Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,570,584	T→A	15.4%	L135Q (CTG→CAG)	treY →	maltooligosyl trehalose synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,570,584	0	T	A	15.4%	65.3 / 4.9	26	L135Q (CTG→CAG)	treY	maltooligosyl trehalose synthase
Reads supporting (aligned to +/- strand):  ref base T (13/9);  new base A (2/2);  total (15/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

CCTCGACACGGTGTCCAACCACATGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGCCCGGTCGATTACGGCTGGATTC  >  NC_002947/4570435‑4570727                                                                                                                                                      |                                                                                                                                                ccTCGACACGGTGTCCAACCACATGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCTACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAActgct                                                                                                                                                 <  1:493253/150‑1 (MQ=255)         cGGTGTCCAACCACATGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACAGCAGTTGcccg                                                                                                                                         <  2:192381/150‑3 (MQ=255)           gtgtCCAACCACATGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCTGGCAACTGCTGTTGCCGTTc                                                                                                                                       <  2:443812/150‑1 (MQ=255)              tCCAACCACATGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTc                                                                                                                                    <  2:105761/150‑1 (MQ=255)                    cacaTGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGc                                                                                                                              <  2:138810/150‑1 (MQ=255)                                                     tggCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCGTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTNCCGNTCCGNGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATa                                                                                             <  1:450440/150‑1 (MQ=255)                                                         aaaGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCAc                                                                                         >  1:233553/1‑150 (MQ=255)                                                            gCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGc                                                                                      >  2:147973/1‑150 (MQ=255)                                                              ctgctgGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAg                                                                                    <  1:147973/150‑1 (MQ=255)                                                                                 gcAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAGTTCGACAAACAGCAGGGgc                                                                 >  1:206674/1‑150 (MQ=255)                                                                                      ccGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAGTTCGACAAACAGCAGGGGctgctg                                                            >  1:25972/1‑150 (MQ=255)                                                                                              agagTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAGTTc                                                                                 <  1:332435/121‑1 (MQ=255)                                                                                              agagTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAGTTc                                                                                 >  2:332435/1‑121 (MQ=255)                                                                                                     ttcGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTTCTCGGCAGCGACTACTGCGTGGCGCTCAGGAATGGCGAGATACCCCTGCAGTTCGACACACAGCAGGGGCTGCTGCAAGTGGCCCATTAc                                             >  1:433423/1‑150 (MQ=255)                                                                                                     ttcGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTAc                                             >  2:171477/1‑150 (MQ=255)                                                                                                                       tCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATc                           <  2:25972/150‑1 (MQ=255)                                                                                                                          aGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGc                        >  1:547255/1‑150 (MQ=255)                                                                                                                          aGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGc                        <  1:171477/150‑1 (MQ=255)                                                                                                                               cccACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGCCCGGt                   >  1:11911/1‑150 (MQ=255)                                                                                                                                  aCTGCGGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGGTCAGGAATGGCGAGATCGGGCGGGATGGCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGGTTCCCGATCTGCCCGGTCGa                >  2:163015/1‑150 (MQ=255)                                                                                                                                      gaggaacggCAACAGCAGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGCCCGGTCGATTAc            >  1:288420/8‑150 (MQ=255)                                                                                                                                           cGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGccc                      <  1:536230/135‑1 (MQ=255)                                                                                                                                           cGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGccc                      >  2:536230/1‑135 (MQ=255)                                                                                                                                           acggCAACAGCAGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCga                                                                                                 <  2:245645/58‑1 (MQ=38)                                                                                                                                           acggCAACAGCAGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCga                                                                                                 >  1:245645/3‑60 (MQ=39)                                                                                                                                                aaCTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGCCCGGTCGATTACGGCTGGATtc  >  2:395209/1‑150 (MQ=255)                                                                                                                                                aaCTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGACCGAAAGATTACGGCTGGtttt  >  2:31536/1‑149 (MQ=255)                                                                                                                                                      |                                                                                                                                                CCTCGACACGGTGTCCAACCACATGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACCACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGCCCGGTCGATTACGGCTGGATTC  >  NC_002947/4570435‑4570727

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: ‑