Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,105,994 T→C 100% T12T (ACT→ACC)  pdhD → Dihydrolipoyl dehydrogenase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,105,9940TC100.0% 131.7 / ‑6.5 42T12T (ACT→ACC) pdhDDihydrolipoyl dehydrogenase
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (18/23);  total (18/24)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTGACCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACTATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTCAAAAG  >  USA300TCH1516_ALE/1105857‑1106127
                                                                                                                                         |                                                                                                                                     
tttGACCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACcata                                                                                                                                    >  1:479524/1‑141 (MQ=255)
  tGACCACACACAAATTGGTGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGt                                                                                                                                  <  2:430089/141‑1 (MQ=255)
   gACCACAGACCAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTACATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTa                                                                                                                                 <  1:469122/141‑1 (MQ=255)
   gACCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTACATAATCGAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTa                                                                                                                                 >  2:75747/1‑141 (MQ=255)
     ccACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAAt                                                                                                                               >  2:211199/1‑141 (MQ=255)
                      gTGCAACTGGCCAACATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCGAATTGAAACGAATACCATAGTAATCGGAGAAGGTCCtggtg                                                                                                              >  2:417347/1‑141 (MQ=255)
                         cAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATACCGAATTGTGATTAATGGAGGGTGAGAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGAt                                                                                                           <  1:302587/141‑1 (MQ=255)
                           aCTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATAc                                                                                                         >  1:220816/1‑141 (MQ=255)
                                gaaaaaTGCAATTAATCAAATTAAACGTTTATCAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTCCCCAATTGAAACAGATACCATAGTACTCGGAGCAGGTCCTGGTGGATACGTTgc                                                                                                    <  2:110418/139‑1 (MQ=255)
                                        cAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTc                                                                                            >  1:688623/1‑141 (MQ=255)
                                        cAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCAGAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTc                                                                                            <  1:41848/141‑1 (MQ=255)
                                           tGAATCACATTAGACGTTTATTAAATAATCCAGGATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTg                                                                                         <  2:53811/141‑1 (MQ=255)
                                             aaTCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCa                                                                                       <  1:222399/141‑1 (MQ=255)
                                             aaTCACATTAAACGGTTATTAAATAACCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCa                                                                                       <  1:575600/141‑1 (MQ=255)
                                              aTCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAg                                                                                      >  1:212502/1‑141 (MQ=255)
                                                      aaaCGTTTATTAAATAATACAGAATTATTATTAATGGAGGGGTAAAACATGTTAATTGGAGATTTTCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCCATTa                                                                              <  1:473299/141‑1 (MQ=255)
                                                      aaaCGGTTATTAAACAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTa                                                                              <  2:19182/141‑1 (MQ=255)
                                                                taAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAg                                                                    >  1:517102/1‑141 (MQ=255)
                                                                   ataatCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTaa                                                                 <  1:211199/141‑1 (MQ=255)
                                                                        ccAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGTACAAAAGGTAAGAAtg                                                            >  1:675959/1‑140 (MQ=255)
                                                                        ccAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATc                                                            <  1:280418/141‑1 (MQ=255)
                                                                        ccAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATc                                                            >  1:111383/1‑141 (MQ=255)
                                                                             attattattAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGTATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTga                                                       <  1:462907/141‑1 (MQ=255)
                                                                              ttattattaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTgag                                                      >  1:135674/1‑141 (MQ=255)
                                                                              ttattattaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTgag                                                      >  1:388934/1‑141 (MQ=255)
                                                                              ttattattaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTgag                                                      >  1:304084/1‑141 (MQ=255)
                                                                              ttattattaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTgag                                                      >  1:206784/1‑141 (MQ=255)
                                                                                   attaATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGGCCGGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAgg                                                 >  1:317265/1‑141 (MQ=255)
                                                                                          gAGTGGTAAAACATGGTAGATGGAGATTTCACAAATGATACAGATACCATAGTAATTGGAGCAAGACCTGGTGGATACGGTGCAACAATTCGTGCAGCTCAATTAAGACAAAAAGTAACAATCGTTGAGAAAGGTAATCtt                                          <  2:256230/141‑1 (MQ=255)
                                                                                          gAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCtt                                          <  1:30036/141‑1 (MQ=255)
                                                                                             ggagaaaaCATGGTAGTTGGAGCGTTCCGAATTGAAACAGATACCAGATTAATCGTAGAAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGATCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggt                                       <  2:693011/137‑1 (MQ=255)
                                                                                               gtacaccATGGTAGTTGGACATTGCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggtgg                                     <  2:368459/135‑1 (MQ=255)
                                                                                               gTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggtgg                                     <  1:19406/141‑1 (MQ=255)
                                                                                               atAACACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGGCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTtggtgg                                     <  2:95088/140‑1 (MQ=255)
                                                                                                  aaaCCTGGTAGTTTGAGATTTCCCAATTTAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGgtgt                                  <  2:67272/141‑1 (MQ=255)
                                                                                                   aaCATGGTAGTTGGAGATTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTgttgtt                                 >  1:434123/1‑141 (MQ=255)
                                                                                                              tggttaTTTCCTAATTGTAACAGACACCATAGTAATGGTAGCGGGTCCTGATGAAAACGATGCAGCAATTCGTGGCGCTCGATTAGGCCAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGt                      <  2:425606/136‑1 (MQ=255)
                                                                                                                 agaTTTCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAgg                   >  2:343906/1‑141 (MQ=255)
                                                                                                                     ttCCCAATTGAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGt               >  1:80291/1‑141 (MQ=255)
                                                                                                                      tcacAATTGAAACAGATACTCTATGAGGCGTAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTa              <  2:484950/138‑1 (MQ=255)
                                                                                                                              gAAACAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATACCTTCa      >  2:588510/1‑141 (MQ=255)
                                                                                                                                  cAGATACCATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCAAAAAAAAAAAAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTCAAAAg  <  2:688623/141‑1 (MQ=255)
                                                                                                                                  cAGAGACCATAGTAATTGGAGCAGGTGCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAACGTAACGATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTCAAAAg  <  2:212502/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                     
TTTGACCACAGACAAATTGATGGTGCAACTGGCCAAAATGCAATGAATCACATTAAACGTTTATTAAATAATCCAGAATTATTATTAATGGAGGGGTAAAACATGGTAGTTGGAGATTTCCCAATTGAAACAGATACTATAGTAATCGGAGCAGGTCCTGGTGGATACGTTGCAGCAATTCGTGCAGCTCAATTAGGACAAAAAGTAACAATCGTTGAGAAAGGTAATCTTGGTGGTGTTTGCTTAAACGTAGGATGTATTCCTTCAAAAG  >  USA300TCH1516_ALE/1105857‑1106127

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: ‑