Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,570,537	T→A	9.5%	L134Q (CTG→CAG)	treY →	maltooligosyl trehalose synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,570,537	0	T	A	9.5%	149.2 / 4.4	52	L134Q (CTG→CAG)	treY	maltooligosyl trehalose synthase
Reads supporting (aligned to +/- strand):  ref base T (24/23);  new base A (2/3);  total (26/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACACGGTGTCCAACCACATGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGCCCGGTCGATTACGGCTGGA  >  NC_002947/4570396‑4570680                                                                                                                                              |                                                                                                                                                 acacGGTGTCCAACCACATGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTg                                                                                                                                           >  2:39525/1‑149 (MQ=255)       tgtCCAACCACATGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACAGCAGTTGcccggc                                                                                                                                     <  4:67762/149‑5 (MQ=255)           cAACCACATGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCg                                                                                                                                 >  8:52980/1‑149 (MQ=255)           cAACCACATGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCg                                                                                                                                 <  6:155048/149‑1 (MQ=255)            aaCCACATGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCgg                                                                                                                                <  7:35463/149‑1 (MQ=255)                  aTGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCgg                                                                                                                                >  7:334069/1‑143 (MQ=255)                  aTGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCgg                                                                                                                                <  8:334069/143‑1 (MQ=255)                            gCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTg                                                                                                                <  7:52980/149‑1 (MQ=255)                            gCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTg                                                                                                                <  3:342655/149‑1 (MQ=255)                                          cccTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATgg                                                                                                  >  3:2556/1‑149 (MQ=255)                                          cccTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATgg                                                                                                  >  5:618/1‑149 (MQ=255)                                           ccTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGc                                                                                                 <  2:277100/149‑1 (MQ=255)                                           ccTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGc                                                                                                 <  8:191170/149‑1 (MQ=255)                                            cTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGc                                                                                                 >  3:131888/1‑148 (MQ=255)                                                      aGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACt                                                                                     >  3:92968/1‑149 (MQ=255)                                                          tgctgGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAg                                                                                 >  7:220615/1‑149 (MQ=255)                                                                 cTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGtt                                                                                                                                            >  7:199641/1‑84 (MQ=255)                                                                 cTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGtt                                                                                                                                            <  8:199641/84‑1 (MQ=255)                                                                 cTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACa                                                                          <  2:106881/149‑1 (MQ=255)                                                                    gggACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACAGCAGTTGcccg                                                                                                                                       <  8:48801/86‑3 (MQ=255)                                                                        cGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTg                                                                                    >  3:298053/1‑132 (MQ=255)                                                                        cGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTg                                                                                    <  4:298053/132‑1 (MQ=255)                                                                         ggCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAAcagcag                                                                  <  6:97783/149‑1 (MQ=255)                                                                          gcgcAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAgg                                                                 >  5:71635/1‑149 (MQ=255)                                                                                  cGTATGCAGAGTTCTTAGACATCCAGTGGCACTACAGCGACCAAATGCTGGCCGGGCAACTGCTGTTGCAGTTCCTAGGCAGCGACTACTGCGTGGCGCTCAGGAAGGGCGAGATAC‑CACTGCAGATCGACAAACAGCAGGCGcagctg                                                         >  8:337640/1‑149 (MQ=255)                                                                                      tGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCaa                                                      <  4:131888/148‑1 (MQ=255)                                                                                      tGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCaa                                                      <  4:2556/148‑1 (MQ=255)                                                                                        cAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CAc                                                                                      <  6:62337/114‑1 (MQ=255)                                                                                        cAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CAc                                                                                      >  5:62337/1‑114 (MQ=255)                                                                                           agTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTCGcc                                                >  8:228322/1‑149 (MQ=255)                                                                                                ttcGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCtgctgc                                                        >  7:115751/1‑136 (MQ=255)                                                                                                ttcGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCtgctgc                                                        <  8:115751/136‑1 (MQ=255)                                                                                                ttcGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTa                                           >  7:215285/1‑149 (MQ=255)                                                                                                  cGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGTGGCTGCTGCAAGTGGCCCATTa                                           <  8:220615/147‑1 (MQ=255)                                                                                                  cGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCAtt                                            <  1:39525/146‑1 (MQ=255)                                                                                                        ccAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTACAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATc                                   >  5:286823/1‑149 (MQ=255)                                                                                                         cAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCg                                  <  7:337640/149‑1 (MQ=255)                                                                                                            tGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGttt                               <  6:618/149‑1 (MQ=255)                                                                                                                aCTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTccc                            >  2:191741/1‑148 (MQ=255)                                                                                                                    cAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCt                       >  2:339009/1‑149 (MQ=255)                                                                                                                      gCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTAcgc                                        <  5:156239/130‑1 (MQ=255)                                                                                                                      gCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTAcgc                                        >  6:156239/1‑130 (MQ=255)                                                                                                                           ccACTGCTGGCCGGGCAACTGCTGTTGCCGTTGCTCGGCAGCGTCTTCGGCGTGGCGCTCAGGAATGGCGAGATAG‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACTCGCATCGTTTCCCGATCTGCCCg                  <  8:247425/147‑1 (MQ=255)                                                                                                                           ccACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGCCCGGt                >  1:231460/1‑149 (MQ=255)                                                                                                                           ccACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGCCCGGt                <  6:71635/149‑1 (MQ=255)                                                                                                                           ccACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGACATAC‑GACTGCAGATCGACAAACAGCAGGGGCTGCTGCAAGAGGCCCATTACGCGCATCGATTCCCGATCTGCCCg                  >  7:247425/1‑147 (MQ=255)                                                                                                                             aCTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGCCCGGTc               >  8:117111/1‑148 (MQ=255)                                                                                                                                      cGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAgg                                                                 >  4:85728/1‑89 (MQ=255)                                                                                                                                      cGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAgg                                                                 <  3:85728/89‑1 (MQ=255)                                                                                                                                      acggCAACAGCAGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATACGGACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGCCCGGTCGATTACGGc      >  1:107139/3‑149 (MQ=255)                                                                                                                                      acggCAACAGCAGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGCCCGGTCGATTACGGCt     >  8:98129/3‑149 (MQ=255)                                                                                                                                         gCAACAGCAGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGCCCGGTCGATTACGGCTGGa  <  7:98129/149‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                 ACACGGTGTCCAACCACATGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGCCCGGTCGATTACGGCTGGA  >  NC_002947/4570396‑4570680

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑