Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,973,308:1	+T	12.0%	coding (609/1713 nt)	PP_2600 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,973,308	1	.	T	12.0%	166.5 / 19.7	50	coding (609/1713 nt)	PP_2600	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (23/21);  new base T (3/3);  total (26/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01

CGACCCACGCCCCGCGCACCTGGCCACCCTCGATCAGCAGGCGTTTGGCCGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGCCCATGAACGAGGTTTCGCGCATGGTC  >  NC_002947/2973160‑2973449                                                                                                                                                      |                                                                                                                                              cgACCCCCGCCCCGCGCACCTGGCCACCCTCGATCAGCAGGCGTTTGGCCGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑c                                                                                                                                              <  1:228568/150‑1 (MQ=255)     ccACGCCCCGCGCACCTGGCCACCCTCGATCAGCAGGCGTTTGGCCGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCGGGTGCATGGCCCGACCATAG‑CGGGc                                                                                                                                          >  2:164669/1‑150 (MQ=255)      cACGCCCCGCGCACCTGGCCACCCTCGATCAGCAGGCGTTTGGCCGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGcc                                                                                                                                         >  1:279693/1‑150 (MQ=255)       aCGCCCCGCGCACCTGGCCACCCTCGATCAGCAGGCGTTTGGCCGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCa                                                                                                                                        >  2:524669/1‑150 (MQ=255)           cccGCGCACCTGGCCACCCTCGATCAGCAGGCGTTTGGCCGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGACCGACCATGG‑CGGGCCAggtg                                                                                                                                    <  1:358589/150‑1 (MQ=255)            ccGCGCACCTGGCCACCCTCGATCAGCAGGCGTTTGGCCGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAggtgg                                                                                                                                   >  2:180085/1‑150 (MQ=255)            ccGCGCACCTGGCCACCCTCGATCAGCAGGCGTTTGGCCGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAggtgg                                                                                                                                   <  1:180085/150‑1 (MQ=255)            ccGCGCACCTGGCCACCCTCGATCAGCAGGCGTTTGGCCGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCG‑CCATGGTCGGGCCatgcac                                                                                                                                   <  1:47748/150‑6 (MQ=255)              gcgcACCTGGCCACCCTCGATCAGCAGGCGTTTGGCCGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCAGACCATTG‑CGGGCCAGGTGGTa                                                                                                                                 <  2:361848/150‑1 (MQ=255)                                   cagcagGCGTTTGGCCGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCtt                                                                                                            <  2:319078/150‑1 (MQ=255)                                   cagcagGCGTTTGGCCGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCtt                                                                                                            <  1:376683/150‑1 (MQ=255)                                      cagGCGTTTGGCCGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCCTGGCCCG‑CCATGGTCGGGCCatg                                                                                                                                      >  1:130963/1‑119 (MQ=255)                                      cagGCGTTTGGCCGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCCTGGCCCG‑CCATGGTCGGGCCatg                                                                                                                                      <  2:130963/121‑3 (MQ=255)                                                 ccGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAg                                                                                                                 <  1:537215/131‑1 (MQ=255)                                                 ccGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAg                                                                                                                 >  2:537215/1‑131 (MQ=255)                                                 ccGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTgcagca                                                                                              >  2:41008/1‑150 (MQ=255)                                                  cGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGcagcag                                                                                             <  2:492801/150‑1 (MQ=255)                                                        cGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCttt                                                                                       >  2:324660/1‑150 (MQ=255)                                                         gACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTg                                                                                      >  1:83680/1‑150 (MQ=255)                                                          aCGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTgg                                                                                     <  1:234672/150‑1 (MQ=255)                                                          aCGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTGTgg                                                                                     >  1:434267/1‑150 (MQ=255)                                                          aCGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTGTgg                                                                                     >  1:169431/1‑150 (MQ=255)                                                          aCGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGAGCGAGCGCGTTGTCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTgg                                                                                     <  2:323913/150‑1 (MQ=255)                                                               tGCAGGTGCCCACCCACGTCCTGTGCCGATTTAGCCAGGCGCCCAACCAGTGCCACACCGTTGACCAGGTGCATGTCCCGACCATGG‑CGGGCCAGGTTGTACAGGGGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAg                                                                                <  1:547463/150‑1 (MQ=255)                                                                  aGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCgg                                                                             <  2:345935/150‑1 (MQ=255)                                                                          cccgaGGTCCTGTGCTGATTTAGCCAGGCGCGCCACCCGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑AGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGtt                                                                     <  2:434267/146‑1 (MQ=255)                                                                                         cGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGCAGGCGGCAAg                                                      >  1:182342/1‑150 (MQ=255)                                                                                                 ccAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCAc                                              >  1:388011/1‑150 (MQ=255)                                                                                                   aGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCg                                            >  2:185513/1‑150 (MQ=255)                                                                                                      cgcgcCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGcc                                         <  2:388011/150‑1 (MQ=255)                                                                                                                gTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCtt                                                                                                            >  1:61172/1‑73 (MQ=255)                                                                                                                gTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCtt                                                                                                            <  2:61172/73‑1 (MQ=255)                                                                                                                 tGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCAt                              <  2:83680/150‑1 (MQ=255)                                                                                                                    cacaCCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGcc                           >  2:400980/1‑150 (MQ=255)                                                                                                                    cacaCCGTTAACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGcc                           >  1:542256/1‑150 (MQ=255)                                                                                                                               ccAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGCCCATGAACGAgg                <  1:185513/150‑1 (MQ=255)                                                                                                                                   gTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGCCCATGAAc                    <  1:510585/142‑1 (MQ=255)                                                                                                                                   gTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGCCCATGAAc                    >  2:510585/1‑142 (MQ=255)                                                                                                                                    cacATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGCCCATGAACGAGGTTTcg           >  1:411224/3‑150 (MQ=255)                                                                                                                                     gCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCTCTTGCACACGTGCAGCAGGGCTTTGATCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGCCCATGAACGAGGTTTcgc          <  1:41008/150‑1 (MQ=255)                                                                                                                                      cATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCTGCATGCCCATGAACGAGGTTTcgcg         >  2:137864/1‑150 (MQ=255)                                                                                                                                        tGGCCCG‑CCATGGTCGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGCCCATGAACGAGGTTTCGCGCa       >  2:370302/1‑150 (MQ=255)                                                                                                                                         ggCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGCCCATGAACGAGGTTTCGCGCAt      <  1:524669/150‑1 (MQ=255)                                                                                                                                         ggCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGCCCATGAACGAGGTTTCGCGCAt      <  2:411224/150‑1 (MQ=255)                                                                                                                                          gCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGCCCATGAACGAGGTTTCGCGCATg     <  2:182342/150‑1 (MQ=255)                                                                                                                                           gcccgccATGGTCGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCgg                                                 <  2:137290/101‑1 (MQ=255)                                                                                                                                           gcccgccATGGTCGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCgg                                                 >  1:137290/6‑106 (MQ=255)                                                                                                                                            ccGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGCCCATGAACGCGGTTTAGAGCATGGt   >  2:341177/1‑150 (MQ=255)                                                                                                                                            ccGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGCCCATGAACGAGGTTTCGCGCATGGt   >  2:574349/1‑150 (MQ=255)                                                                                                                                            ccGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGCCCATGAACGAGGTTTCGCGCATGGt   >  1:420754/1‑150 (MQ=255)                                                                                                                                             cGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGCCCATGAACGAGGTTTCGCGCATGGTc  >  2:222959/1‑150 (MQ=255)                                                                                                                                                      |                                                                                                                                              CGACCCACGCCCCGCGCACCTGGCCACCCTCGATCAGCAGGCGTTTGGCCGGCGCCGACGCTTGCAGGTGCACACCCAGGTCCTGTGCCGATTTAGCCAGGCGCGCCACCAGTGCCACACCGTTGACCAGGTGCATGGCCCGACCATGG‑CGGGCCAGGTGGTACAGGTGGCGGCCAAAGCGCTTGCACACGTGCAGCAGGGCTTTGGGCGAGCGGGTCATGTTGAGGAAGGCGGCAAGGTCGGCACCGGCCATGATCGGCATGCCCATGAACGAGGTTTCGCGCATGGTC  >  NC_002947/2973160‑2973449

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: ‑