Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,352,815 G→A 100% A92V (GCA→GTA)  rpsI ← 30S ribosomal protein S9

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,352,8150GA100.0% 120.7 / ‑6.5 45A92V (GCA→GTA) rpsI30S ribosomal protein S9
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (24/20);  minor base T (0/1);  total (24/21)
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.

CGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTA  >  USA300TCH1516_ALE/2352681‑2352941
                                                                                                                                      |                                                                                                                              
cGTCCGACAATTAACGTTTTGAGAATTGATGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCt                                                                                                                           <  1:94743/140‑1 (MQ=255)
 gTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCta                                                                                                                          >  2:427649/1‑140 (MQ=255)
         aTTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTTTTTATTCAGGATCTACTTCTAATAATGCa                                                                                                                  >  1:121243/1‑140 (MQ=255)
          ttAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCAc                                                                                                                 >  1:417486/1‑140 (MQ=255)
           tAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATAAGTGGGTCACGAGTAAGTAATCCAGCGTGTTTTAAAGAACCTCTGTATTTAGGATCTTTTTTTAATATTGCaag                                                                                                                <  2:282875/140‑3 (MQ=37)
            aaCGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGa                                                                                                               <  2:177964/140‑1 (MQ=255)
             aCGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAACACCTGGTTTTTTACGTCCTTTCCTACGTGGGTCACGACTACGTAATCCAGCGCGTCTTAAAGCAACTATGTATTCAGGATTTACTCCTAATAATGCACGAg                                                                                                              <  2:459177/140‑1 (MQ=37)
                     agaATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCg                                                                                                      >  1:360020/1‑140 (MQ=255)
                     agaATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTAGTCAGGATCTACTTCTAATCATGCACGAGCGAttggg                                                                                                      >  2:486386/1‑137 (MQ=255)
                             ggTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTTACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGAt                                                                                              <  1:538380/140‑1 (MQ=255)
                             ggTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGAt                                                                                              <  1:8869/140‑1 (MQ=255)
                              gTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATa                                                                                             >  1:290155/1‑140 (MQ=255)
                                      cgaGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGAGTCACGAGTCAGTAATCCATCGCGTTTTAAAGAACCTCTGTATTCATGATCTACTACTAATAAAGCACGACCGATGCCATGACGGATagcttgggc                                                                                     >  1:128415/1‑140 (MQ=255)
                                       gaGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagct                                                                                    <  1:388952/140‑1 (MQ=255)
                                       gaGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagct                                                                                    >  2:144434/1‑140 (MQ=255)
                                          ctgctTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTGTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGt                                                                                 >  2:528576/1‑140 (MQ=255)
                                                   gACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGGTAGCTTGCGCTTGTCCAGTGaaa                                                                        >  2:117012/1‑140 (MQ=255)
                                                   gACCTGGTTTTTTAAGTTATTTCATACGTGGGTCAGGAGTAAGTAATACAGAGTGTTTTAAAGAACCTCTGTATTCAGGATCTAATTCTAATAATGCACGAGCGATTTGCGGAAGGATAGGTTAAGCTTGTCGAGTGaaa                                                                        >  2:117084/1‑140 (MQ=255)
                                                           ttttttCGTTCTTTAGTGCGGTGGTTACGAGTAATTAATCTAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCAAGAGCGTGTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccaccacc                                                                <  1:242507/140‑1 (MQ=255)
                                                             tttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGTACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCAt                                                              <  1:201044/140‑1 (MQ=255)
                                                              ttACGTTCTTTCATATGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCATGATCTACTTCTAATAATGCACGAGCGATTCCGGGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATg                                                             <  1:141901/140‑1 (MQ=255)
                                                                aCGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTTCGTGACGGTTAGCTTGAGCTTGTCCAGTTAAACCACACCCATaaa                                                           >  2:382355/1‑140 (MQ=255)
                                                                       ttCATACGGTGGTCACGTTTAAGTAATCCTGCGTGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGGGAAACCACCACCATGAACGTTAAc                                                    <  2:128415/140‑1 (MQ=255)
                                                                        tCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACt                                                   <  1:290196/140‑1 (MQ=255)
                                                                          aTACGTGGGTCACGAGGGGGTAATCCAGCGCGTTTTATAGAACCGGTGTATACAGGATGTACTTGTAATAATGCAAGAGCGATTCGTAGACGGATAGCTTGAGCTTGTCCAGTGGAACCACCGCCATGGACGTCTACTaa                                                 >  2:303370/1‑140 (MQ=255)
                                                                             cGTGGGCCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTTAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAc                                              <  2:2133/140‑1 (MQ=255)
                                                                                  gTCACGAGTAAGTAATCCAGCGAGGTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTAACGGGTAGCTTGAGATTGTCCGGTGCAACCACCGCCATGCACTTTAACTAAAActtctt                                         >  2:92752/1‑138 (MQ=255)
                                                                                  gTCACGAGGAAGTAATCCAGCGCGTGTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcatcat                                         <  2:174905/140‑1 (MQ=255)
                                                                                      cGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGtt                                     >  2:175348/1‑140 (MQ=255)
                                                                                      cGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGtt                                     >  2:279578/1‑140 (MQ=255)
                                                                                      cGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCCTGACGGATCGCTTGAGCTTGTCCTGTGAAACCACCACCATGAACGTTAACTACAGCTTCATGGtt                                     >  1:171729/1‑140 (MQ=255)
                                                                                              taaTCCAGCGCGTCTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCGCCACCATAAACGTTAACTAAAACATCATAGTTACCGTTAg                             <  1:393558/140‑1 (MQ=255)
                                                                                               aaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGATCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGt                            >  1:213321/1‑140 (MQ=255)
                                                                                                  ccAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGAGAAACCTCCCCCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTc                         <  1:402989/140‑1 (MQ=255)
                                                                                                             tAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATAATAGTTACCTATAGTTTCAGTTACAtaac              >  2:208558/1‑137 (MQ=255)
                                                                                                              aaaTAACCTCTGTATTCAGGATCTACTTCTAATAATGCACTAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCaaa             <  1:387428/140‑1 (MQ=255)
                                                                                                              aaaGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATACCTGGAGCTTGTCCAGGGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTCGTTTCAGTTACACCaaa             >  2:169514/1‑140 (MQ=255)
                                                                                                              aaaGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTACGTGACGGATAGCTTGGGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCaaa             >  2:514362/1‑140 (MQ=255)
                                                                                                               aaGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAATTCACCACCATGATCGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAt            <  1:144434/140‑1 (MQ=255)
                                                                                                                 gAACCTCTGTAGTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCGTGAGCTTGTCCAGTGAAACCACCACCATGACCGTTAACTAAAGCATCATAGTTACCTTTAGTTTCAGTTACATCAAAtgg          <  2:209026/140‑1 (MQ=255)
                                                                                                                    ccTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAtggttg       <  1:519613/140‑1 (MQ=255)
                                                                                                                     ctctGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCTGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAtggttgg      <  1:252335/140‑1 (MQ=255)
                                                                                                                       ctGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCGTTTACATCAAATggttgttt    >  2:33707/1‑140 (MQ=255)
                                                                                                                        tGTATTCAGGATCTACTTCTACTAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGttt   >  1:59987/1‑140 (MQ=255)
                                                                                                                         gTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTa  >  1:289711/1‑140 (MQ=255)
                                                                                                                                      |                                                                                                                              
CGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTA  >  USA300TCH1516_ALE/2352681‑2352941

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑