Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,924,907	T→A	15.4%	*543L (TAA→TTA)	peaA ←	quinohemoprotein amine dehydrogenase subunit alpha

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,924,907	0	T	A	15.4%	98.9 / 10.6	39	*543L (TAA→TTA)	peaA	quinohemoprotein amine dehydrogenase subunit alpha
Reads supporting (aligned to +/- strand):  ref base T (18/15);  new base A (2/4);  total (20/19)
Fisher's exact test for biased strand distribution p-value = 4.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.43e-01

AGCGAACTGCTGGGGATATGGAACAGCATGCGGTCGGCATCAACCTGTACTTCGTGCAGGTTGCGTTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGTGGCGATGACCTTCAGGTTACCGGCGTTGTTGGTCATCATCTTGCGCTCAGGGTTGGGCCCGG  >  NC_002947/3924766‑3925048                                                                                                                                              |                                                                                                                                              aGCGAACTGCTGGGGATATGGAACAGCATGCGGTCGGCATCAACCTGTACTTCGTGCAGGTTGCGTTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAgc                                                                                                                                       >  1:658155/1‑150 (MQ=255)   cGAACTGCTGGGGATATGGAACAGCATGCGGTCGGCATCAACCTGTACTTCGTGCAGGTTGCGCTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTAACGGCAggct                                                                                                                                     <  1:77554/150‑4 (MQ=255)                 tatGGAACAGCATGCGGTCGGCATCAACCTGTACTTCGTGCAGGTTGCGTTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAgc                                                                                                                       >  2:339018/1‑150 (MQ=255)                     gAACAGCATGCGGTCGGCATCAACCTGTACTTCGTGCAGGTTGCGTTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTg                                                                                                                   <  2:694899/150‑1 (MQ=255)                            aTGCGGTCGGCATCAACCTGTACTTCGTGCAGGTTGCGTTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTg                                                                                                            <  2:985059/150‑1 (MQ=255)                              gCGGTCGGCATCAACCTGTACTTCGTGCAGGTTGCGTTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGAc                                                                                                          <  1:458767/150‑1 (MQ=255)                                ggTCGGCATCAACCTGTACTTCGTGCAGGTTGCGTTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGa                                                                                                        >  2:997409/1‑150 (MQ=255)                                      cATCAACCTGTACTTCGTGCAGGTTGCGTTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCAtgt                                                                                                  <  1:339018/150‑1 (MQ=255)                                       aTCAACCTGTACTTCGTGCAGGTTGCGTTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCAtgtg                                                                                                 >  1:233761/1‑150 (MQ=255)                                        tCAACCTGTACTTCGTGCAGGTTGCGTTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGc                                                                                                <  2:233761/150‑1 (MQ=255)                                         cAATCTTTACTTCGTGCAGGTTTCGTTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGcc                                                                                               <  2:433841/150‑1 (MQ=255)                                                  cTTCGTGCAGGTTGCGTTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTAGCCgg                                                                                      >  1:423437/1‑150 (MQ=255)                                                          aGGTTGCGTTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCa                                                                              >  1:525867/1‑150 (MQ=255)                                                           ggTTGCGTTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCAc                                                                             <  2:1064285/150‑1 (MQ=255)                                                                cGTTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCg                                                                        <  2:407911/150‑1 (MQ=255)                                                                     gACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGc                                                                                                >  1:89139/1‑121 (MQ=255)                                                                     gACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGCTGTTCCAGCGCTGTACGGTGACGATCATGTGc                                                                                                <  2:89139/121‑1 (MQ=255)                                                                      aCCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGc                                                                  >  2:243303/1‑150 (MQ=255)                                                                       ccAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTAACGGCAgg                                                                                                                                       <  1:695757/80‑2 (MQ=255)                                                                       ccAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAAGCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTAACGGCAgg                                                                                                                                       >  2:695757/1‑79 (MQ=255)                                                                        cAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGt                                                                >  2:824976/1‑150 (MQ=255)                                                                        cAGGTTCAGTAGTACGCCCATGGCAACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTCGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGt                                                                >  2:246531/1‑150 (MQ=255)                                                                          ggTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGTgg                                                              <  2:326277/150‑1 (MQ=255)                                                                                gtagtaCGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTGCGCCGGTGTGTTCATCTTCGGCCAGCGTGGCGATGa                                                        >  2:498671/1‑150 (MQ=255)                                                                                     aCGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGTGGCGATGACCTTc                                                   >  1:476519/1‑150 (MQ=255)                                                                                     aCGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGTGGCGATGACCTTc                                                   <  2:658155/150‑1 (MQ=255)                                                                                      cGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGTGGCGATGACCTTCa                                                  <  2:476519/150‑1 (MQ=255)                                                                                         ccATGGCGACCTCCCGATAATCGATCCGTTGGACAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCGGCGCTGTCCGGTCACGATCATGTGCCCTTCGCCGGTGTGGCCACCGTCGTCCAGCGTGGCGATGACCTTCAGGt                                               >  2:461724/1‑150 (MQ=255)                                                                                           aTGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGTGGCGATGACCTTCAGGTTa                                             <  1:498671/150‑1 (MQ=255)                                                                                              gCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCTTCGGCCAGCGTGGCGATGACCTTCAGGTTACCg                                          <  1:400655/150‑1 (MQ=255)                                                                                                gACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGTGGCGATGACCTTCAGGTTACCGGc                                        >  1:987723/1‑150 (MQ=255)                                                                                                      ccGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGTGGCGATGACCTTCAGGTTACCGGCgttgtt                                  >  1:970439/1‑150 (MQ=255)                                                                                                       cGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGTGGCGATGACCTTCAGGTTACCGGCGttgttg                                 >  2:1038960/1‑150 (MQ=255)                                                                                                               gATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGTGGCGATGACCTTCAGGTTACCGGCGTTGTTGGTcatcat                         >  1:518281/1‑150 (MQ=255)                                                                                                                         aaaaCCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGTGGCGATGACCTTCAGGTTACCGGCGTTGTTGGTCATCATCTTGCGCTCa               <  1:243303/150‑1 (MQ=255)                                                                                                                                   gccgcTGCCGTAACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGTGGCGAt                                                          <  2:515111/93‑1 (MQ=255)                                                                                                                                   gccgcTGCCGTAACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGTGGCGAt                                                          >  1:515111/5‑97 (MQ=255)                                                                                                                                    aGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGTGGCGATGACCTTCAGGTTACCGGCGTTGTTGGTCATCATCTTGCGCTCAGGGTTGGGccc    >  2:368922/1‑150 (MQ=255)                                                                                                                                      ccTGCCGTAACGGCAGCGGCGGGTTGTTCCAGCTGTGTGCGGTGACGATCATGTGCCTTTCGCCGGTCTGGCCACCGTCGGCCAGCGTGGCGATGACCTTCAGGTTACCGGCGTTGTTGGTCATCATCTTGCGCTCAGGGTTGGGCCCgg  <  2:518281/150‑1 (MQ=255)                                                                                                                                              |                                                                                                                                              AGCGAACTGCTGGGGATATGGAACAGCATGCGGTCGGCATCAACCTGTACTTCGTGCAGGTTGCGTTCGACCAGGTTCAGTAGTACGCCCATGGCGACCTCCCGATAATCGATCCGTTGGAAAACCGTTGCAGCCTGCCGTTACGGCAGCGGCGGGTTGTTCCAGCGCTGTACGGTGACGATCATGTGCCCTTCGCCGGTCTGGCCACCGTCGGCCAGCGTGGCGATGACCTTCAGGTTACCGGCGTTGTTGGTCATCATCTTGCGCTCAGGGTTGGGCCCGG  >  NC_002947/3924766‑3925048

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: ‑