Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,416,458 A→T 100% I216N (ATT→AAT)  oppD_4 ← Oligopeptide transport ATP‑binding protein OppD

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,416,4580AT100.0% 145.4 / ‑6.5 50I216N (ATT→AAT) oppD_4Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (29/20);  minor base G (1/0);  total (30/20)
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.

TTTAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTC  >  USA300TCH1516_ALE/1416322‑1416594
                                                                                                                                        |                                                                                                                                        
tttAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAACTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTa                                                                                                                                      >  2:506475/1‑141 (MQ=255)
 ttAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTAACCTTCTTTTAAAACATAATTGTAc                                                                                                                                     >  1:522563/1‑141 (MQ=255)
    aCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAACGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGa                                                                                                                                  <  2:722598/141‑1 (MQ=255)
      tCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACa                                                                                                                                <  1:437484/141‑1 (MQ=255)
        aaTCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAat                                                                                                                              <  2:731657/141‑1 (MQ=255)
         aTCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAAGGCTCATACTTGAAATGATGTATATTACCTCGTTCACTGATTTGACCTTCTTTTAAACCATAATTTTACTTGCAata                                                                                                                             >  2:212512/1‑141 (MQ=255)
                 aaTCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATa                                                                                                                     >  1:277888/1‑141 (MQ=255)
                       tctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAGTATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACagaac                                                                                                               >  2:332582/1‑137 (MQ=255)
                       tctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCATTAAATGAc                                                                                                               >  2:548464/1‑141 (MQ=255)
                       tctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGAc                                                                                                               >  2:269574/1‑141 (MQ=255)
                       tctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGAc                                                                                                               >  2:548434/1‑141 (MQ=255)
                         tttGATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGAGTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATAACtt                                                                                                             >  1:567003/1‑141 (MQ=255)
                         tttAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACtt                                                                                                             >  1:106652/1‑141 (MQ=255)
                           tAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGACATGATTAATATGACCGCGCACAGGGAGCCTAGCTTCTTTTAAAACATAATTGTACTGACAATCGTTCCATACATGACttgc                                                                                                           >  2:359504/1‑139 (MQ=255)
                           tAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTaa                                                                                                           <  2:429365/141‑1 (MQ=255)
                             aTTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGt                                                                                                         <  2:627054/141‑1 (MQ=255)
                                 tgtTCTATATTTAATTAGACGTTCAGTATACGGATGCCAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAtg                                                                                                     <  2:32431/141‑1 (MQ=255)
                                    tCTATATGTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAtgtgt                                                                                                  <  2:469390/141‑1 (MQ=255)
                                     cTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAGGTTAcgtgtg                                                                                                 >  2:611220/1‑141 (MQ=255)
                                              aTTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATaataaat                                                                                        <  2:277888/141‑1 (MQ=255)
                                               ttAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCACTACATGACTTAAGTTATGTGTGATaataaata                                                                                       >  2:12943/1‑141 (MQ=255)
                                               ttAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGGTATaataaata                                                                                       >  2:247684/1‑141 (MQ=255)
                                               ttAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGGGATaataaata                                                                                       >  1:172340/1‑141 (MQ=255)
                                               ttAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAGTGTACTGACAAGATTTAAATACATGACTTAAGTTATGTGTGATaataaata                                                                                       >  2:375975/1‑141 (MQ=255)
                                                  gACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATg                                                                                    >  1:520197/1‑141 (MQ=255)
                                                     gTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGttt                                                                                 <  1:760508/141‑1 (MQ=255)
                                                     gTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGttt                                                                                 <  1:301599/141‑1 (MQ=255)
                                                      ttCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTg                                                                                >  2:361950/1‑141 (MQ=255)
                                                       tCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGa                                                                               <  1:352007/141‑1 (MQ=255)
                                                          gTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCa                                                                            >  1:563133/1‑141 (MQ=255)
                                                           tataCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCAt                                                                           >  1:351688/1‑141 (MQ=255)
                                                              aCGGATCCAAATGCACATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGtt                                                                        <  1:598/141‑1 (MQ=255)
                                                               cGGATGCAAATGCTCATAATTACGCTCTGCAGTATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAATGTATGTATGATAATAAATAATGTTTGACCATGttt                                                                       >  1:580427/1‑140 (MQ=255)
                                                                        aTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTATTACAat                                                              >  2:66199/1‑141 (MQ=255)
                                                                            tCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGc                                                          >  1:387252/1‑141 (MQ=255)
                                                                               tACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGt                                                       >  2:164797/1‑141 (MQ=255)
                                                                                    gAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGtaataa                                                  >  1:675555/1‑141 (MQ=255)
                                                                                    gAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGtaataa                                                  >  1:59548/1‑141 (MQ=255)
                                                                                           ttAATATTACCTCGTTAAATGATTTGACCTTCTTTTAAAACATACTTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATc                                           <  2:590827/141‑1 (MQ=255)
                                                                                                     ccctttCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTAc                                 <  2:496102/137‑1 (MQ=255)
                                                                                                         ttCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCACTACGTGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGtt                             >  1:523620/1‑141 (MQ=255)
                                                                                                          tCAATGATTATACTATCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTc                            <  1:117320/141‑1 (MQ=255)
                                                                                                               gATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAga                       >  1:206151/1‑140 (MQ=255)
                                                                                                                        ttcttTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAATCATCCAatga              <  2:563133/141‑1 (MQ=255)
                                                                                                                         tcttTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAatgat             >  1:315432/1‑141 (MQ=255)
                                                                                                                                aaaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTg      >  2:400380/1‑141 (MQ=255)
                                                                                                                                    aTAATTGTTCTGACAATATTTCAATACATGACTTAAGTTATTTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTc  <  2:415564/141‑1 (MQ=255)
                                                                                                                                    aTAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTc  <  1:424340/141‑1 (MQ=255)
                                                                                                                                    aTAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTc  <  2:433561/141‑1 (MQ=255)
                                                                                                                                    aTAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTc  <  1:381804/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                        
TTTAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTTC  >  USA300TCH1516_ALE/1416322‑1416594

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑