Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 478,502 C→A 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_ALE478,5020CA97.6% 140.2 / ‑5.5 41D342E (GAC→GAA) nuoLNADH‑quinone oxidoreductase subunit L
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base A (21/19);  minor base T (0/1);  total (21/20)
Fisher's exact test for biased strand distribution p-value = 4.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTATGTTAGTTCAATGTGCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGACGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTGTATCTTGGAATCAA  >  USA300TCH1516_ALE/478357‑478640
                                                                                                                                                 |                                                                                                                                          
ttATGTTAGTTCAATGTGCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCt                                                                                                                                         >  2:151705/1‑149 (MQ=255)
ttATGTTAGTTCAATGTGCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCt                                                                                                                                         >  1:254450/1‑149 (MQ=255)
 tATGTTAGTTCAATGTGCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCATGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCtt                                                                                                                                        <  2:267694/149‑1 (MQ=255)
    gTTAGTTCAATGTGCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATg                                                                                                                                     >  1:164018/1‑149 (MQ=255)
     ttAGTTCAATGTGCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATgg                                                                                                                                    >  1:237780/1‑149 (MQ=255)
         ttCAATGTGCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTgg                                                                                                                                >  1:208460/1‑149 (MQ=255)
            aaTGTGCATTGGGTGTATATTCAGCAGCGAGTAGTCATTGAATAGTGCACGGTATTTGTAAAGCGGCATGTTGTTTACAATCAGGTTCTTCCTTTAAGCGAGTCAGTGTTCGAAAACAAGCATCTGCTAAAGAAGCTTATGTCTGTAtt                                                                                                                             >  1:278755/1‑149 (MQ=255)
                        gtgtATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACgt                                                                                                                 <  1:59445/149‑1 (MQ=255)
                           tataTTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTa                                                                                                              >  2:36018/1‑149 (MQ=255)
                                  agcagcGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCta                                                                                                       >  2:253175/1‑149 (MQ=255)
                                   gcagcGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATCCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCtat                                                                                                      >  2:147753/1‑149 (MQ=255)
                                           tattCATTTAATATTGCACGGTATTTTTTAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTgg                                                                                              <  1:46615/149‑1 (MQ=255)
                                           tattCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTgg                                                                                              <  1:242370/149‑1 (MQ=255)
                                                  ttAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCt                                                                                       >  1:27132/1‑149 (MQ=255)
                                                  ttAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCt                                                                                       >  2:40184/1‑149 (MQ=255)
                                                  ttAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCt                                                                                       >  1:168648/1‑149 (MQ=255)
                                                     atatTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTAtt                                                                                    >  2:47731/1‑149 (MQ=255)
                                                       atTGCACGGTATTTTTAAAGCAACATTATTTTTTTTTTTTTTTTCTATCGTGAAGCGATTCAATATTTCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGTATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTAtttt                                                                                  >  2:244869/1‑149 (MQ=255)
                                                       atTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTAtttt                                                                                  <  2:235740/149‑1 (MQ=255)
                                                          gCACGGTATTTTTAAAGCAACATTATTTTTTTTTTTTTTTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTggt                                                                               >  2:56215/1‑148 (MQ=255)
                                                           cACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGAt                                                                              >  2:137929/1‑149 (MQ=255)
                                                                         aGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGaa                                                                >  2:85089/1‑149 (MQ=255)
                                                                            aaCATTATTTTTACCATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGTGTAGTGACAGAAGTg                                                             <  1:221798/149‑1 (MQ=255)
                                                                            aaCATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTg                                                             <  2:200459/149‑1 (MQ=255)
                                                                            aaCATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTg                                                             <  2:131074/149‑1 (MQ=255)
                                                                            aaCATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTg                                                             <  2:113330/149‑1 (MQ=255)
                                                                              cATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCa                                                           <  2:140642/149‑1 (MQ=255)
                                                                               attattTTTACAATCAGGTTCTAACGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCat                                                          <  2:26709/149‑1 (MQ=255)
                                                                                      ttACAATCAGGTTGTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAgt                                                   <  2:50169/149‑1 (MQ=255)
                                                                                        aCAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAgtgt                                                 >  2:232677/1‑149 (MQ=255)
                                                                                        aCAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAgtgt                                                 <  2:7520/149‑1 (MQ=255)
                                                                                        aCAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAgtgt                                                 >  2:270899/1‑149 (MQ=255)
                                                                                        aCAATCAGGTGCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAgtgt                                                 <  2:96533/149‑1 (MQ=255)
                                                                                                      tCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCAtt                                   <  1:36018/149‑1 (MQ=255)
                                                                                                      tCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCAtt                                   >  1:85366/1‑149 (MQ=255)
                                                                                                        gTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCt                                 >  2:242735/1‑149 (MQ=255)
                                                                                                                    aaTATTGCAGAACTAGCATGTGCTTATGATACTTATGGCTCATTTGGTATTGGTGTTGTATTATTGATTATCGGGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCAtt                     <  1:126711/149‑1 (MQ=255)
                                                                                                                            aaaaCAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTGTAt             <  1:244801/149‑1 (MQ=255)
                                                                                                                                       cTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTGTATCTTGGAATCaa  <  2:27132/149‑1 (MQ=255)
                                                                                                                                       cTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTGTATCTTGGAATCaa  <  1:40184/149‑1 (MQ=255)
                                                                                                                                       cTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGCTAAGTGCACTCATTCTAGGATGGTCATTACTTGTATCTTGGAATCaa  <  2:168648/149‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                          
TTATGTTAGTTCAATGTGCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGACGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTGTATCTTGGAATCAA  >  USA300TCH1516_ALE/478357‑478640

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: ‑