Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 2,931,907 T→A 8.7% N732I (AAT→ATT)  PP_2566 ← leucine‑rich repeat‑containing protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029472,931,9070TA 8.7% 126.9 / 3.4 46N732I (AAT→ATT) PP_2566leucine‑rich repeat‑containing protein
Reads supporting (aligned to +/- strand):  ref base T (23/19);  new base A (2/2);  total (25/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.67e-01

GAACAGCGCCTCGCGATGCTGTTCCAGGTGTTGCGCGAGTTTGTTGTTCAGTGCGGACGCTCGGTGCTCGGTTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTCCCCTCGGGCCACCCCGGCAGGCGCAGCAACTCA  >  NC_002947/2931762‑2932053
                                                                                                                                                 |                                                                                                                                                  
gAACAGCGCCTCGCGATGCTGTTCCAGGTGTTGCGCGAGTTTGTTGTTCAGTGCGGACGCTCGGTGCTCGGTTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCAtt                                                                                                                                                   <  4:241905/147‑1 (MQ=255)
gAACAGCGCCTCGCGATGCTGTTCCAGGTGTTGCGCGAGTTTGTTGTTCAGTGCGGACGCTCGGTGCTCGGTTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCAtt                                                                                                                                                   >  3:241905/1‑147 (MQ=255)
              gATGCTGTTCCAGGTGTTGCGCGAGTTTGTTGTTCAGTGCGGACGCTCGGTGCTCGGTTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCAtt                                                                                                                                                   >  4:105022/1‑133 (MQ=255)
              gATGCTGTTCCAGGTGTTGCGCGAGTTTGTTGTTCAGTGCGGACGCTCGGTGCTCGGTTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCAtt                                                                                                                                                   <  3:105022/133‑1 (MQ=255)
                       ccAGGTGTTGCGCGAGTTTGTTGTTCAGTGCGGACGCTCGGTGCTCGGTTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTc                                                                                                                           >  6:3361/1‑148 (MQ=255)
                              ttGCGCGAGTTTGTTGTTCAGTGCGGACGCTCGGTGCTCGGTTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTtct                                                                                                                    <  8:71381/148‑1 (MQ=255)
                                 cgcgAGTTTGTTGTTCAGTGCGGACGCTCGGTGCTCGGTTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTtctgtct                                                                                                                >  4:327633/1‑149 (MQ=255)
                                 cgcgAGTTTGTTGTTCAGTGCGGACGCTCGGTGCTCGGTTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTtctgtct                                                                                                                >  6:249158/1‑149 (MQ=255)
                                  gcgAGTTTGTTGTTCAGTGCGGACGCTCGGTGCTCGGTTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCAAGGTCGGTACGGGAAATTTCGATTtctgtctg                                                                                                               >  6:46271/1‑149 (MQ=255)
                                    gAGTTTGTTGTTCAGTGCGGACGCTCGGTGCTCGGTTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGc                                                                                                             <  5:249158/149‑1 (MQ=255)
                                    gAGTTTGTTGTTCAGTGCGGACGCTCGGTGCTCGGTTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGc                                                                                                             <  3:327633/149‑1 (MQ=255)
                                             gttCAGTGCGGACGCTCGGTGCTCGGTTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCgtgt                                                                                                    >  6:214233/1‑149 (MQ=255)
                                              ttCAGTGCGGACGCTCGGTGCTCGGTTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCgtgt                                                                                                    >  3:148603/1‑148 (MQ=255)
                                                 aGTGCGGACGCTCGGTGCTCGGTTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAg                                                                                                 <  4:148603/148‑1 (MQ=255)
                                                   tGCGGACGCTCGGTGCTCGGTTGGTGTCTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCGAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGTGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAgggg                                                                                              <  5:46271/149‑1 (MQ=255)
                                                                     ggtTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAggg                                                                                               >  3:117779/1‑130 (MQ=255)
                                                                     ggtTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAggg                                                                                               <  4:117779/130‑1 (MQ=255)
                                                                      gtTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCAc                                                                                 >  1:10957/1‑143 (MQ=255)
                                                                      gtTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCAc                                                                                 <  2:10957/143‑1 (MQ=255)
                                                                                cACCGAGCAACAGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGt                                                                 <  7:142853/149‑1 (MQ=255)
                                                                                 aCCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGtt                                                                >  2:177737/1‑149 (MQ=255)
                                                                                             cTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTg                                                      <  1:177737/147‑1 (MQ=255)
                                                                                              tCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGt                                                    >  7:112478/1‑148 (MQ=255)
                                                                                                aaTGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCACGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCAAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTaaa                                                 >  7:111804/1‑149 (MQ=255)
                                                                                                 aTGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTg                                                      <  7:138305/143‑1 (MQ=255)
                                                                                                 aTGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTg                                                      >  8:138305/1‑143 (MQ=255)
                                                                                                      ttcttcATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCtt                                             >  5:92571/1‑147 (MQ=255)
                                                                                                         ttcATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCCGGCCCTTg                                                      <  1:84522/135‑1 (MQ=255)
                                                                                                         ttcATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCACAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCCGGCCCTTg                                                      >  2:84522/1‑135 (MQ=255)
                                                                                                              ccatcTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAACCCTTCAGCACGTTc                                   >  4:222997/1‑149 (MQ=255)
                                                                                                               catcTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTc                                   <  8:112478/148‑1 (MQ=255)
                                                                                                               catcTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTc                                   <  5:214233/148‑1 (MQ=255)
                                                                                                                atcTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTgg                                                            >  3:105501/1‑122 (MQ=255)
                                                                                                                atcTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTgg                                                            <  4:105501/122‑1 (MQ=255)
                                                                                                                       ccAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTATCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTCCCCTCGGGc                          >  4:300982/1‑149 (MQ=255)
                                                                                                                        cAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTCCCCTCGGGc                          <  5:3361/148‑1 (MQ=255)
                                                                                                                         aGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTCCCCTCGGGCCa                        >  6:165452/1‑149 (MQ=255)
                                                                                                                         aGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTCCCCTCGGGCCa                        >  6:79915/1‑149 (MQ=255)
                                                                                                                            aCGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTCCCCTCGGGCCAccc                     >  8:40562/1‑149 (MQ=255)
                                                                                                                                      tCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTCCCCTCGGGCCACCCCgg                  >  6:295510/1‑142 (MQ=255)
                                                                                                                                      tCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTCCCCTCGGGCCACCCCgg                  <  5:295510/142‑1 (MQ=255)
                                                                                                                                       gaccTGGACAATGGCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTc                                   <  4:144111/121‑1 (MQ=255)
                                                                                                                                       gaccTGGACAATGGCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTc                                   >  3:144111/4‑124 (MQ=255)
                                                                                                                                       gaccTGGACAATGGCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTCCCCTCGGGCCa                        >  1:54106/4‑135 (MQ=255)
                                                                                                                                       gaccTGGACAATGGCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTCCCCTCGGGCCa                        <  2:54106/132‑1 (MQ=255)
                                                                                                                                         aCTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTCCCCTCGGGCCACCCCGGCAGGCgcagc        <  6:92571/149‑1 (MQ=255)
                                                                                                                                             gCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTCCCCTCgg                            >  1:18041/1‑125 (MQ=255)
                                                                                                                                             gCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTCCCCTCgg                            <  2:18041/125‑1 (MQ=255)
                                                                                                                                             gCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTCCCCTCGGGCCACCCCGGCAGGCGCAGCAACt    >  5:177701/1‑149 (MQ=255)
                                                                                                                                               cATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTCCCCTCGGGCCACCCCGGCAGGCGCAGCAACTCa  <  6:123176/149‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                  
GAACAGCGCCTCGCGATGCTGTTCCAGGTGTTGCGCGAGTTTGTTGTTCAGTGCGGACGCTCGGTGCTCGGTTGGTGTGTCACCGAGCAACTGCTCAATGGCTTCTTCATCCATCTGATCCAGCACGGTTTGGCTCAACTGGCCATTGTCCAGGTCGGTACGGGTAATTTCGATTTCTGTCTGGCCCAGCGTGTGAGGGGGGCCGTAGCGCACCGATTCGCCCCAGGGTTCTGGCCCTTGGTAAACCTTCAGCACGTTCCCCTCGGGCCACCCCGGCAGGCGCAGCAACTCA  >  NC_002947/2931762‑2932053

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: ‑