Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,929,212	T→C	8.3%	*1630W (TGA→TGG)	PP_2566 ←	leucine‑rich repeat‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,929,212	0	T	C	8.3%	125.7 / 2.5	48	*1630W (TGA→TGG)	PP_2566	leucine‑rich repeat‑containing protein
Reads supporting (aligned to +/- strand):  ref base T (22/22);  new base C (2/2);  total (24/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.76e-01

CTACGTGGCGGTGACCCGTGCAGTACAGCACTGCTATTGGCACGTGGAGGCCGCCAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGATACTGCTGCTCGTTGAGCACTACGCGACGTAGCCTGCCGTCAGCATC  >  NC_002947/2929067‑2929355                                                                                                                                                  |                                                                                                                                                  cTACGTGGCGGTGACCCGTGCAGTACAGCACTGCTATTGGCACGTGGAGGCCGCCAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAg                                                                                                                                                <  8:4198/149‑1 (MQ=255)   aCGTGGCGGTGACCCGTGCAGTACAGCACTGCTATTGGCACGTGGAGGCCGCCAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCg                                                                                                                                              >  5:102551/1‑149 (MQ=255)     gTGGCGGTGACCCGTGCAGTACAGCACTGCTATTGGCACGTGGAGGCCGCCAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGc                                                                                                                                            <  5:258249/149‑1 (MQ=255)        gCGGTGACCCGTGCAGTACAGCACTGCTATTGGCACGTGGAGGCCGCCAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCg                                                                                                                                          <  5:158343/148‑1 (MQ=255)        gCGGTGACCCGTGCAGTACAGCACTGCTATTGGCACGTGGAGGCCGCCAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGa                                                                                                                                         >  2:39984/1‑149 (MQ=255)                ccGTGCAGTACAGCACTGCTATTGGCACGTGGAGGCCGCCAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGACAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGc                                                                                                                                 >  4:174968/1‑149 (MQ=255)                      aGTACAGCACTGCTATTGGCACGTGGAGGCCGCCAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGT‑‑GTCTgg                                                                                                                         >  5:222454/1‑149 (MQ=255)                        tACAGCACTGCTATTGGCACGTGGAGGCCGCCAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCg                                                                                                                       >  5:299210/1‑149 (MQ=255)                           aGCACTGCTATTGGCACGTGGAGGCCGCCAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGt                                                                                                                    >  1:53594/1‑149 (MQ=255)                               cTGCTATTGGCACGTGGAGGCCGCCAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAgg                                                                                                                <  3:170588/149‑1 (MQ=255)                                          aCGTGGAGGCCGCCAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATcag                                                                                                        >  8:221570/1‑146 (MQ=255)                                                    cgccAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTc                                                                                            >  4:58151/1‑148 (MQ=255)                                                     gccAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGACAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCaa                                                                                          <  3:174968/149‑1 (MQ=255)                                                      ccAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAAc                                                                                         <  2:176558/149‑1 (MQ=255)                                                      ccAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAAc                                                                                         <  2:240613/149‑1 (MQ=255)                                                       cAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAAcc                                                                                        >  6:57296/1‑149 (MQ=255)                                                          tGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACctgc                                                                                     <  6:299210/149‑1 (MQ=255)                                                                  ccgcAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTc                                                                             <  3:258376/149‑1 (MQ=255)                                                                      aGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCa                                                                         <  7:221570/149‑1 (MQ=255)                                                                      aGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCa                                                                         <  5:57296/149‑1 (MQ=255)                                                                                   gCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCaa                                                            >  3:9987/1‑149 (MQ=255)                                                                                        cAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTc                                                                             >  6:52090/1‑127 (MQ=255)                                                                                        cAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTc                                                                             <  5:52090/127‑1 (MQ=255)                                                                                        cAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGccc                                                       <  3:55830/149‑1 (MQ=255)                                                                                        cAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGccc                                                       >  2:203121/1‑149 (MQ=255)                                                                                         aGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGCCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCt                                                      >  2:162250/1‑149 (MQ=255)                                                                                         aGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGCCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCt                                                      >  2:157345/1‑149 (MQ=255)                                                                                            cACGTGGACGGCAATCAGGACTTCTTCGAAGACCTGCTCGGGCAGTGAGTTGTGTCAGCTGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGc                                                   <  6:261802/149‑1 (MQ=255)                                                                                            cACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCCGTCAGCGCGTCAACGCCCTGGc                                                   <  7:49538/149‑1 (MQ=255)                                                                                            cACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGCCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGc                                                   <  1:162250/149‑1 (MQ=255)                                                                                            cACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGCCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGc                                                   <  1:157345/149‑1 (MQ=255)                                                                                             aCGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGc                                                   >  6:284297/1‑148 (MQ=255)                                                                                              cGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGa                                                 <  2:80852/149‑1 (MQ=255)                                                                                                tGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGATa                                               <  6:102551/149‑1 (MQ=255)                                                                                                  gACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGCGTGTGTGGCGGGTGAGGCTGATAAGCAGACCGGTTTAAAACATCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGATa                                               >  1:264776/1‑149 (MQ=255)                                                                                                   aCGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGATActg                                            <  4:9987/149‑1 (MQ=255)                                                                                                    cGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGATActgc                                           >  5:115468/1‑149 (MQ=255)                                                                                                      gCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGATActgctg                                         <  5:8348/149‑1 (MQ=255)                                                                                                         aGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGATACTGCTGCTc                                      >  3:24409/1‑149 (MQ=255)                                                                                                           cAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGATACTGCTGCTCGt                                    <  1:203121/149‑1 (MQ=255)                                                                                                            aGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGATACTGCTGCTCGtt                                   >  6:321033/1‑149 (MQ=255)                                                                                                              gCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGAACGGTTTAAACCTGCTGCTGCTCGTCAGTAAGCGCGTAAACGCCCTgc                                                    >  1:99003/1‑129 (MQ=255)                                                                                                                    ttcGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGATACTGCTGCTCGTTGAGCACTa                           >  3:219834/1‑149 (MQ=255)                                                                                                                         aGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGATACTGCTGCTCGTTGAGCACTACGCGa                      >  3:110703/1‑149 (MQ=255)                                                                                                                             cTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTGCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGATACTGCTGCTCGTTGAGCACTACGCGACGTa                  <  1:39984/149‑1 (MQ=255)                                                                                                                                cgcgGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGATACTGCTGCTCGTTGAGCACTACGCGACGTAg                 <  2:53594/147‑1 (MQ=255)                                                                                                                                    ggCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGATACTGCTGCTCGTTGAGCACTACGCGACGTAGCCTGcc           >  3:286581/1‑149 (MQ=255)                                                                                                                                              ggggTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGATACTGCTGCTCGTTGAGCACTACGCGACGTAGCCTGCCGTCAGCATc  >  7:254981/1‑148 (MQ=255)                                                                                                                                                  |                                                                                                                                                  CTACGTGGCGGTGACCCGTGCAGTACAGCACTGCTATTGGCACGTGGAGGCCGCCAATGGTGACGCCGCAGCGGCCCCACGGGCGTCCAGCCACGTGGACGGCAAGCAGGCCTTCTTCGAAGACCTGCGCGGGCAGTGAGTGGGGTCAGCGGCCGATTGTTTGC‑‑GTCTGGCGGGTGAGGCTGATCAGCAGACCGGTTTCAACCTGCTGCTGCTCGGCAGTCAGCGCGTCAACGCCCTGGCGATACTGCTGCTCGTTGAGCACTACGCGACGTAGCCTGCCGTCAGCATC  >  NC_002947/2929067‑2929355

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: ‑