGGCGCCAc                        >  2:155746/1‑150 (MQ=255)                                                                                                                                tgatgaAAACGCCCACCCGC‑ATCGATTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAAACGCAATTTGCTGGTAATCGGCCTGGCGGTCATGCTCAGCGCCTGCGGTTTCCAGCTGCGCGGCACCGGCGCCACCGa                     >  2:476538/1‑150 (MQ=255)                                                                                                                                  atgaAAACCCCCACCCGC‑ATCGATTGCGGGTGGGCGGAAGAGGCCCAAAAGGGAGCAACAACATGATCAAACGCAATTTGCTGGTAACCGGCCTGGCGGTCATGCTCAGCGCCTGCGGTTTCCAGCTGCGCGGCACCGGCGCCACCGAGc                   <  2:401681/150‑1 (MQ=255)                                                                                                                                    gaAAACGCCCACCCGC‑ATCGATTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAAACGCAATTTGCTGGTAATc                                                                                <  1:428148/87‑1 (MQ=255)                                                                                                                                    gaAAACGCCCACCCGC‑ATCGATTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAAACGCAATTTGCTGGTAATc                                                                                >  2:428148/1‑87 (MQ=255)                                                                                                                                          gCCCACCCGCAATCGA‑TGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAAACGCAATTTGCTGGTAATCGGCCTGGCGGTCATGCTCAGCGCCTGCGGTTTCCAGCTGCGCGGCACCGGCGCCACCGAGCTGAGCgcg           >  2:2004/1‑148 (MQ=255)                                                                                                                                            ccACCCGCAATCGA‑TGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAAACGCAATTTGCTGGTAATCGGCCTGGCGGTCATGCTCAGCGCCTGCGGTTTCCAGCt                                          >  1:46308/1‑117 (MQ=255)                                                                                                                                            ccACCCGCAATCGA‑TGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAAACGCAATTTGCTGGTAATCGGCCTGGCGGTCATGCTCAGCGCCTGCGGTTTCCAGCt                                          <  2:46308/117‑1 (MQ=255)                                                                                                                                             cACCCGC‑ATCGATTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAAACGCAATTTGCTGGTAATCGGCCTGGCGGTCATGCTCAGCGCCTGCGGTTTCCAGCTGCGCGGCACCGGCGCCACCGAGCTGAGCGTGAAg        <  1:476538/150‑1 (MQ=255)                                                                                                                                              aCCCGC‑ATCGATTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAAACGCAATTTGCTGGTAATCGGCCTGGCGGTCATGCTCAGCGCCTGCGGTTTCCAGCTGCGCGCGACCTCCGCCACCGAGCTGAGCGTGAAgg       >  1:308323/1‑150 (MQ=255)                                                                                                                                                 cGC‑ATCGATTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACCACATGATCAAACGCAATTTGCTGGTAATCGGCCTGGCGGTCATGCTCAGCGCCTGCGGTTTCCAGCTGCGCGGCACCGGCGCCACCGAGCTGAGCGTGAAGGaaa    <  2:442395/150‑1 (MQ=255)                                                                                                                                                   c‑ATCGATTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAAACGCAATTTGCTGGTAATCGGCCTGGCGGTCATGCTCAGCGCCTGCGGTTTCCAGCGGCGCGGCACCGGCGCCACCGAGCTGAGCGTGAAGGAAATg  <  2:48829/150‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                      CGCTGCCAGCCGCGAAGAAGTCGAAGCCGCTGCCCGCAGCAACGAGAATGTCCTGCGCTTCATCGATGGCCTGACCATCCGCAAGGTCATCGTGGTACCGGGCAAGCTGGTCAACATCGTCGCCAACTGATGAAAACGCCCACCCGC‑ATCGATTGCGGGTGGGCGGAACAGGCCCAAAAGGGAGCAACAACATGATCAAACGCAATTTGCTGGTAATCGGCCTGGCGGTCATGCTCAGCGCCTGCGGTTTCCAGCTGCGCGGCACCGGCGCCACCGAGCTGAGCGTGAAGGAAATG  >  NC_002947/5458794‑5459089

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑