Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,559,537 G→A 6.7% A125V (GCA→GTA)  ddpC ← D,D‑dipeptide ABC transporter permease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,559,5370GA 6.7% 196.2 / 3.4 60A125V (GCA→GTA) ddpCD,D‑dipeptide ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base G (31/25);  new base A (2/2);  total (33/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.27e-01

AAAAGGGAATTCGCACAATAGCAATAGCCAGCATGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACTTCATC  >  NC_000913/1559400‑1559676
                                                                                                                                         |                                                                                                                                           
aaaaGGGAATTCGCACAATAGCAATAGCCAGCATGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTACGCGTccacca                                                                                                                                  >  2:160222/1‑149 (MQ=255)
aaaaGGGAATTCGCACAATAGCAATAGCCAGCATGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTACGCGTccacca                                                                                                                                  >  4:236621/1‑149 (MQ=255)
      gcaTTCGCACAATAGCAATAGCCAGCATGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGcaca                                                                                                                            >  3:353536/3‑149 (MQ=255)
      gAATTCGCACAATAGCAATAGCCAGCATGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGcaca                                                                                                                            >  1:216185/1‑149 (MQ=255)
       aaTTCGCACAATAGCAATAGCCAGCATGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCacac                                                                                                                           <  2:216185/149‑1 (MQ=255)
        aTTCGCACAATAGCAATAGCCAGCATGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACAcc                                                                                                                          >  2:214818/1‑149 (MQ=255)
         ttCGCACAATAGCAATAGCCAGCATGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCg                                                                                                                         >  2:184329/1‑149 (MQ=255)
              acaATAGCAATAGCCAGCATGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAg                                                                                                                    <  1:214818/149‑1 (MQ=255)
                aatagcaatagcCAGCATGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGAc                                                                                                                  >  1:395485/1‑149 (MQ=255)
                  tagcaatagcCAGCATGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACAt                                                                                                                >  2:340018/1‑149 (MQ=255)
                        tagcCAGCATGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGt                                                                                                          >  4:361445/1‑149 (MQ=255)
                              gCATGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGaa                                                                                                    <  2:198296/149‑1 (MQ=255)
                              gCATGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGaa                                                                                                    <  3:310615/149‑1 (MQ=255)
                                aTGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGATATCCGAGTAGCGAAcc                                                                                                  >  1:406619/1‑149 (MQ=255)
                                 tGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCa                                                                                                 <  1:89376/149‑1 (MQ=255)
                                  ggCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCaa                                                                                                <  3:13149/149‑1 (MQ=255)
                                      ttAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCAt                                                                                            <  1:177196/149‑1 (MQ=255)
                                       tAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATa                                                                                           <  3:122517/149‑1 (MQ=255)
                                        aaacaaacTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATAc                                                                                          <  4:561158/149‑1 (MQ=255)
                                            aaacTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGc                                                                                      >  2:310374/1‑149 (MQ=255)
                                             aacTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAAt                                                                                               >  4:150992/1‑139 (MQ=255)
                                             aacTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAAt                                                                                               <  3:250480/139‑1 (MQ=255)
                                             aacTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAAt                                                                                               <  3:150992/139‑1 (MQ=255)
                                             aacTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAAt                                                                                               >  4:250480/1‑139 (MQ=255)
                                               cTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAAt                                                                                   <  1:141941/149‑1 (MQ=255)
                                                 cGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATgg                                                                                 <  4:404807/149‑1 (MQ=255)
                                                     ccGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAAc                                                                             >  2:44455/1‑149 (MQ=255)
                                                        agagCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCAc                                                                          >  2:245078/1‑149 (MQ=255)
                                                              gCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCaa                                                                              >  2:454158/1‑139 (MQ=255)
                                                              gCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCaa                                                                              <  1:454158/139‑1 (MQ=255)
                                                                  ccAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCg                                                                <  4:462165/149‑1 (MQ=255)
                                                                         cATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGATATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGaa                                                         <  2:406619/149‑1 (MQ=255)
                                                                            tGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAattg                                                      <  3:203576/149‑1 (MQ=255)
                                                                             gTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAattga                                                     <  2:349383/149‑1 (MQ=255)
                                                                             gTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAattga                                                     <  1:62408/149‑1 (MQ=255)
                                                                              tCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAattgat                                                    <  4:506060/149‑1 (MQ=255)
                                                                               cAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTACGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAattgatt                                                   <  1:160222/149‑1 (MQ=255)
                                                                               cAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTACGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAattgatt                                                   <  3:236621/149‑1 (MQ=255)
                                                                                   aCCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGCATTGATTGCTg                                               >  3:367762/1‑149 (MQ=255)
                                                                                   aCCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTg                                               >  3:101729/1‑149 (MQ=255)
                                                                                    ccAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGa                                              >  3:42535/1‑149 (MQ=255)
                                                                                    ccAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGa                                              >  1:457434/1‑149 (MQ=255)
                                                                                      aaCGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACt                                            >  1:332250/1‑149 (MQ=255)
                                                                                       aCGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTg                                           <  3:104550/149‑1 (MQ=255)
                                                                                         gAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGcc                                         >  4:304714/1‑149 (MQ=255)
                                                                                            ggAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGAc                                      <  1:51723/149‑1 (MQ=255)
                                                                                              aaTCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCa                                    <  3:58987/149‑1 (MQ=255)
                                                                                               aTCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAg                                   >  4:472804/1‑149 (MQ=255)
                                                                                                  gACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTAc                                >  3:517509/1‑149 (MQ=255)
                                                                                                  gACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTAc                                >  3:529686/1‑149 (MQ=255)
                                                                                                         tAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTa                         >  3:495456/1‑149 (MQ=255)
                                                                                                          aaTGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCtga                        >  1:409726/1‑147 (MQ=255)
                                                                                                          aaTGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTaa                        >  4:78287/1‑149 (MQ=255)
                                                                                                          aaTGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTaa                        >  4:79683/1‑149 (MQ=255)
                                                                                                                cATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGAt                  <  3:23891/149‑1 (MQ=255)
                                                                                                                   gatgCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATcgc               >  4:107661/1‑149 (MQ=255)
                                                                                                                        gcATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTccc          >  3:525496/1‑149 (MQ=255)
                                                                                                                           tgatgatgGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACt       >  2:264268/1‑149 (MQ=255)
                                                                                                                            gatgatgGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACtt      >  4:48851/1‑149 (MQ=255)
                                                                                                                                atgGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACTTCATc  <  1:245078/149‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                           
AAAAGGGAATTCGCACAATAGCAATAGCCAGCATGGCGTTAAACAAACTCGGCCCGAGAGCGGCAGCCAGTGCCATTGTCAGTACCAACGAAGGAATCGACAGCATAATGTCCATGATGCGCATGATGATGGCGTCTGCGCGTCCACCAAGCACACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACTTCATC  >  NC_000913/1559400‑1559676

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑