Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,768,318	C→A	11.3%	P97Q (CCG→CAG)	PP_5600 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,768,318	0	C	A	11.3%	148.0 / 6.5	53	P97Q (CCG→CAG)	PP_5600	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (24/23);  new base A (3/3);  total (27/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.87e-01

CACGGCCGACAGCAGCGGCATGGTCCAAGGTGAGCAAGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTCCCCGTGCCGCCTGATCGGCAGCGGGCGT  >  NC_002947/3768169‑3768458                                                                                                                                                      |                                                                                                                                              cACGGCCGACAGCAGCGGCATGGTCCAAGGTGAGCAAGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGcc                                                                                                                                               <  1:1059900/150‑1 (MQ=255)   cgcccGACACCCGCTGCATGGTCCAAGGTTCGCAATATTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCTAGCCTGTTCATCGCCACACTGCTTGCCCTCTTTTTCGGCCTGCTGACCCTTCCCGCCGTCGAGCCgg                                                                                                                                             <  2:423370/147‑1 (MQ=255)        gACAGCAGCGGCATGGTCCAAGGTGAGCAAGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCGGCTCGCCGGCGAGCAgggtcag                                                                                                                                        <  2:1175124/150‑5 (MQ=255)         ccagcagCGGCATGGTCCACGGTGAGCAAGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGcc                                                                                                                                      >  2:1087097/2‑150 (MQ=255)              agcGGCATGGTCCAAGGTGAGCAAGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTa                                                                                                                                 >  1:1223901/1‑150 (MQ=255)                cGGCATGGTCCAAGGTGAGCAAGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTAcc                                                                                                                               <  2:1079767/150‑1 (MQ=255)                           aaGGTGAGCAAGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGc                                                                                                                                       >  2:569642/1‑131 (MQ=255)                           aaGGTGAGCAAGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGc                                                                                                                                       <  1:569642/131‑1 (MQ=255)                              gTGAGCAAGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTCCTGACCCTGCTCTCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGc                                                                                                                 <  1:81391/150‑1 (MQ=255)                                  gCAAGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACg                                                                                                             >  1:5057/1‑150 (MQ=255)                                   cAAGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGc                                                                                                            >  2:638968/1‑150 (MQ=255)                                   cAAGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGc                                                                                                            >  1:660513/1‑150 (MQ=255)                                         ttCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGccc                                                                                                      >  2:30271/1‑150 (MQ=255)                                          tCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCAgg                                                                                                                                             <  2:182861/111‑1 (MQ=255)                                          tCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGAGGCCCTGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCa                                                                                                     >  1:306434/1‑150 (MQ=255)                                           cAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCaa                                                                                                    <  1:661148/150‑1 (MQ=255)                                            aGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTcc                                                                                                                   <  1:215984/134‑1 (MQ=255)                                            aGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTcc                                                                                                                   >  2:215984/1‑134 (MQ=255)                                            aGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAag                                                                                                   >  2:1212792/1‑150 (MQ=255)                                            aGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAag                                                                                                   <  2:1108982/150‑1 (MQ=255)                                                       ccTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCcaaccaac                                                                                                                       >  2:411923/1‑119 (MQ=255)                                                       ccTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCcaaccaac                                                                                                                       <  1:411923/119‑1 (MQ=255)                                                        cTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCa                                                                                       >  1:1189691/1‑150 (MQ=255)                                                           tCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTg                                                                                    <  2:1332226/150‑1 (MQ=255)                                                             tGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGt                                                                                  <  1:1180386/150‑1 (MQ=255)                                                                     gTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGc                                                                                                                 >  1:453945/1‑111 (MQ=255)                                                                     gTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGc                                                                                                                 <  2:453945/111‑1 (MQ=255)                                                                                aTCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTccc                                                               >  2:1121320/1‑150 (MQ=255)                                                                                   gCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCcgct                                                            >  2:987274/1‑150 (MQ=255)                                                                                    ccAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTTGTCAATCCCCGCGCCTCTCCcgctt                                                           <  1:1406954/150‑1 (MQ=255)                                                                                    ccAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCcgctt                                                           >  2:110180/1‑150 (MQ=255)                                                                                       gCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCGACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCcccttcgc                                                        <  1:702806/150‑1 (MQ=255)                                                                                          tGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCgcttcgcttc                                                     >  1:478612/1‑150 (MQ=255)                                                                                           gTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTtct                                                    >  1:446460/1‑150 (MQ=255)                                                                                            ttCAGCGCCACACTGCTGGCCGTCTTTCTCGCCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCCATCCCCGCGCCTCTCCCGCTTCGCTtctc                                                   <  2:34147/150‑1 (MQ=255)                                                                                            ttCAGCGCCACACTGCTGGCCGTCGTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTtctc                                                   <  2:643850/150‑1 (MQ=255)                                                                                                gcgcCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGt                                               <  1:694942/150‑1 (MQ=255)                                                                                                      cacTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTccc                                                               <  2:1068589/128‑1 (MQ=255)                                                                                                      cacTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTccc                                                               >  1:1068589/1‑128 (MQ=255)                                                                                                           ctgGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTtctc                                                   <  2:1058707/135‑1 (MQ=255)                                                                                                           ctgGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTtctc                                                   >  1:1058707/1‑135 (MQ=255)                                                                                                              gCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGGAACTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCAc                                 >  1:435311/1‑150 (MQ=255)                                                                                                                 gTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTc                              >  1:217612/1‑150 (MQ=255)                                                                                                                    tttttCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTtctc                                                   <  1:1098546/126‑1 (MQ=255)                                                                                                                    tttttCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTtctc                                                   >  2:1098546/1‑126 (MQ=255)                                                                                                                           gCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCTCTTCTCGCGTTCTGACATCGCCACGTCCCCGTgccgc                    <  2:1189691/150‑1 (MQ=255)                                                                                                                              tgctgACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTGTGACATCGCCACGTCCCCGTGCCGCCTg                 >  1:489/1‑150 (MQ=255)                                                                                                                                  tgcccGGCTCGCCGGCGAGCAGGG‑TAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTCCCCGTGCCGCCTGATCg             >  2:1370109/3‑150 (MQ=255)                                                                                                                                   aCCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCTCGCCTGCCCAAGCAGCGCTGGCCACGGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTCCCCGTGCCGCCTGATCgg            <  1:1087097/150‑1 (MQ=255)                                                                                                                                     ccggCTCGCCGGCGAGCAGGGTCAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTCCCCGTGCCGCCTGATCggg           >  1:417571/4‑149 (MQ=255)                                                                                                                                      cggCTCGCCGGCGAGCAGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTCCCCGTgccgc                    >  1:502980/3‑139 (MQ=255)                                                                                                                                      cggCTCGCCGGCGAGCAGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTCCCCGTgccgc                    <  2:502980/137‑1 (MQ=255)                                                                                                                                             ccGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTCCCCGTGCCGCCTGATCGGCAGCGGGCgt  <  2:5057/150‑1 (MQ=255)                                                                                                                                             ccGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCCGACATCGCCACGTCCCCGTGCCGCCTGATCGGCAGCGGGCgt  <  1:110180/150‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                              CACGGCCGACAGCAGCGGCATGGTCCAAGGTGAGCAAGACTTCAGCGATCCGACCCTGTCTGCCGGCGGTGACTGCGTGATCGCCAGCCTGTTCAGCGCCACACTGCTGGCCGTCTTTTTCGGCCTGCTGACCCTGCTCGCCGGCGAGCCGGG‑CAGCCCCTTACCCAACCAACCTCCGCCACGCCTGCCCAAGCAGCGCTGGCCACTGGTCAATCCCCGCGCCTCTCCCGCTTCGCTTCTCGCGTTCTGACATCGCCACGTCCCCGTGCCGCCTGATCGGCAGCGGGCGT  >  NC_002947/3768169‑3768458

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑