Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,265,392	C→A	14.3%	L140L (CTG→CTT)	PP_2857 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,265,392	0	C	A	14.3%	79.7 / 3.4	28	L140L (CTG→CTT)	PP_2857	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (10/14);  new base A (2/2);  total (12/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.43e-01

GTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCTGATGCTCAGTGCGTTGGCTTGCTGGGTGTTGGCACCTGCGCTCTGGTTGACGCCCAGGGCGCCGCTGCCG  >  NC_002947/3265258‑3265524                                                                                                                                       |                                                                                                                                     gtgtTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCa                                                                                                                                     <  1:4390/136‑1 (MQ=255)   gtTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCTCCCGTCGGCTACCGGTGAAGGCCTGGTGACTGGTAGTGACCTGGCGATAGCCTGCTGGATTGTCAGTTGCTCCTGAGTTGTTGTTCAgc                                                                                                                                   <  1:502746/136‑1 (MQ=255)      ggCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGcc                                                                                                                                <  1:189857/136‑1 (MQ=255)       gCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCa                                                                                                                               >  2:24221/1‑136 (MQ=255)         cATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACg                                                                                                                             >  2:638932/1‑136 (MQ=255)           ttCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGtt                                                                                                                           <  1:264514/136‑1 (MQ=255)               gTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGt                                                                                                                       >  2:523949/1‑136 (MQ=255)                          cGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGAc                                                                                                            <  1:634550/136‑1 (MQ=255)                           ggCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACg                                                                                                           >  1:405951/1‑136 (MQ=255)                                    gTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGtcgtcg                                                                                                  <  2:658623/136‑1 (MQ=255)                                     ttCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGATCCTGAGTTGTTGATCAGCGACACGTTCTGTTGCATGAGGACGCTgtcgtagg                                                                                                 >  1:626354/1‑133 (MQ=255)                                          cTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCtt                                                                                            >  1:564174/1‑136 (MQ=255)                                               tCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCgg                                                                                       <  1:156771/136‑1 (MQ=255)                                               tCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCgg                                                                                       <  1:496799/136‑1 (MQ=255)                                               tCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCgg                                                                                       <  2:466495/136‑1 (MQ=255)                                                  ccccTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATAAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTtg                                                                                    >  2:576879/1‑136 (MQ=255)                                                  ccccTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATAAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTtg                                                                                    >  2:480311/1‑136 (MQ=255)                                                                  gAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCTGATg                                                                    <  2:401005/136‑1 (MQ=255)                                                                  gAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCTGATg                                                                    <  2:448190/136‑1 (MQ=255)                                                                                         ccTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCTGATGCTCAGTGCGTTGGCTTGCTGGgt                                             <  2:639503/136‑1 (MQ=255)                                                                                         ccTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCTGATGCTCAGTGCGTTGGCTTGCTGGgt                                             <  2:112808/136‑1 (MQ=255)                                                                                              ggATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCTGATGCTCAGTGCGTTGGCTTGCTGGGTGTTgg                                        <  1:24221/135‑1 (MQ=255)                                                                                                aTAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCTGATGCTCAGTGCGTTGGCTTGCTGGGTGTTGGCa                                      >  2:306594/1‑136 (MQ=255)                                                                                                     ctgctgGAATGTCAGTTGCTCCTGAGTTGTTGATAAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCTGATGCTCAGTGCGTTGGCTTGCTGGGTGTTGGCACCTgc                                 <  1:576879/136‑1 (MQ=255)                                                                                                     ctgctgGAATGTCAGTTGCTCCTGAGTTGTTGATAAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCTGATGCTCAGTGCGTTGGCTTGCTGGGTGTTGGCACCTgc                                 <  1:480311/136‑1 (MQ=255)                                                                                                                     tGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCTGATGCTCAGTGCGTTGGCTTGCTGGGTGTTGGCACCTGCGCTCTGGTTGACGccc                 >  1:595098/1‑136 (MQ=255)                                                                                                                          cTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCTGATGCTCAGTGCGTTGGCTTGCTGGGTGTTGGCACCTGCGCTCTGGTTGACGCCCAGGgc            >  1:652340/1‑136 (MQ=255)                                                                                                                                    gATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCTGATGCTCAGTGCGTTGGCTTGCTGGGTGTTGGCACCTGCGCTCTGGTTGACGCCCAGGGCGCCGCTGCCg  >  1:291918/1‑136 (MQ=255)                                                                                                                                       |                                                                                                                                     GTGTTGGCCATTCGGTTTCCCACCCCGGCACTCTGGTTCAACTGGATCACCCCTCGGCTACCGGTGAAGGCCTGGTCACTGGTAGTGACCTGGCGATAGCCTGCTGGAATGTCAGTTGCTCCTGAGTTGTTGATCAGCGCCACGTTCTGTTGCATGAGGACGCTGTCGTCGATGCTTTGCGGTTGTGCACCAATGCTGATGCTCAGTGCGTTGGCTTGCTGGGTGTTGGCACCTGCGCTCTGGTTGACGCCCAGGGCGCCGCTGCCG  >  NC_002947/3265258‑3265524

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑