Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,570,540	T→A	9.6%	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	4,570,540	0	T	A	9.6%	148.8 / 5.9	52	L135Q (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 = 9.84e-01

ACACGGTGTCCAACCACATGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGCCCGGTCGATTACGGCTGGATTCTC  >  NC_002947/4570396‑4570685                                                                                                                                                 |                                                                                                                                                   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                                                                                                                                     <  8:334069/143‑1 (MQ=255)                  aTGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCgg                                                                                                                                     >  7:334069/1‑143 (MQ=255)                            gCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTg                                                                                                                     <  7:52980/149‑1 (MQ=255)                            gCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTg                                                                                                                     <  3:342655/149‑1 (MQ=255)                                          cccTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATgg                                                                                                       >  5:618/1‑149 (MQ=255)                                          cccTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATgg                                                                                                       >  3:2556/1‑149 (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                                                                                                                                                 <  8:199641/84‑1 (MQ=255)                                                                 cTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGtt                                                                                                                                                 >  7:199641/1‑84 (MQ=255)                                                                 cTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACa                                                                               <  2:106881/149‑1 (MQ=255)                                                                    gggACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACAGCAGTTGcccg                                                                                                                                            <  8:48801/86‑3 (MQ=255)                                                                        cGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTg                                                                                         <  4:298053/132‑1 (MQ=255)                                                                        cGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTg                                                                                         >  3:298053/1‑132 (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                                                           <  4:2556/148‑1 (MQ=255)                                                                                      tGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCaa                                                           <  4:131888/148‑1 (MQ=255)                                                                                        cAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CAc                                                                                           >  5:62337/1‑114 (MQ=255)                                                                                        cAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CAc                                                                                           <  6:62337/114‑1 (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                                             >  6:156239/1‑130 (MQ=255)                                                                                                                      gCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTAcgc                                             <  5:156239/130‑1 (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)                                                                                                                                                ctgTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGCCCGGTCGATTACGGCTGGATtctc  <  4:92968/147‑1 (MQ=255)                                                                                                                                                 tgTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGcc                         <  4:333141/123‑1 (MQ=255)                                                                                                                                                 tgTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGcc                         >  3:333141/1‑123 (MQ=255)                                                                                                                                                 |                                                                                                                                                   ACACGGTGTCCAACCACATGGCCGTAGGCGGTGCCGACAACCCCTGGTGGCAAAGCCTGCTGGCCTGGGGACGGCGCAGTCCGTATGCAGAGTTCTTCGACATCCAGTGGCACTCCAGCGACCCACTGCTGGCCGGGCAACTGCTGTTGCCGTTCCTCGGCAGCGACTACGGCGTGGCGCTCAGGAATGGCGAGATAC‑CACTGCAGTTCGACAAACAGCAGGGGCTGCTGCAAGTGGCCCATTACGCGCATCGTTTCCCGATCTGCCCGGTCGATTACGGCTGGATTCTC  >  NC_002947/4570396‑4570685

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: ‑