Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,511,113	C→T	7.4%	G103G (GGC→GGT)	PP_3107 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,511,113	0	C	T	7.4%	154.8 / 2.1	54	G103G (GGC→GGT)	PP_3107	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (24/26);  new base T (2/2);  total (26/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.25e-01

ACCATCTCGCGTGACACCTTGCTGCCGGACGAAGCGCTGCAGGCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGCACAGGCCGACTTCAGTGCCCAGCAGAACCAGGACTGGGA  >  NC_002947/3510967‑3511256                                                                                                                                                   |                                                                                                                                                acaaTCTCGCGTGACACCTTGCTGCCGGACGAAGCTCTGCAGGCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGAGGCTACACCAGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCAt                                                                                                                                               >  8:38148/4‑149 (MQ=255)  ccATCTCGCGTGACACCTTGCTGCCGGACGTAGCGCTGCAGGCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAACCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATc                                                                                                                                              <  5:239340/149‑1 (MQ=255)   cATCTCGCGTGACACCTTGCTGCCGGACGAAGCGCTGCAGGCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATc                                                                                                                                              >  1:66082/1‑148 (MQ=255)   cATCTCGCGTGACACCTTGCTGCCGGACGAAGCGCTGCAGGCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATc                                                                                                                                              >  3:175465/1‑148 (MQ=255)         gcgTGACACCTTGCTGCCGGACGAAGCGCTGCAGGCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGAt                                                                                                                                         <  2:176297/147‑1 (MQ=255)         gcgTGACACCTTGCCGCCGGACGAAGCGCTGCAGGCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATc                                                                                                                                        >  8:245895/1‑148 (MQ=255)          cgTGACACCTTGCTGCCGGACGAAGCGCTGCAGGCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGa                                                                                                                                      <  1:137292/149‑1 (MQ=255)             gACACCTTGCTGCCGGACGAAGCGCTGCAGGCCTATTTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGc                                                                                                                                   <  7:139733/149‑1 (MQ=255)                 ccTTGCTGCCGGACGAAGCGCTGCAGGCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTAt                                                                                                                               <  3:147298/149‑1 (MQ=255)                     gctgcCGGACGAAGCGCTGCAGGCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTAc                                                                                                                            <  4:175465/148‑1 (MQ=255)                          cGGACGAAGCGCTGCAGGCCTATGTCGATCGCCATGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAAc                                                                                                                      <  5:231857/149‑1 (MQ=255)                              cGAAGCGCTGCAGGCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAgg                                                                                                                  >  4:77223/1‑149 (MQ=255)                               gAAGCGCTGCAGGCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAggg                                                                                                                 >  1:254391/1‑149 (MQ=255)                                 aGCGCTGCAGGCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGgcc                                                                                                               <  2:66082/149‑1 (MQ=255)                                         aGGCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGTATCCAGATCGACGCCTATTACATGAACCAggg                                                                                                                 >  2:21409/1‑139 (MQ=255)                                         aGGCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGTATCCAGATCGACGCCTATTACATGAACCAggg                                                                                                                 <  1:21409/139‑1 (MQ=255)                                           gCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTAtt                                                                                                                              >  3:270676/1‑124 (MQ=255)                                           gCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTAtt                                                                                                                              <  4:270676/124‑1 (MQ=255)                                             cTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTAc                                                                                                    >  3:183350/1‑148 (MQ=255)                                                tGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAgc                                                                                                <  7:245895/149‑1 (MQ=255)                                                      tCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAgg                                                                                          >  7:107913/1‑149 (MQ=255)                                                        gCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGgcc                                                                                        <  3:77223/149‑1 (MQ=255)                                                         ccAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGgccg                                                                                       >  5:76144/1‑149 (MQ=255)                                                         ccAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGgccg                                                                                       >  8:214181/1‑149 (MQ=255)                                                          cAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGgccgc                                                                                      <  8:107913/149‑1 (MQ=255)                                                            ggTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGTATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCt                                                                                    >  5:100368/1‑149 (MQ=255)                                                              tCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCtt                                                                                   >  5:43124/1‑148 (MQ=255)                                                                aaGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTtca                                                                                 <  7:214181/148‑1 (MQ=255)                                                                           cTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCg                                                                     >  2:113407/1‑149 (MQ=255)                                                                            tCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCgg                                                                    >  4:294707/1‑149 (MQ=255)                                                                                 gCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGTATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTg                                                               <  6:100368/149‑1 (MQ=255)                                                                                       cgGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCTCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGa                                                         <  6:76144/149‑1 (MQ=255)                                                                                         gCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGAtc                                                       <  4:183350/149‑1 (MQ=255)                                                                                          cTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGAt                                                        >  4:84338/1‑147 (MQ=255)                                                                                          cTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGAt                                                        <  3:84338/147‑1 (MQ=255)                                                                                                     tGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACt                                           <  1:113407/149‑1 (MQ=255)                                                                                                        gCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGca                                        >  3:282649/1‑149 (MQ=255)                                                                                                          aacaaGGCCGTCACGCTCTCGGTTACCGCACCAATTGCCGGCATCCAGATCGACGCCTATTACATGAACCATGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGcaca                                      <  4:14863/149‑1 (MQ=255)                                                                                                            caaGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGCACAgg                                    >  4:118914/1‑149 (MQ=255)                                                                                                             aaGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGCACAGGc                                   <  3:118914/149‑1 (MQ=255)                                                                                                               ggCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCATATCCACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGCACAGGCCg                                 <  7:38148/149‑1 (MQ=255)                                                                                                                gCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGCACAGGCCGa                                <  4:282649/149‑1 (MQ=255)                                                                                                                   gTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGCACAGGCCGACtt                             <  3:294707/149‑1 (MQ=255)                                                                                                                         ctctCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGCACAGGCCGAc                               >  8:153362/1‑141 (MQ=255)                                                                                                                         ctctCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGCACAGGCCGAc                               <  7:153362/141‑1 (MQ=255)                                                                                                                          tctcGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGCACAGGCCGACTTCAGTGcc                      >  5:35786/1‑149 (MQ=255)                                                                                                                                  aCCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGCACAGGCCGACTTCAGTGCCCAGCAGaa              >  3:116502/1‑149 (MQ=255)                                                                                                                                  aCCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGCACAGGCCGACTTCAGTGCCCAGCAGa               <  6:43124/148‑1 (MQ=255)                                                                                                                                     gCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTtcatcat                                                                             <  5:272083/83‑1 (MQ=255)                                                                                                                                     gCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTtcatcat                                                                             >  6:272083/1‑83 (MQ=255)                                                                                                                                     gCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGCACAGGCCGACTTCAGTGCCCAGCAGAAc             >  4:212833/1‑147 (MQ=255)                                                                                                                                       aCCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCCTCATCAGCCCCGGGCGTGCGCTGATGTTCTCCACCCCTGCACAGGCCGACTACAGTGCCCAGCAGAGCCAgg         >  8:195257/1‑149 (MQ=255)                                                                                                                                            ttGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGCACAGGCCGACTTCAGTGCCCAGCAGAACCAGGACTgg    <  2:254391/149‑1 (MQ=255)                                                                                                                                               ccGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGCACAGGCCGACTTCAGTGCCCAGCAGAACCAGGACTGGGa  >  2:28868/1‑148 (MQ=255)                                                                                                                                                   |                                                                                                                                                ACCATCTCGCGTGACACCTTGCTGCCGGACGAAGCGCTGCAGGCCTATGTCGATCGCCAGGTCAAGCTGCTCACCTCCAAGCTGCGCGGCTACACCCGCATGGGCAACAAGGCCGTCACGCTCTCGGTTACCGCACCCATTGCCGGCATCCAGATCGACGCCTATTACATGAACCAGGGCCGCCCGCTGTACCAGCGCCAGGCCGCCTTCATCATCAGCCCCGGGCGTGCCCTGATCTTCTCCACCACTGCACAGGCCGACTTCAGTGCCCAGCAGAACCAGGACTGGGA  >  NC_002947/3510967‑3511256

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑