Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 2,224,391 A→C 8.9% I52M (ATT→ATG)  PP_1962 ← site‑specific recombinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029472,224,3910AC 8.9% 136.9 / 5.5 45I52M (ATT→ATG) PP_1962site‑specific recombinase
Reads supporting (aligned to +/- strand):  ref base A (22/19);  new base C (2/2);  total (24/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.58e-01

GTAAATTTCGATAAACCGATAGTCGTGAGATTTCGCTTTGGATGATACGAAGGAACGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGCGTAAGAAGCTTGATAAGTAGGCCGCTCTTCGAGGACTCAAGTTCTCCGGCGGT  >  NC_002947/2224244‑2224537
                                                                                                                                                   |                                                                                                                                                  
gTAAATTTCGATAAACCGATAGTCGTGAGATTTCGCTTTGGATGATACGAAGGAACGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGaa                                                                                                                                                   >  1:46506/1‑149 (MQ=255)
 tAAATTTCGATAAACCGATAGTCGTGAGATTTCGCTTTGGATGATACGAAGGAACGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAAt                                                                                                                                                  <  1:233084/149‑1 (MQ=255)
     tttCGATAAACCGATAGTCGTGAGATTTCGCTTTGGATGATACGAAGGAACGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGtt                                                                                                                                               >  7:229135/1‑148 (MQ=255)
                 gATAGTCGTGAGATTTCGCTTTGGATGATACGAAGGAACGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTttgt                                                                                                                                  >  7:113906/1‑149 (MQ=255)
                         tGAGATTTCGCTTTGGATGATACGAAGGAACGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTc                                                                                                                          >  4:301139/1‑149 (MQ=255)
                         tGAGATTTCGCTTTGGATGATACGAAGGAACGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTc                                                                                                                          <  2:162364/149‑1 (MQ=255)
                                  gCTTTGGATGATACGAAGGAACGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGtt                                                                                                                  <  8:113906/148‑1 (MQ=255)
                                   cTTTGGATGATACGAAGGAACGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTc                                                                                                                >  4:26564/1‑149 (MQ=255)
                                          tgatACGAAGGAACGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGc                                                                                                         >  3:33659/1‑149 (MQ=255)
                                             tACGAAGGAACGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGCATGTAACATtcgc                                                                                                                                       >  5:263020/1‑116 (MQ=255)
                                             tACGAAGGAACGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGCATGTAACATtcgc                                                                                                                                       <  6:263020/116‑1 (MQ=255)
                                               cGACGGCACGACTACGATTGAAGGGAGGAAATGCAGGGAGCAAATGGTAACCAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGGCCGCAAGTTTCCAAATGCTGgct                                                                                                    <  2:126956/149‑1 (MQ=255)
                                                 aaGGAACGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTctct                                                                                                  <  1:10142/149‑1 (MQ=255)
                                                 aaGGAACGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTctct                                                                                                  <  3:301139/149‑1 (MQ=255)
                                                   ggAACGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTg                                                                                                 >  6:237410/1‑148 (MQ=255)
                                                       cGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTc                                                                                            <  4:88991/149‑1 (MQ=255)
                                                          aTACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGa                                                                                         <  2:46506/149‑1 (MQ=255)
                                                                   aaGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAAt                                                                                  >  1:299777/1‑147 (MQ=255)
                                                                     gggAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATgaga                                                                              >  6:200107/1‑149 (MQ=255)
                                                                       gAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGaa                                                                                               <  5:80178/130‑1 (MQ=255)
                                                                       gAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGaa                                                                                               >  6:80178/1‑130 (MQ=255)
                                                                         gTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACggg                                                                          <  1:202148/149‑1 (MQ=255)
                                                                                   ggAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGATTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCg                                                                >  3:306268/1‑149 (MQ=255)
                                                                                       cAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTg                                                            <  8:229135/149‑1 (MQ=255)
                                                                                        ataTGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGaa                                                                                               >  8:293919/3‑113 (MQ=255)
                                                                                        ataTGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGaa                                                                                               <  7:293919/111‑1 (MQ=255)
                                                                                        aaaTGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTgg                                                           >  3:176009/1‑149 (MQ=255)
                                                                                           tGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAg                                                        >  5:94976/1‑149 (MQ=255)
                                                                                                aaCAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGCGTa                                                    <  3:26564/148‑1 (MQ=255)
                                                                                                        cccTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGCGTAAGAAGCTTg                                           <  5:237410/149‑1 (MQ=255)
                                                                                                                aGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGCGTAAGAAGCTTGATAAGTa                                    <  4:33659/148‑1 (MQ=255)
                                                                                                                 ggTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTgg                                                           <  4:258593/124‑1 (MQ=255)
                                                                                                                 ggTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTgg                                                           >  3:258593/1‑124 (MQ=255)
                                                                                                                 ggTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTCAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGCGTAAGAAGCTTGATAAGTAgg                                  >  7:75423/1‑149 (MQ=255)
                                                                                                                  gTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGCGTAAGAAGCTTGATAAGTAGGc                                 >  3:93650/1‑149 (MQ=255)
                                                                                                                           aCCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGCGTAAGAAGCTTGATAAGTAGGCCGCTCTTCg                        >  4:96890/1‑149 (MQ=255)
                                                                                                                                     tctcGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGCGTAAGAAGCTTGATAAg                                      <  3:305740/125‑1 (MQ=255)
                                                                                                                                     tctcGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGCGTAAGAAGCTTGATAAg                                      >  4:305740/1‑125 (MQ=255)
                                                                                                                                       tcGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGCGTAAGAAGCTTGATAAGTAGGCCGCTCTTCGAGGACTCaa               <  5:200107/146‑1 (MQ=255)
                                                                                                                                       tcGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGCGTAAGAAGCTTGATAAGTAGGCCGCTCTTCGAGGACTCAAGt             >  4:78000/1‑148 (MQ=255)
                                                                                                                                        aacacAAAGCGCATGTAACATTCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGc                                                       <  2:237121/101‑1 (MQ=39)
                                                                                                                                        aacacAAAGCGCATGTAACATTCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGc                                                       >  1:237121/5‑105 (MQ=39)
                                                                                                                                             aaaGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGCGTAAGAAGCTTGATAAGTAGGCCGCTCTTCGa                       >  4:124816/1‑132 (MQ=255)
                                                                                                                                             aaaGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGCGTAAGAAGCTTGATAAGTAGGCCGCTCTTCGa                       <  3:124816/132‑1 (MQ=255)
                                                                                                                                              aaGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGCGTAAGAAGCTTGATAAGTAGGCCGCTCTTCGAGGACTCAAGTTCTCcggc     >  6:280055/1‑149 (MQ=255)
                                                                                                                                                 cGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGCGTAAGAAGCTTGATAAGTAGGCCGCTCTTCGAGGACTCAAGTTCTCCGGCGGt  >  2:114141/1‑149 (MQ=255)
                                                                                                                                                   |                                                                                                                                                  
GTAAATTTCGATAAACCGATAGTCGTGAGATTTCGCTTTGGATGATACGAAGGAACGAATACGATTGAAGGGAGTAAATGCAGGGAGCAAATGGTAAACAATTGCCCTTTTCAGGTCGTTCCCACCTGGTATCTCTCGATCAAAGCGAATGTTACATGCGCTTTGTGTTGTGTCCGCAAGTTTCCAAATGCTGTCTCTGAATTCCGACTCTAATGAGACGGGGAAATCTCCGCCTGGGAGCGTAAGAAGCTTGATAAGTAGGCCGCTCTTCGAGGACTCAAGTTCTCCGGCGGT  >  NC_002947/2224244‑2224537

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑