Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,848,513	A→T	10.4%	P78P (CCA→CCT)	PP_3397 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,848,513	0	A	T	10.4%	136.0 / 7.9	48	P78P (CCA→CCT)	PP_3397	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (23/20);  new base T (2/3);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 6.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.87e-01

CGCCGCGTTCGCCGCGCTGTCTGATGTCGATCCGGGGCCCTACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCGCTGGTATTTCCAGATAACTGGCCACCCGAGATGTTCTGGTTCCTGGCCGAAACCTCGATACCACAAGTCGGTAACA  >  NC_002947/3848375‑3848661                                                                                                                                           |                                                                                                                                                     cgccgcGTTCGCCGCGCTGTCTGATGTCGATCCGGGGCCCTACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCTGGCGCAcgggt                                                                                                                                           <  1:160838/150‑5 (MQ=255)           gccgcGCTGTCTGATGTCGATCCGGGGCCCTACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGcgcccgcc                                                                                                                                 >  1:538286/1‑150 (MQ=255)             cgcgCTGTCTGATGTCGATCCGGGGCCCTACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTa                                                                                                                               >  1:337014/1‑150 (MQ=255)              gcgcTGTCTGATGTCGATCCGGGGCCCTACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTAc                                                                                                                              >  2:744794/1‑150 (MQ=255)                gcTGTCTGATGTCGATCCGGGGCCCTACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACAt                                                                                                                            <  2:549583/150‑1 (MQ=255)                 cTGTCTGATGTCGATCCGGGGCCCTACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACAtg                                                                                                                           <  2:85393/150‑1 (MQ=255)                       gATGTCGATCCGGGGCCCTACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCg                                                                                                                                            <  2:473990/127‑1 (MQ=255)                       gATGTCGATCCGGGGCCCTACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCg                                                                                                                                            >  1:473990/1‑127 (MQ=255)                        aTGTCGATCCGGGGCCCTACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGgcgc                                                                                                                                      <  1:476125/132‑1 (MQ=255)                        aTGTCGATCCGGGGCCCTACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGgcgc                                                                                                                                      >  2:476125/1‑132 (MQ=255)                               tCCGGGGCCCTACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCTGGCGCAcgg                                                                                                                                             >  2:322146/1‑116 (MQ=255)                               tCCGGGGCCCTACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCTGGCGCAcgg                                                                                                                                             <  1:322146/118‑3 (MQ=255)                                  ggggCCCTACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGa                                                                                                          >  2:511719/1‑150 (MQ=255)                                         tACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTTCATTTGCACCTTGTTGCCCGAGCCCggg                                                                                                   <  1:744794/150‑1 (MQ=255)                                         tACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCggg                                                                                                   <  2:337014/150‑1 (MQ=255)                                          acacCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCggg                                                                                                   <  2:217158/149‑1 (MQ=255)                                          acacCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCggg                                                                                                   >  1:217158/1‑149 (MQ=255)                                               ttCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTAt                                                                                             >  1:304734/1‑150 (MQ=255)                                               ttCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTAt                                                                                             >  2:18270/1‑150 (MQ=255)                                                 cGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGa                                                                                           <  1:511719/150‑1 (MQ=255)                                                     acaGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGAt                                                                                       <  1:18270/150‑1 (MQ=255)                                                              tATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCg                                                                              >  1:113239/1‑150 (MQ=255)                                                              tATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGACGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGc                                                                                                        <  1:427074/124‑1 (MQ=255)                                                              tATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGACGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGc                                                                                                        >  2:427074/1‑124 (MQ=255)                                                              tATCCGATGTGGTACAAGGACAGCATCGACCCATCCCTGAACGGGTTCCATGGGCGTGGTAAATGCACCCGTGAGAAACGGTAACCAACACCGCCCACCCACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTAAGACCATGcctgcccg                                                                              >  1:181750/1‑144 (MQ=255)                                                                  cGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCggg                                                                                                                                          >  1:437579/1‑86 (MQ=255)                                                                  cGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCggg                                                                                                                                          <  2:437579/86‑1 (MQ=255)                                                                         gTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGgc                                                                                                                                                   <  1:30390/70‑1 (MQ=255)                                                                         gTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGgc                                                                                                                                                   >  2:30390/1‑70 (MQ=255)                                                                          tACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCGCTGGTATTTCCa                                                                  <  2:360244/150‑1 (MQ=255)                                                                                     ccTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCGCTGGTATTTCCAGATAACTGGcc                                                       >  2:138712/1‑150 (MQ=255)                                                                                     ccTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCGCTGGTATTTACAGATAACTGGcc                                                       >  1:530623/1‑150 (MQ=255)                                                                                             aaTCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCGCTGGTATTTCCAGATAACTGGCCACCCgaga                                               >  2:510272/1‑150 (MQ=255)                                                                                              aTCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACAtgtg                                                                                                                         <  1:703419/75‑1 (MQ=255)                                                                                              aTCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACAtgtg                                                                                                                         >  2:703419/1‑75 (MQ=255)                                                                                                cccTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCGCTGGTATTTCCAGATAACTGGCCACCCGAGATGt                                            <  1:138712/150‑1 (MQ=255)                                                                                                   tGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCGCTGGTATTTCCAGATAACTGGCCACCCGAGATGTTCt                                         <  2:150434/150‑1 (MQ=255)                                                                                                        cTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCGCTGGTATTTCCAGATAACTGGCCACCCGAGATGTTCTGGTTc                                    <  2:538286/150‑1 (MQ=255)                                                                                                          gtgCCAGTCGCGTGCCACCAGCACCCGTGCGCCTGGCGCAcgg                                                                                                                                             <  2:291853/43‑3 (MQ=255)                                                                                                          gtgCCAGTCGCGTGCCACCAGCACCCGTGCGCCTGGCGCAcgg                                                                                                                                             >  1:291853/1‑41 (MQ=255)                                                                                                          gtgCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCGCTGGTATTTCCAGATAACTGGCCACCCGAAATGTTCTGGTTCCt                                  >  2:277985/1‑150 (MQ=255)                                                                                                           tgCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCGCTGGTATTTCCAGATAACTGGCCACCCGAGATGTTCTgg                                       <  2:313234/144‑1 (MQ=255)                                                                                                           tgCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCGCTGGTATTTCCAGATAACTGGCCACCCGAGATGTTCTgg                                       >  1:313234/1‑144 (MQ=255)                                                                                                           tgCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCGCTGGTATTTCCAGATAACTGGCCACCCGAGATGTTCTGGTTCCTg                                 <  2:204471/150‑1 (MQ=255)                                                                                                                         caccaGCACCCGTGCGCCAGGCGCACACGGCACGCTCGCCTATATGTGCACCTGGTTGCCCGAGCCCGACGGCTATGCCGATGCCCGGCCGCTGGGATTTCCAGATAACTGGCCACCCGAGATGTTCTGGTTACTGGCGGAAACCGCGAt                   >  1:654899/1‑150 (MQ=255)                                                                                                                             aGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCGCTGGTATTTCCAGATAACTGGCCACCCGAGATGTTCTGGTTCCTGGCCGAAACCTCGATACca               >  2:71358/1‑150 (MQ=255)                                                                                                                                          cAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCGCTGGTATTTCCAGATAACTGGCCACCCGAGATGTTCTGGTTCCTGGCCGAAACCTCGATACCCCAAGCCGGGAAcc  >  2:291818/1‑149 (MQ=255)                                                                                                                                          cAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCGCTGGTATTTCCAGATAACTGGCCACCCGAGATGTTCTGGTTCCTGGCCGAAACCTCGATACCACAAGTCGGTAACa  <  2:181750/150‑1 (MQ=255)                                                                                                                                           |                                                                                                                                                     CGCCGCGTTCGCCGCGCTGTCTGATGTCGATCCGGGGCCCTACACCTTCGCCACAGGTGGCTATCCGATGTGGTACAAGGACAGCCTCGACCAATCCCTGGAGCTGTGCCAGTCGCGTGCCACCAGCACCCGTGCGCCAGGCGCACCCGGGGCGCCCGCCTACATGTGCACCTTGTTGCCCGAGCCCGGGGTCTATGACGATGCCCTGCCGCTGGTATTTCCAGATAACTGGCCACCCGAGATGTTCTGGTTCCTGGCCGAAACCTCGATACCACAAGTCGGTAACA  >  NC_002947/3848375‑3848661

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