Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 478,502 C→A 100% D342E (GAC→GAA)  nuoL → NADH‑quinone oxidoreductase subunit L

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE478,5020CA100.0% 113.6 / NA 38D342E (GAC→GAA) nuoLNADH‑quinone oxidoreductase subunit L
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (21/17);  total (21/17)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGTGCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGACGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTGTATCTTGG  >  USA300TCH1516_ALE/478371‑478634
                                                                                                                                   |                                                                                                                                      
tgtgCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGc                                                                                                                               >  1:129975/1‑141 (MQ=255)
tgtgCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGc                                                                                                                               >  1:299566/1‑141 (MQ=255)
   gCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGCAGCTTATGGCTgg                                                                                                                            >  2:267975/1‑141 (MQ=255)
      ttGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGAtt                                                                                                                         >  1:124200/1‑141 (MQ=255)
          gtgtATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCa                                                                                                                    <  1:373249/141‑1 (MQ=255)
                                   tttAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGt                                                                                           >  1:24104/1‑141 (MQ=255)
                                           tGCACGGTATTTTTAATGCAACGTTTTTTTTACAATCAGGTTTTATCGTGAAGTGATTCAATATTCCATAACAAGCATATGCTATTCAAGCTGATGGGTGGTTTG‑TCATGGGGTGTGTGTTAGCTATTATCGTGGCATTTc                                                                                   <  2:60201/141‑1 (MQ=255)
                                           tGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCCGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTc                                                                                   <  1:230681/141‑1 (MQ=255)
                                                  tATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTAAGGCTGGATTG‑TCATGGGACGTGTATTAGCAATTATCGTGGCATTTCTAATTTg                                                                            >  1:283343/1‑141 (MQ=255)
                                                     ttttAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGAt                                                                         >  1:276355/1‑141 (MQ=255)
                                                      tttAAAGCAACATTATTTTTACATTCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGATGGATTG‑TCATGGGACGTGTCTTAGCTATTAGCGTGGCCTTTGTAGTTTgtgtg                                                                        >  2:65535/1‑137 (MQ=255)
                                                       ttAAAGCAACATTATTTTTATGTTCATTTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGGTGa                                                                       >  2:361366/1‑141 (MQ=255)
                                                        tAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCGTTTCTATTTTGGATGag                                                                      >  2:98729/1‑141 (MQ=255)
                                                        tAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATggg                                                                      >  2:175746/1‑139 (MQ=255)
                                                              aaCATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTAATTGCTATTATCGTGGCTTTTCTATTTTGGATGAG‑TAGTGa                                                               >  2:57027/1‑141 (MQ=255)
                                                                aattattTGTTCCATCAGGTTCTACCGTGAAGCGATTCAATATTGCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACa                                                             <  1:138266/140‑1 (MQ=255)
                                                                 attattTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAg                                                            <  1:60636/141‑1 (MQ=255)
                                                                    attTTTGCATTCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTACTATTTTGGATGAG‑TAGTGACAGAAg                                                         >  1:274058/1‑141 (MQ=255)
                                                                          aCAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCata                                                   <  1:363246/141‑1 (MQ=255)
                                                                          aCAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTCCTAAAGAAGCTTATGGCTGGATGG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCata                                                   <  1:368937/141‑1 (MQ=255)
                                                                          aCAATACGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCata                                                   <  1:322253/141‑1 (MQ=255)
                                                                                 ggTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCATATGAAgtg                                            <  1:23584/141‑1 (MQ=255)
                                                                                   ttCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCATATGAAGTGtt                                          >  2:188218/1‑141 (MQ=255)
                                                                                     cTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCATATGAAGTGTTaa                                        <  2:338557/141‑1 (MQ=255)
                                                                                          gTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATAGCTGGATTG‑TCATGGGACGTGTCTTAGCTATTATCGTGGCCTTACTATTTTGGATGAG‑GAGTGACATCAGTGCATATGCAGTGTTAGGTgaa                                   >  2:200388/1‑139 (MQ=255)
                                                                                           tGAAGCGATTCAATATTCCAAAACAAGCACCTGCCAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCATATGAAGTGTTAAGTGCAc                                  <  1:189993/141‑1 (MQ=255)
                                                                                                  cttCAATATGCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCt                           <  2:92286/140‑1 (MQ=255)
                                                                                                    tCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCATATGAAGTGTTAAGTGCAATccttatcg                         >  2:182893/1‑134 (MQ=255)
                                                                                                        tatTCCAAAACAAGCGTCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCATATGAAGAGATAAGTGCACTCATTCTAGGATg                     >  1:186706/1‑141 (MQ=255)
                                                                                                        tatTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATg                     >  2:120202/1‑141 (MQ=255)
                                                                                                           tCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTc                  <  2:276355/141‑1 (MQ=255)
                                                                                                            ccAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCa                 <  2:186262/141‑1 (MQ=255)
                                                                                                             cAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGCCAGGAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCAt                <  1:163522/141‑1 (MQ=255)
                                                                                                               aaaCAAGCATCTGCTAAAGAAGCTTATGGCTGGCTTGATTAT‑TGTCGTGTATTGGCGATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTa              >  1:178801/1‑141 (MQ=255)
                                                                                                                     gCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGCGCTAG‑GACGGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTGTa        >  1:271119/1‑141 (MQ=255)
                                                                                                                     gCATCTGCTAAAGAAGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAA‑CATACACTTAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTGTa        >  1:271155/1‑141 (MQ=255)
                                                                                                                       aTCTGCTAAAGAAGCCTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTGTATc      <  1:124218/141‑1 (MQ=255)
                                                                                                                           gcgaaaGAAGCTTATGGCTGGAGTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTGTATCTTgg  <  1:65535/138‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                      
TGTGCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGACGCTTATGGCTGGATTG‑TCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAG‑TAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTGTATCTTGG  >  USA300TCH1516_ALE/478371‑478634

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑