Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,553,793 C→T 11.6% R154C (CGC→TGC)  PP_3138 → VirK domain‑containing protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,553,7930CT11.6% 111.3 / 4.7 43R154C (CGC→TGC) PP_3138VirK domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base C (21/17);  new base T (3/2);  total (24/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.55e-01

CTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTGCTCGAA  >  NC_002947/3553649‑3553933
                                                                                                                                                |                                                                                                                                             
cTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAg                                                                                                                                           >  2:327621/1‑149 (MQ=255)
     gCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAgg                                                                                                                                     <  6:315637/149‑1 (MQ=255)
           tgACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCT‑GGCTGCGGCCCAGGGTGaag                                                                                                                               <  1:260912/149‑2 (MQ=255)
                         aCTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCAtt                                                                                                                 >  4:229390/1‑149 (MQ=255)
                              ccGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTggtgc                                                                                                            >  2:188231/1‑149 (MQ=255)
                                    tGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAg                                                                                                                                           <  1:301840/113‑1 (MQ=255)
                                    tGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAg                                                                                                                                           >  2:301840/1‑113 (MQ=255)
                                             gTGCTGGACCGGCCAATCTGGTTCAAGCTCGATGGCGAGCTGGTGGTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGTGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATc                                                                                               <  6:180694/147‑1 (MQ=255)
                                                cTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTggtgcggt                                                                                                         <  8:13508/134‑1 (MQ=255)
                                                cTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTggtgcggt                                                                                                         >  7:13508/1‑134 (MQ=255)
                                                 tGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAAcctgc                                                                                                                          >  6:227537/1‑116 (MQ=255)
                                                 tGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAAcctgc                                                                                                                          <  5:227537/116‑1 (MQ=255)
                                                       ggCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGATCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTAt                                                                                    >  7:125415/1‑148 (MQ=255)
                                                            aTCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGATGCAGGGCATCCACAAAGGTATCGACAg                                                                              <  8:312619/149‑1 (MQ=255)
                                                                  ttCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAAc                                                                        >  8:92591/1‑149 (MQ=255)
                                                                     aaGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCACAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTc                                                                     >  8:36873/1‑149 (MQ=255)
                                                                        cgcgAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCt                                                                  <  1:188231/149‑1 (MQ=255)
                                                                          cgAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCACAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTgg                                                                <  7:36873/149‑1 (MQ=255)
                                                                               gCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATc                                                           >  6:170474/1‑149 (MQ=255)
                                                                                           tGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGtgacct                                                >  3:179583/1‑148 (MQ=255)
                                                                                             aaCCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGtgccctgac                                             >  8:333658/1‑149 (MQ=255)
                                                                                             aaCCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGtgacctga                                              <  7:92591/148‑1 (MQ=255)
                                                                                                   atCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAg                                         <  8:125415/146‑1 (MQ=255)
                                                                                                     ccAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAAc                                                                        >  4:63822/1‑114 (MQ=255)
                                                                                                     ccAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAg                                         <  6:27282/145‑1 (MQ=255)
                                                                                                     ccAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAg                                         >  5:27282/1‑145 (MQ=255)
                                                                                                     ccAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACt                                     >  5:269931/1‑149 (MQ=255)
                                                                                                      cAGGCCGACCTGCGGGTTGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGGGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACt                                     <  3:180937/148‑1 (MQ=255)
                                                                                                                        gCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGCCCTGACCAAGGACTTCGAAGGGCTGCGGCCACg                  >  7:83479/1‑149 (MQ=255)
                                                                                                                              cTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCt            <  6:269931/149‑1 (MQ=255)
                                                                                                                              cTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCt            >  7:86756/1‑149 (MQ=255)
                                                                                                                                aggtttCACCCT‑GGCTGCGGCCCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGt          >  4:234533/5‑149 (MQ=255)
                                                                                                                                  gtttCACCCT‑GGCTGCGGCCCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCAc                   <  8:280961/136‑1 (MQ=255)
                                                                                                                                  gtttCACCCT‑GGCTGCGGCCCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCAc                   >  7:280961/3‑138 (MQ=255)
                                                                                                                                  gtttCACCCT‑GGCTGCGGCCCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTg        >  5:116268/3‑149 (MQ=255)
                                                                                                                                    ttCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTGCt      >  1:61560/1‑149 (MQ=255)
                                                                                                                                    ttCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTGCt      >  3:268533/1‑149 (MQ=255)
                                                                                                                                     tCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTGCt      <  7:273898/148‑1 (MQ=255)
                                                                                                                                     tCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTGCt      >  8:273898/1‑148 (MQ=255)
                                                                                                                                        cccTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTGCTCGaa  <  3:229390/149‑1 (MQ=255)
                                                                                                                                        cccTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTGCTCGaa  <  5:170474/149‑1 (MQ=255)
                                                                                                                                              gCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGc              <  2:3631/131‑1 (MQ=255)
                                                                                                                                              gCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGc              >  1:3631/1‑131 (MQ=255)
                                                                                                                                                |                                                                                                                                             
CTGAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTGCTCGAA  >  NC_002947/3553649‑3553933

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: ‑