Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,260,381	T→A	12.3%	Q161L (CAG→CTG)	PP_2857 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,260,381	0	T	A	12.3%	85.4 / 2.3	32	Q161L (CAG→CTG)	PP_2857	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (14/13);  new base A (2/2);  total (17/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCTCCGTACGCTATTAGGTTAAGTGTCGTTCTTAACTGCAGGGTCAATCCGCGACCCGGATGCTCAAGGTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCTGATGCTCAGTGCGTTGGCTTGCTGG  >  NC_002947/3260241‑3260530                                                                                                                                             |                                                                                                                                                      tctcCGTACGCTATTAGGTTAAGTGTCGTTCTTAACTGCAGGGTCAATCCGCGACCCGGATGCTCAAGGTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCAGGTCACtac                                                                                                                                              >  1:215137/1‑148 (MQ=255)           cTATTAGGTTAAGTGTCGTTCTTAACTGCAGGGTCAATCCGCGACCCGGATGCTCAAGGTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGCTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCAGGTCACTACCAGTGAccag                                                                                                                                    <  1:427308/150‑3 (MQ=255)                  gTTAAGTGTCGTTCTTAACTGCAGGGTCAATCCGCGACCCGGATGCTCAAGGTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAg                                                                                                                             >  2:54731/1‑150 (MQ=255)                          tCGTTCTTAACTGCAGGGTCAATCCGCGACCCGGATGCTCAAGGTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTg                                                                                                                                               >  2:300443/1‑124 (MQ=255)                          tCGTTCTTAACTGCAGGGTCAATCCGCGACCCGGATGCTCAAGGTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTg                                                                                                                                               <  1:300443/124‑1 (MQ=255)                            gTTCTTAACTGCAGGGTCAATCCGCGACCCGGATGCTCAAGGTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGaa                                                                                                                   <  1:54731/150‑1 (MQ=255)                                  aaCTGCAGGGTCAATCCGCGACCCGGATGCTCAAGGTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAg                                                                                                             >  1:536918/1‑150 (MQ=255)                                        aGGGTCAATCCGCGACCCGGATGCTCAAGGTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGACCTCAGAGGCACGGCTAGTAACCTTGCGATAGCCTGCTGGAATGTCAGTTGCTc                                                                                                       >  2:222822/1‑150 (MQ=255)                                                 ccGCGACCCGGATGCTCAAGGTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAgttgt                                                                                              <  2:536918/150‑1 (MQ=255)                                                  cgggtcgcGGATGCTCAAGGTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAgttgtt                                                                                             <  2:767225/143‑1 (MQ=255)                                                         cGGATGCTCAAGGTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAgc                                                                                      >  2:5519/1‑150 (MQ=255)                                                         cGGATGCTCAAGGTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAgc                                                                                      >  2:405035/1‑150 (MQ=255)                                                                tCAAGGTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCAc                                                                                 <  1:457720/148‑1 (MQ=255)                                                                tCAAGGTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCAc                                                                                 >  2:457720/1‑148 (MQ=255)                                                                           gCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATg                                                                    >  1:203874/1‑150 (MQ=255)                                                                            ccATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGa                                                                   >  1:106798/1‑150 (MQ=255)                                                                               ttCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTa                                                                                                                                            <  2:579535/74‑1 (MQ=255)                                                                               ttCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTa                                                                                                                                            >  1:579535/1‑74 (MQ=255)                                                                                         cACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCAGGTCACTACCAGTGAccag                                                                                                                                    <  2:776284/72‑3 (MQ=37)                                                                                         cACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCAGGTCACTACCAGTGAccag                                                                                                                                    >  1:776284/1‑70 (MQ=37)                                                                                            cccGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGAt                                                   >  1:688716/1‑150 (MQ=255)                                                                                                       ggTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGtt                                        <  2:203874/150‑1 (MQ=255)                                                                                                        gTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTtg                                       <  1:5519/150‑1 (MQ=255)                                                                                                        gTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTtg                                       <  1:405035/150‑1 (MQ=255)                                                                                                                  aTCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCAGACGTCGATGCTTTGCGGTTGTGCACCAATg                             <  1:222822/150‑1 (MQ=255)                                                                                                                   tCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAg                                                                                       >  1:730072/1‑91 (MQ=255)                                                                                                                   tCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAg                                                                                       <  2:730072/91‑1 (MQ=255)                                                                                                                    cACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCt                           >  1:784174/1‑150 (MQ=255)                                                                                                                              cTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGtt                                                                         >  1:769751/1‑94 (MQ=255)                                                                                                                              cTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGtt                                                                         <  2:769751/94‑1 (MQ=255)                                                                                                                               tACCGGTGAAGGCCTGGTCACTGGTAGTGATCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAAt                              >  2:10658/1‑136 (MQ=255)                                                                                                                               tACCGGTGAAGGCCTGGTCACTGGTAGTGATCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAAt                              <  1:10658/136‑1 (MQ=255)                                                                                                                                             tGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCTGATGCTCAGTGCGTTGGCTTGCTgg  <  2:784174/150‑1 (MQ=255)                                                                                                                                             |                                                                                                                                                      TCTCCGTACGCTATTAGGTTAAGTGTCGTTCTTAACTGCAGGGTCAATCCGCGACCCGGATGCTCAAGGTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCTGATGCTCAGTGCGTTGGCTTGCTGG  >  NC_002947/3260241‑3260530

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: ‑