Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,425,129 T→C 8.3% M69T (ATG→ACG)  PP_3040 → holin

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,425,1290TC 8.3% 133.9 / 2.9 48M69T (ATG→ACG) PP_3040holin
Reads supporting (aligned to +/- strand):  ref base T (19/25);  new base C (2/2);  total (21/27)
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

TCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGCCAAGCGGCTGGGCGTCTGCGATGTCACGTCCCGTAGCGGCGAACCTGGACAGTGACC  >  NC_002947/3424981‑3425273
                                                                                                                                                    |                                                                                                                                                
tCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCAt                                                                                                                                                  >  5:23147/1‑149 (MQ=255)
   cTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTc                                                                                                                                               >  5:322632/1‑149 (MQ=255)
   cTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTc                                                                                                                                               <  4:301643/149‑1 (MQ=255)
         ggcggGGTGTCAGGCGAGATGTGGCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGAtgtg                                                                                                                                         <  3:127214/149‑1 (MQ=255)
          ggggggTGTCAGGCGAGATTTGGCGGGCCGACATGGCCGGCGGTAGCGGCTGGTTCATTTTCCGCGAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTTCTGTACTCGGCGGGGATGTCGATGTgg                                                                                                                                        <  2:114323/147‑1 (MQ=255)
               gtgtCAGGCGAGATGTGGCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGc                                                                                                                                   >  2:318248/1‑149 (MQ=255)
                  tCAGGCGAGATGTGGCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCa                                                                                                                                 <  7:203048/148‑1 (MQ=255)
                  tCAGGCGAGATGTGGCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCACGTCGATGTGGTCGGCCAg                                                                                                                                >  6:163804/1‑149 (MQ=255)
                  tCAGGCGAGAAGTGGCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTAGACCATCATGATGCTGTACTCGGCGGGCACGTCGATGTCGTCGGCCAg                                                                                                                                >  8:160719/1‑149 (MQ=255)
                      gCGAGATGTGGCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGc                                                                                                                             >  7:305111/1‑148 (MQ=255)
                        gagaTGTGGCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCAt                                                                                                                          >  3:222410/1‑149 (MQ=255)
                           aTGTGGCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTg                                                                                                                        <  8:293826/148‑1 (MQ=255)
                             gtgGCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCACGTCGATGTGGTCGGCCAGTGCCATTGGtt                                                                                                                     <  7:160719/149‑1 (MQ=255)
                              tgGCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGtt                                                                                                                     <  6:23147/148‑1 (MQ=255)
                              tgGCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCACGTCGATGTGGTCGGCCAGTGCCATTGGtt                                                                                                                     <  5:163804/148‑1 (MQ=255)
                                gCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGt                                                                                                                   <  1:277310/148‑1 (MQ=255)
                                       gACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTcactgc                                                                                                           <  6:366503/149‑1 (MQ=255)
                                             gCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTcactgccactgc                                                                                                     <  6:343895/149‑1 (MQ=255)
                                                   gTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGc                                                                                               <  5:48947/149‑1 (MQ=255)
                                                               ttCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCCCTGCCGGTGCGGATGTGGCCa                                                                                    >  3:285775/1‑148 (MQ=255)
                                                               ttCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTg                                                                                                <  8:15709/136‑1 (MQ=255)
                                                               ttCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTg                                                                                                >  7:15709/1‑136 (MQ=255)
                                                                        cGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTa                                                                          <  6:322632/149‑1 (MQ=255)
                                                                          ccAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTAc                                                                         >  1:168444/1‑148 (MQ=255)
                                                                                  tgctgcGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACaa                                                                       >  1:48849/1‑142 (MQ=255)
                                                                                  tgctgcGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACaa                                                                       <  2:48849/142‑1 (MQ=255)
                                                                                  tgctgcGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATACTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTTCGGATGTGGCCATAggg                                                                               <  6:231374/134‑1 (MQ=255)
                                                                                  tgctgcGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATACTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAggg                                                                               >  5:226293/1‑134 (MQ=255)
                                                                                  tgctgcGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATACTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAggg                                                                               <  6:226293/134‑1 (MQ=255)
                                                                                  tgctgcGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATACTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAggg                                                                               >  5:231374/1‑134 (MQ=255)
                                                                                   gctgcGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTggg                                                               >  8:128345/1‑149 (MQ=255)
                                                                                    ctgcGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTACCACTGCCGGTGCGGATGTGGCCTTAGGGTTGTACAAGCGTTgg                                                                <  4:123965/147‑1 (MQ=255)
                                                                                          tCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCa                                                                                                                                 >  6:174407/1‑76 (MQ=255)
                                                                                          tCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCa                                                                                                                                 <  5:174407/76‑1 (MQ=255)
                                                                                          tCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGcc                                                          >  7:31640/1‑147 (MQ=255)
                                                                                                 ccTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGCCAAGCGGCTg                                                 <  1:318248/149‑1 (MQ=255)
                                                                                                                gACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGCCAAGCGGCTGGGCGTCTGCGATGTc                                  <  2:168444/149‑1 (MQ=255)
                                                                                                                  atGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGCCAAGCGGCTGGGCGTCTGCGATGTCAc                                <  8:305111/148‑1 (MQ=255)
                                                                                                                     tCGACCATCATGCTGCTGTACTCGTCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGCCAAGCGGCTGGGCGTCTGCGATGTCACg                               <  6:302100/147‑1 (MQ=255)
                                                                                                                       gACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGCCAAGCGGCTGGGCGTCTGCGATGTCACGTccc                           >  3:322180/1‑149 (MQ=255)
                                                                                                                       gACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGCCAAGCGGCTGGGCGTCTGCGATGTCACGTccc                           >  8:246086/1‑149 (MQ=255)
                                                                                                                        aCCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGCCAAGCGGCTGGGCGTCTGCGATGTCACGTCCCg                          >  5:3925/1‑149 (MQ=255)
                                                                                                                         ccATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGCCAAGCGGCTGGGCGTCTGCGATGTCACGTCCCg                          >  5:295323/1‑148 (MQ=255)
                                                                                                                            tcatGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGCCAAGCGGCTGGGCGTCTGCGATGTCACGTCCCGTAgc                      <  2:222367/149‑1 (MQ=255)
                                                                                                                                  tgctgTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGCCAAGCGGCTGGGCGTCTGCGAt                                     >  6:91155/1‑128 (MQ=255)
                                                                                                                                  tgctgTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGCCAAGCGGCTGGGCGTCTGCGAt                                     <  5:91155/128‑1 (MQ=255)
                                                                                                                                       tACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGCCAAGCGGCTGGGCGTCTGCGATGTCACGTCCCGTAGCGGCGAACCTg            >  6:6616/1‑148 (MQ=255)
                                                                                                                                                ggCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGCCAAGCGGCTGGGCGTCTGCGATGTCACGTCCCGTAGCGGCGAACCTGGACAGTGAcc  <  7:128345/149‑1 (MQ=255)
                                                                                                                                                ggCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGCCAAGCGGCTGGGCGTCTGCGATGTCACGTCCCGTAGCGGCGAACCTGGACAGTGAcc  <  4:222410/149‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                                
TCCCTGGTCGGCGGGGTGTCAGGCGAGATGTGGCGGGCCGACATGGCCGGCGTTAGCGGCTGGTTCATTTTCCGCCAGGTGCTGCTGCGCTCCGGTGCCTGCGTCGTATGCGGACTGTCGACCATCATGCTGCTGTACTCGGCGGGCATGTCGATGTGGTCGGCCAGTGCCATTGGTTGTCTCACTGCCACTGCCGGTGCGGATGTGGCCATAGGGTTGTACAAGCGTTGGGTCGCCAAGCGGCTGGGCGTCTGCGATGTCACGTCCCGTAGCGGCGAACCTGGACAGTGACC  >  NC_002947/3424981‑3425273

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: ‑