Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,898,692	C→A	6.8%	R164L (CGC→CTC)	PP_3441 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,898,692	0	C	A	6.8%	184.4 / 3.2	59	R164L (CGC→CTC)	PP_3441	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (33/22);  new base A (2/2);  total (35/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.19e-01

CACTTCACACCCCAGGTGGCAGCCAATCACCTCATCGCCCAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAATGCTGCGCCGCAGTTCGCTGTCGTAGCGGGCAGTGATGTCTTCCAGTGGGCGCCCCAGCGGC  >  NC_002947/3898550‑3898835                                                                                                                                               |                                                                                                                                                cACTTCACACCCCAGGTGGCAGCCAATCACCTCATCGCCCAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGcagcag                                                                                                                                          >  1:611039/1‑150 (MQ=255)       acacCCCAGGTGGCAGCCAATCACCTCATCGCCCAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCg                                                                                                                                    <  1:1119177/150‑1 (MQ=255)        cacCCCAGGTGGCAGCCAATCACCTCATCGCCCAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCgg                                                                                                                                   >  1:961238/1‑150 (MQ=255)         acCCCAGGTGGCAGCCAATCACCTCATCGCCCAGCATGATCAAGTCAAGCCGGCCTACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGt                                                                                                                                  >  1:139501/1‑150 (MQ=255)          ccccAGGTGGCAGCCAATCACCTCATCGCCCAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTc                                                                                                                                 >  1:398649/1‑150 (MQ=255)                 tGGCAGCCAATCACCTCATCGCCCAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATg                                                                                                                          <  1:867681/150‑1 (MQ=255)                   gCAGCCAATCACCTCATCGCCCAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGc                                                                                                                        >  1:446449/1‑150 (MQ=255)                     aGCCAATCACCTCATCGCCCAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGGATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGa                                                                                                                      >  1:197099/1‑150 (MQ=255)                         aaTCACCTCATCGCCCAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATttc                                                                                                                  <  2:961238/150‑1 (MQ=255)                         aaTCACCTCATCGCCCAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATttc                                                                                                                  >  2:894645/1‑150 (MQ=255)                           tcacctcaccGCCCAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATttctt                                                                                                                <  1:128293/150‑1 (MQ=255)                            cACCTCATCGCCCAGAATGATCAAGTCAAGACGGCGGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATttcttc                                                                                                               <  2:398649/150‑1 (MQ=255)                             aCCTCATCGCCCAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCg                                                                                                              >  1:863457/1‑150 (MQ=255)                              ccTCATCGCCCAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGt                                                                                                             >  2:285966/1‑150 (MQ=255)                              ccTCATCGCCCAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGt                                                                                                             >  2:25404/1‑150 (MQ=255)                               cTCATCGCCCAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTc                                                                                                            <  2:446449/150‑1 (MQ=255)                                      cccAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAgg                                                                                                     >  1:125321/1‑150 (MQ=255)                                      cccAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAgg                                                                                                     <  1:55330/150‑1 (MQ=255)                                      cccAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAgg                                                                                                     >  2:208076/1‑150 (MQ=255)                                      cccAGCATGATCAAGGCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAgg                                                                                                     <  1:55325/150‑1 (MQ=255)                                        cAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGAGCAGCAGATCCCGGTc                                                                                                                                 <  1:503643/120‑1 (MQ=255)                                        cAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGAGCAGCAGATCCCGGTc                                                                                                                                 <  1:504102/120‑1 (MQ=255)                                        cAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGAGCAGCAGATCCCGGTc                                                                                                                                 >  2:503643/1‑120 (MQ=255)                                        cAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGAGCAGCAGATCCCGGTc                                                                                                                                 >  2:504102/1‑120 (MQ=255)                                                    gtcaagCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCAtgtg                                                                                       >  2:210488/1‑150 (MQ=255)                                                     tcaagCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAgg                                                                                                     <  2:821721/135‑1 (MQ=255)                                                     tcaagCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAgg                                                                                                     >  1:821721/1‑135 (MQ=255)                                                     tcaagCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGa                                                                                      <  1:25404/150‑1 (MQ=255)                                                     tcaagCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGa                                                                                      >  1:389812/1‑150 (MQ=255)                                                     tcaagCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGa                                                                                      >  2:354126/1‑150 (MQ=255)                                                                gACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCAtgt                                                                                        >  2:718882/1‑137 (MQ=255)                                                                gACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCAtgt                                                                                        <  1:718882/137‑1 (MQ=255)                                                                 acacTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCgg                                                                          >  2:216156/1‑150 (MQ=255)                                                                       ttGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTg                                                                    <  1:285966/150‑1 (MQ=255)                                                                        tGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATcc                                                                                                                                      <  2:817542/83‑1 (MQ=255)                                                                        tGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATcc                                                                                                                                      >  1:817542/1‑83 (MQ=255)                                                                           cAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGaa                                                                <  1:323497/150‑1 (MQ=255)                                                                                cGGAACACATCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAAtgctg                                                           <  2:611039/150‑1 (MQ=255)                                                                                     cacCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGc                                                                             >  2:1052747/1‑127 (MQ=255)                                                                                     cacCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGc                                                                             <  1:1052747/127‑1 (MQ=255)                                                                                        ctctTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATgg                                                                                                                         <  2:1035796/80‑1 (MQ=255)                                                                                        ctctTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATgg                                                                                                                         >  1:1035796/1‑80 (MQ=255)                                                                                               gTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAGTGCTGCGCCGCAGTTCGCTg                                            >  1:9764/1‑150 (MQ=255)                                                                                                              gCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAATGCTGCGCCGCAGTTCGCTGTCGTAGCGGGCAGTg                             <  1:261105/150‑1 (MQ=255)                                                                                                               cATGAATGACCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAATGCTGCGCCGCAGTTCGCTGTCGTAGCGGGCAGTGa                            >  2:405025/1‑150 (MQ=255)                                                                                                                aTGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAATGCTGCGCCGCAGTTCGCTGTCGTAGCGGGCAGTGAt                           <  1:208076/150‑1 (MQ=255)                                                                                                                 gggaTGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAATGCTGCGCCGCAGTTCGCTGTCGTAGCGGGCAGTGATg                          <  2:197099/147‑1 (MQ=255)                                                                                                                   aaTGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAATGCTGCGCCGCAGTTCGCTGTCGTAGCGGGCAGTGATGTc                        >  1:904090/1‑150 (MQ=255)                                                                                                                    aTGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCAt                                                                                          >  1:957982/1‑83 (MQ=255)                                                                                                                    aTGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCAt                                                                                          <  2:957982/83‑1 (MQ=255)                                                                                                                     tGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAATGCTGCGCCGCAGTTCGCTGTCGTAGCGGGCAGTGATGTCtt                      >  2:200688/1‑150 (MQ=255)                                                                                                                        ccTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAATGCTGCGCCGCAGTTCGCTGTCGTAGCGGGCAGTGATGTCTTCCa                   >  2:920422/1‑150 (MQ=255)                                                                                                                                  cGAAGCATAAGGGCGCAGCAGTTCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAATGCTGCGCCGCAGTTCTCTGGCGTAGCGGGCAGTGATGTCTTCCAGTGGGCGccc         >  1:58228/1‑150 (MQ=255)                                                                                                                                   gAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAATGCTGCGCCGCAGTTCGCTGTCGTAGCGGGCAGTGATGTCTTCCAGTGGGCGcccc        >  1:460446/1‑150 (MQ=255)                                                                                                                                    aaGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAATGCTGCGCCGCAGTTCGCTGTCGTAGCGGGCAGTGATGTCTTCCAGTGGGCGCCCCa       >  2:519836/1‑150 (MQ=255)                                                                                                                                        aTAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAATGCTGCGCCGCAGTTCGCTGTCGTAGCGGGCAGTGATGTCTTCCAGTGGGCGCCCCAGCgg   >  2:1109791/1‑150 (MQ=255)                                                                                                                                         tAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAATGCTGCGCCGCAGTTCGCTGTCGTAGCGGGCAGTGATGTCTTCCAGTGGGCGCCCCAGCGGc  >  1:419524/1‑150 (MQ=255)                                                                                                                                             ggCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAATGCTGCGCCGCAGTTCGCt                                             >  2:1036215/1‑103 (MQ=255)                                                                                                                                             ggCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAATGCTGCGCCGCAGTTCGCt                                             <  1:1036215/103‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                CACTTCACACCCCAGGTGGCAGCCAATCACCTCATCGCCCAGCATGATCAAGTCAAGCCGGCCGACACTCTTGGCAATACGGAACACCTCTTCGGTAGGAAACTGCGCGGCATGAATGCCCTGACGGGCCGAAGCATAAGGGCGCAGCAGATCCCGGTCGGCCATGGCGATTTCTTCGTCCGAAAGGGCTTGGCGCATGTGATAAAGCGGCCGGTTCTTGCGAATGCTGCGCCGCAGTTCGCTGTCGTAGCGGGCAGTGATGTCTTCCAGTGGGCGCCCCAGCGGC  >  NC_002947/3898550‑3898835

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑