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% 121.7 / NA 40I216N (ATT→AAT) oppD_4Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (19/21);  total (19/21)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAA  >  USA300TCH1516_ALE/1416336‑1416587
                                                                                                                          |                                                                                                                                 
attAATTCCTTTTTAATTGTGCTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACaa                                                                                                                        <  1:3397/132‑1 (MQ=255)
attAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACaa                                                                                                                        <  1:88566/132‑1 (MQ=255)
aGTAATCCCTCTTTGATTGTGTTCTATATTGAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACaa                                                                                                                        <  1:250016/134‑1 (MQ=255)
aGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAACTGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACaa                                                                                                                        >  2:28045/1‑134 (MQ=255)
aGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACaa                                                                                                                        <  1:428337/134‑1 (MQ=255)
 gTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAACTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAat                                                                                                                       >  2:534511/1‑134 (MQ=255)
 gTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTAGCTCGCCCAATGATTTGTGTTGCTTTAAAAACATAATTGTACTGACAat                                                                                                                       >  1:83192/1‑134 (MQ=255)
 gTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAat                                                                                                                       <  1:227842/134‑1 (MQ=255)
   aaTCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAatat                                                                                                                     <  1:222809/134‑1 (MQ=255)
      tccTGTTTAAGTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTc                                                                                                                  <  2:426562/133‑1 (MQ=255)
      tccTCGTTAATTGTGCTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTc                                                                                                                  <  2:168133/133‑1 (MQ=255)
      ctctctTTAAGTGTGTTTTATTTTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATGACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTc                                                                                                                  <  2:411677/132‑1 (MQ=255)
          ctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATa                                                                                                              <  1:293385/134‑1 (MQ=255)
            ttAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACa                                                                                                            <  1:389108/134‑1 (MQ=255)
                ttGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGAc                                                                                                        <  2:473648/134‑1 (MQ=255)
                 tgtgTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGTCAATATTTCAATCCATTAcc                                                                                                       >  1:43091/1‑133 (MQ=255)
                           atTTACTTAGCCGTTCAGTATACGCATGCAAATGATCATACTTGAAATGATTAATCTTACCTCATTCAATGATTTTACCTTCCTTTAATACATAATTTGACTGTCACTGTTCCCATACATTACTCAACTTAtgt                                                                                             >  2:236294/1‑134 (MQ=255)
                                        ttCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCCATACCTGCCTTATGTTTTGTGTGATaataaata                                                                                >  1:532849/1‑134 (MQ=255)
                                         tCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTAACAATATTTCAATACATGACTTAAGTTATGTGTGATAataaataa                                                                               >  1:465287/1‑134 (MQ=255)
                                            gTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATCTTTCAATACAGTACTTAAGTTATGTGTAATAAAAAAGAATGt                                                                            >  1:254526/1‑134 (MQ=255)
                                            gTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACTTGAATTAAGTTATGTGGGATAATAAATAATGt                                                                            >  2:544595/1‑134 (MQ=255)
                                                       cAAATGTTCATTCTTTAAATTATTAATATTACCTCGTTCAATGATTTGACTTTCTTTTAAAACATAATTTTATTTTCAATATTTCAATACATGTCTTAAGTTATGTTTTATAATAAATAATGTTTTACCATGtt                                                                 <  2:55268/134‑1 (MQ=255)
                                                       cAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGtt                                                                 <  1:79550/134‑1 (MQ=255)
                                                         aaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCt                                                               >  1:429994/1‑134 (MQ=255)
                                                         aaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGAATTACATTATGTGTGATAATAAATAATGATAGACCATgatat                                                               >  2:504041/1‑130 (MQ=255)
                                                         aaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTAACCTTCTTTTAACACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTCACCAtcttct                                                               >  1:179600/1‑134 (MQ=255)
                                                                aTACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACaa                                                        <  1:561658/134‑1 (MQ=255)
                                                                        aaTGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGt                                                <  2:83192/134‑1 (MQ=255)
                                                                                         ctttCAATGAGTGGAGCTTCTTTTAAAACATGATTGTACTGAGAATATTTCGATACTTGACTTGTGTTATGTGTGATAATAAATAATGTTGTACCATGTTCTGATGCACTATGCTGTAATAAATCCATCACTTg                               <  2:246670/132‑1 (MQ=255)
                                                                                         cGTTCAATGATTTGCCCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTg                               <  2:159348/134‑1 (MQ=255)
                                                                                            tCAATGATTTGACCTTCTTTTAAAAAATAATTGTACTGACAATATTTCAATACATGACTTAAGATATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATTACTTGAtt                            >  2:197619/1‑134 (MQ=255)
                                                                                              aaTGATTTGACCTTCTTTTAAAACATAATTGTACTGACCATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTATAATACAATATGCTGTACTAAACCACTCACTTGagtgc                          >  1:597261/1‑130 (MQ=255)
                                                                                                    ttGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAGTATGCTGTAATAAATCCATCACTTGATTACCGTTCa                    >  1:522532/1‑134 (MQ=255)
                                                                                                    ttGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATTCTGAAATAAATCGATCACTTGATTAcctatca                    >  2:549402/1‑129 (MQ=255)
                                                                                                      gACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCaaa                  <  2:454294/134‑1 (MQ=255)
                                                                                                       aCCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATTTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAg                 <  2:143106/134‑1 (MQ=255)
                                                                                                          ttcttTTAAAACATAATTGTACTGACCCTACTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCAATCAAAGCAt              >  1:116159/1‑134 (MQ=255)
                                                                                                                  aaaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTTATCACCGTTCAAAGCATCCAatgat      >  2:59625/1‑134 (MQ=255)
                                                                                                                  aaaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACAGTTAAAGTCTTCCAatgct      >  2:569955/1‑132 (MQ=255)
                                                                                                                      aTAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGGCCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCaa  <  1:473226/134‑1 (MQ=255)
                                                                                                                          |                                                                                                                                 
AGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAA  >  USA300TCH1516_ALE/1416336‑1416587

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑