Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,996,337	A→G	10.7%	intergenic (+15/+30)	PP_3523 → / ← PP_3524	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,996,337	0	A	G	10.7%	151.0 / 7.8	56	intergenic (+15/+30)	PP_3523/PP_3524	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (23/27);  new base G (3/3);  total (26/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.94e-01

TGAAAAGCTGGTCCGCGATTACATCCATGACGCGCTCAAGGAACTGCGCGTACTGTCCACCGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGAAGGGTGCGTAGACCACGAAGACGATCCACAGCATCTTGCGCTC  >  NC_002947/3996190‑3996483                                                                                                                                                    |                                                                                                                                                   tGAAAAGCTGGTCCGCGATTACATCCATGACGCGCTCAAGGAACTGCGCGTACTGTCCACCGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAg                                                                                                                                                   >  2:215595/1‑149 (MQ=255) tGAAAAGCTGGTCCGCGATTACATCCATGACGCGCTCAAGGAACTGCGCGTACTGTCCACCGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAg                                                                                                                                                   >  5:125588/1‑149 (MQ=255)  gAAAAGCTGGTCCGCGATTACATCCATGACGCGCTCAAGGAACTGCGCGTACTGTCCACCGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAg                                                                                                                                                   <  6:125588/148‑1 (MQ=255)   aaaaGCTGGTCCGCGATTACATCCATGACGCGCTCAAGGAACTGCGCGTACTGTCCACCGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAg                                                                                                                                                   <  3:137771/147‑1 (MQ=255)        cTGGTCCGCGATTACATCCATGACGCGCTCAAGGAACTGCGCGTACTGTCCACCGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGcccc                                                                                                                                            >  3:309196/1‑149 (MQ=255)           gTCCGCGATTACATCCATGACGCGCTCAAGGAACTGCGCGTACTGTCCACCGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGccccc                                                                                                                                           <  6:137123/147‑1 (MQ=255)           gTCCGCGATTACATCCATGACGCGCTCAAGGAACTGCGCGTACTGTCCACCGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCcgc                                                                                                                                         >  1:255244/1‑149 (MQ=255)                       aTCCATGACGCGCTCACGGAACTGCGCGTACTGTCCACCGTGAAGTTCTACGGCTGCCGGATGGTGGACGGGCGGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCGGGCGCGGGGGCGCCTGAGGCCgt                                                                                                                             <  4:22032/149‑2 (MQ=255)                         ccATGACGCGCTCAAGGAACTGCGCGTACTGTCCACCGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCa                                                                                                                            >  5:224433/1‑148 (MQ=255)                               cgcgCTCACGGCACTGCGCGTACTGTCCACCGCGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTc                                                                                                                     <  6:224433/149‑1 (MQ=255)                                    tCAAGGAACTGCGCGTACTGTCCACCGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCGGGCGCGGGGGCGCCTGAGGcc                                                                                                                               >  7:288673/1‑134 (MQ=255)                                    tCAAGGAACTGCGCGTACTGTCCACCGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCGGGCGCGGGGGCGCCTGAGGcc                                                                                                                               <  8:288673/134‑1 (MQ=255)                                      aaGGAACTGCGCGTACTGTCCACCGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTc                                                                                                              <  2:236101/149‑1 (MQ=255)                                          aaCTGCGCGTACTGTCCACCGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGc                                                                                                          <  4:156663/149‑1 (MQ=255)                                                      tGTCCACCGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCgccctg                                                                                              >  3:176400/1‑149 (MQ=255)                                                          cACCGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCgccctgccct                                                                                          >  2:280855/1‑149 (MQ=255)                                                             cGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCa                                                                                       >  1:13928/1‑149 (MQ=255)                                                             cGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCa                                                                                       <  3:180519/149‑1 (MQ=255)                                                               tGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCAcc                                                                                     <  1:55933/149‑1 (MQ=255)                                                               tGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCAcc                                                                                     >  3:230191/1‑149 (MQ=255)                                                                    ttCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCACACGCGCCCCCCCCCCCCACGCCCCAAACCGGCAATTTTACGGCAACCCCGCCCAGCCCTTCCCCGcccg                                                                                >  2:309304/1‑148 (MQ=255)                                                                       tACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCCACCCCGCCCAGCCCTTCCCCGCCCTCgg                                                                             >  2:272912/1‑149 (MQ=255)                                                                         cGGCTGCCAGATGGTGGACGGGCTGGGTCCTGCCATCCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCACCCGCACCCGCACCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTACAACGCCCTCGCAc                                                                           >  4:101083/1‑149 (MQ=255)                                                                                   aTGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCAttttt                                                                                                               <  5:103777/103‑1 (MQ=255)                                                                                   aTGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCAttttt                                                                                                               >  6:103777/1‑103 (MQ=255)                                                                                   aTGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGc                                                                 <  2:255244/149‑1 (MQ=255)                                                                                      gtggACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCa                                                              <  5:35893/149‑1 (MQ=255)                                                                                           cGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACa                                                         <  3:145521/149‑1 (MQ=255)                                                                                                    tCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAATAGCAAACCgg                                                <  1:280855/149‑1 (MQ=255)                                                                                                     ccTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCggg                                               <  3:304006/149‑1 (MQ=255)                                                                                                       tGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCCCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGCACAGCAAACCcggg                                              >  8:219483/1‑148 (MQ=255)                                                                                                         ccATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGAAg                                           >  1:122553/1‑149 (MQ=255)                                                                                                         ccATGCGTTTCGACATCATGCCCACATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGaa                                            <  8:111354/148‑1 (MQ=255)                                                                                                          cATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGAAgg                                          <  2:122553/149‑1 (MQ=255)                                                                                                            tGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCCAACCGGGGAAGGGt                                        >  6:154087/1‑149 (MQ=255)                                                                                                             gCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCgccctgccc                                                                                           <  3:110941/97‑1 (MQ=255)                                                                                                             gCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCgccctgccc                                                                                           >  4:110941/1‑97 (MQ=255)                                                                                                              cGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGAAGGGTGc                                      <  2:13928/149‑1 (MQ=255)                                                                                                               gTTTCGCCATCCTGCCCAAATGCCCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCCTTTTTCCTGCACCACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGACCAGCAAACCGGGGACGGGTGCg                                     >  6:257199/1‑149 (MQ=255)                                                                                                               gTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCCCCCTGCCCTTAACCGCCCTCGGACCGCGCCAGGCCCAGAACACAAAACCCGGGAAGGGTGCg                                     >  6:19436/1‑149 (MQ=255)                                                                                                                tttCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGaa                                            <  1:84981/141‑1 (MQ=255)                                                                                                                tttCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGAAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGaa                                            >  2:84981/1‑141 (MQ=255)                                                                                                                    gACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGAAGGGTGCGTAGAc                                <  3:101083/149‑1 (MQ=255)                                                                                                                      cATCCTGCCCATATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGAAGCGTGCGTAGACCa                              <  3:271691/149‑1 (MQ=255)                                                                                                                        tCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGAAGGGTGCGTAGACCACg                            <  4:309196/149‑1 (MQ=255)                                                                                                                         ccTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCgg                                                <  6:112120/128‑1 (MQ=255)                                                                                                                         ccTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCgg                                                >  5:112120/1‑128 (MQ=255)                                                                                                                         ccTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGAAGGGTGCGTAGACCAc                             <  3:312479/147‑1 (MQ=255)                                                                                                                         ccTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGAAGGGTGCGTAGACCAc                             >  4:312479/1‑147 (MQ=255)                                                                                                                          cTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGAAGGGTGCGTAGACCACGaa                          <  5:107364/149‑1 (MQ=255)                                                                                                                                 aaTGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGAAGGGTGCGTAGACCACGAAGACGATc                   <  1:309304/149‑1 (MQ=255)                                                                                                                                  aTGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGAAGGGTGCGTAGACCACGAAGACGATcc                  <  5:19436/149‑1 (MQ=255)                                                                                                                                          ttgcGGCCTCGGGCGCTGGGGCGCCTGAGGCCGTAAACCGTCATTTTTCCTGAAACACCGCCCTCCCCTACACCGCCCTCGGACCGCGCCAGGCCCAGAACACCAAACCGGCGAATGGTGCGTAGACCACGAAGACGATCCACAGCaac          >  1:319244/4‑147 (MQ=255)                                                                                                                                            gcGGCCTCGGGCGCGGGGGCGCCTGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCa                                                                                       <  3:108121/69‑1 (MQ=18)                                                                                                                                            gcGGCCTCGGGCGCGGGGGCGCCTGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCa                                                                                       >  4:108121/2‑70 (MQ=18)                                                                                                                                                  tCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGAAGGGTGCGTAGACCACGAAGACGATCCACAGCATCTTGCGCTc  >  5:21303/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                   TGAAAAGCTGGTCCGCGATTACATCCATGACGCGCTCAAGGAACTGCGCGTACTGTCCACCGTGAAGTTCTACGGCTGCCTGATGGTGGACGGGCTGGGTCCTGCCATGCGTTTCGACATCCTGCCCAAATGACCCTCGACGGCCTCAGGCGCCCCCGCGCCCGAGGCCGCAAACCGTCATTTTTCCTGCAACACCGCCCTGCCCTTCACCGCCCTCGGACCGCGCCAGGCCCAGAACAGCAAACCGGGGAAGGGTGCGTAGACCACGAAGACGATCCACAGCATCTTGCGCTC  >  NC_002947/3996190‑3996483

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑