Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,452,057 A→T I77N (ATC→AAC)  rplD ← 50S ribosomal subunit protein L4

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,452,0570AT95.8% 231.5 / ‑0.0 71I77N (ATC→AAC) rplD50S ribosomal subunit protein L4
Reads supporting (aligned to +/- strand):  ref base A (0/3);  new base T (35/33);  total (35/36)
Fisher's exact test for biased strand distribution p-value = 2.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.36e-01

CAGGATGCTTTTCAGCGCGCCGCGGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGATCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTACTTCAGCACGAGTCTTCTGAGC  >  NC_000913/3451960‑3452154
                                                                                                 |                                                                                                 
cAGGATGCTTTTCAGCGCGCCGCGGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTc                                                                                                 >  2:323952/1‑100 (MQ=255)
  ggATGCTTTTCAGCGCGCCGCGGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCgg                                                                                               >  1:240068/1‑100 (MQ=255)
  ggATGCTTTTCAGCGCGCCGCGGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCgg                                                                                               >  2:1190267/1‑100 (MQ=255)
  ggATGCTTTTCAGCGCGCCGCGGTACATCTTCTTGTTAACATTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCg                                                                                                >  1:498782/1‑99 (MQ=255)
   gATGCTTTTCAGCGCGCCGCGGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCggg                                                                                              >  2:316738/1‑100 (MQ=255)
      gCTTTTCAGCGCGCCGCGGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGctc                                                                                           >  2:1181340/1‑100 (MQ=255)
        ttttCAGCGCGCCGCGGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCtt                                                                                         >  2:1379611/1‑100 (MQ=255)
         tttCAGCGCGCCGCGGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTg                                                                                        <  1:354227/100‑1 (MQ=255)
           tCAGCGCGCCGCGGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGAt                                                                                      <  1:1181057/100‑1 (MQ=255)
            cAGCGCGCCGCGGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATa                                                                                     <  1:1225070/100‑1 (MQ=255)
            cAGCGCGCCGCGGTACATCTTCTTGTTAACTTTTGGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATa                                                                                     <  2:941137/100‑1 (MQ=255)
             aGCGCGCCGCGGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAg                                                                                    <  1:350258/100‑1 (MQ=255)
             aGCGCGCCGCGGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAg                                                                                    >  1:760475/1‑100 (MQ=255)
              gcgcgcCGCGGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGa                                                                                   <  2:285063/100‑1 (MQ=255)
                  gccgcGGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCa                                                                               <  1:1350110/100‑1 (MQ=255)
                  gccgcGGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCa                                                                               <  2:537096/100‑1 (MQ=255)
                    cgcgGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGATCGGGCTCTTGATAGAACCAGa                                                                             <  2:1173759/100‑1 (MQ=255)
                      cgGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAGAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAAc                                                                           <  2:1472985/100‑1 (MQ=255)
                         tACATCTTCTTGTTAACTTTTTTTTTTTTTTTTTGAGGACGAGCAGCAAAGGTTACTCCACTTTTTCGCCAGTTCGGGCTCTTGATATTTCCAGAActct                                                                        >  2:626983/1‑97 (MQ=255)
                          aCATCTTCTTGTTAACTTTTTTACTTTGTTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACgcgc                                                                       >  2:847051/1‑100 (MQ=255)
                          aCATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACgcgc                                                                       >  1:1360504/1‑100 (MQ=255)
                              cttcttGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACgg                                                                   >  1:1093579/1‑100 (MQ=255)
                              cttcttGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACgg                                                                   >  2:1576950/1‑100 (MQ=255)
                              ctgcttGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAGCGCCAGTTCAGGCTCTTGATAGAACCAGAAcg                                                                          <  2:555788/90‑1 (MQ=255)
                                tcttGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGcc                                                                 >  2:819463/1‑100 (MQ=255)
                                 cttGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCg                                                                >  2:448747/1‑100 (MQ=255)
                                    gTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTg                                                             <  1:699894/100‑1 (MQ=255)
                                      tAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGcc                                                           <  1:281572/100‑1 (MQ=255)
                                       aaCTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCt                                                          >  2:268828/1‑100 (MQ=255)
                                         cTTTTTGACTGTGGTCCTGCGGACGAGCGCCAACGGTCACGCCACCAGAACGCCAGTCCGGCCTCTTGATAGAACCATAACGCGCACGGCCAGTGccct                                                         >  2:10854/1‑97 (MQ=255)
                                           ttttGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCt                                                      <  2:813529/100‑1 (MQ=255)
                                            tttGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTg                                                     <  1:465100/100‑1 (MQ=255)
                                            tttGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTg                                                     <  1:464510/100‑1 (MQ=255)
                                             ttGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTGGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTgg                                                    >  2:293236/1‑100 (MQ=255)
                                              tGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGgc                                                   <  1:334905/100‑1 (MQ=255)
                                              tGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGgc                                                   <  1:756521/100‑1 (MQ=255)
                                              tGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTCCTGgc                                                   >  1:574420/1‑100 (MQ=255)
                                                aCTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGTCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGgcgc                                                 <  2:27627/100‑1 (MQ=255)
                                                 cTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGcc                                                >  1:199219/1‑100 (MQ=255)
                                                   gtgGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTACCTTTCTGGCGCCAc                                              >  1:77933/1‑100 (MQ=255)
                                                      gTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGt                                           >  1:210841/1‑100 (MQ=255)
                                                         cTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGtttt                                        <  1:208398/100‑1 (MQ=255)
                                                          tGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGttttt                                       <  2:16265/100‑1 (MQ=255)
                                                           gCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGtttttt                                      <  2:230677/100‑1 (MQ=255)
                                                             ggACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTAc                                    <  2:1216270/100‑1 (MQ=255)
                                                              gACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTAcc                                   <  1:268828/100‑1 (MQ=255)
                                                                cGAGCAGCAAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCgg                                 <  2:1163834/100‑1 (MQ=255)
                                                                   gcagcaAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAAc                              >  1:1157237/1‑100 (MQ=255)
                                                                    cagcaAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAAcc                             <  1:1576960/100‑1 (MQ=255)
                                                                     agcaAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCa                            >  2:1456414/1‑100 (MQ=255)
                                                                     agcaAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCa                            >  2:459651/1‑100 (MQ=255)
                                                                     agcaAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCa                            >  1:1334760/1‑100 (MQ=255)
                                                                      gcaATGGCCCCGCCACCAAAACGACAGTTCGGGCACTTGAGATAACCAAAACGCGCACGGCCGGGGCCTTTCTGGCGCCACGCGTTTTTACCgg                                 >  2:887581/1‑94 (MQ=255)
                                                                      gcaAAGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAg                           >  1:632121/1‑100 (MQ=255)
                                                                        aaaGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGtt                         >  2:1117043/1‑100 (MQ=255)
                                                                        aaaGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGtt                         <  2:515877/100‑1 (MQ=255)
                                                                          aGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTAc                       >  1:961950/1‑100 (MQ=255)
                                                                          aGGTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTAc                       <  1:485302/100‑1 (MQ=255)
                                                                           ggTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTACt                      <  2:186674/100‑1 (MQ=255)
                                                                            gTCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTACtt                     >  1:814828/1‑100 (MQ=255)
                                                                             tCACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTACTTc                    <  1:44554/100‑1 (MQ=255)
                                                                              cACGCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTACTTCa                   >  1:551138/1‑100 (MQ=255)
                                                                                cGCCACCAGAACGCCAGATCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTACTTCAGc                 <  2:576691/100‑1 (MQ=255)
                                                                                 gCCACCAGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTACTTCAGCa                >  2:164941/1‑100 (MQ=255)
                                                                                  ccaccaGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTACTTCAGCAc               <  1:659846/100‑1 (MQ=255)
                                                                                   caccaGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTACTTCAGCACg              <  1:478069/100‑1 (MQ=255)
                                                                                     ccaGAACGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTACTTCAGCACGAg            <  2:509349/100‑1 (MQ=255)
                                                                                          aCGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTACTTCAGCACGAGtcttc       >  2:83791/1‑100 (MQ=255)
                                                                                          aCGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTACTTCAGCACGAGtcttc       <  1:1330678/100‑1 (MQ=255)
                                                                                           cGCCAGTTCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTACTTCAGCACGAGtcttct      >  2:735936/1‑100 (MQ=255)
                                                                                               aGATCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTACTTCAGCACGAGTCTTCTGAGc  <  2:928497/100‑1 (MQ=255)
                                                                                                 |                                                                                                 
CAGGATGCTTTTCAGCGCGCCGCGGTACATCTTCTTGTTAACTTTTTGACTGTGGTCCTGCGGACGAGCAGCAAAGGTCACGCCACCAGAACGCCAGATCGGGCTCTTGATAGAACCAGAACGCGCACGGCCGGTGCCTTTCTGGCGCCACGGTTTTTTACCGGAACCAGTTACTTCAGCACGAGTCTTCTGAGC  >  NC_000913/3451960‑3452154

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑