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% 150.5 / NA 47A92V (GCA→GTA) rpsI30S ribosomal protein S9
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (20/27);  total (20/27)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTAA  >  USA300TCH1516_ALE/2352687‑2352948
                                                                                                                                |                                                                                                                                     
aCAATTAACGTTTTGAGAATTGAGGTGAACTACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTaataat                                                                                                                            <  1:214050/140‑1 (MQ=255)
aCAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTaataat                                                                                                                            <  1:618615/140‑1 (MQ=255)
 cAATGAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAAGATGTACTTCtaataaat                                                                                                                           >  1:343150/1‑138 (MQ=38)
      aaCGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGa                                                                                                                      <  1:567659/140‑1 (MQ=255)
       aCGTTTTGAGAATTGAGGTGAACGTCGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAg                                                                                                                     <  1:727869/140‑1 (MQ=255)
       aCGTTTTGAGAATTGAGGTGAACGACGAGCTTCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTTACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAg                                                                                                                     <  1:524368/140‑1 (MQ=255)
        cGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGc                                                                                                                    >  1:754448/1‑140 (MQ=255)
         gTTTTGAGAATTGAGGTGAACGCCGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGGGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCg                                                                                                                   <  1:715583/140‑1 (MQ=255)
                taaTTGAGGTGAACGACGGGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCAGTATTCAGGATCTACTTCTAATAATGCACGATCGATTCCGt                                                                                                            <  1:524235/139‑1 (MQ=255)
                    tGAGGTGAACGACGAGCTGCTTTAAGTCTTTGTTTTTTTCGTTCTTTCATAAGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACg                                                                                                        <  1:356191/140‑1 (MQ=255)
                     gAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACgg                                                                                                       <  1:654965/140‑1 (MQ=255)
                                cgaGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagc                                                                                            <  1:661346/140‑1 (MQ=255)
                                cgaGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagc                                                                                            <  1:265137/140‑1 (MQ=255)
                                cgaGCTGCTTCAAGGCCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagc                                                                                            <  1:243836/140‑1 (MQ=255)
                                      gctTCAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGCAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTACTAATGTACGAGCGATTCCGTGACGGATTGCTTGAGCTTGTcc                                                                                      >  1:538980/1‑140 (MQ=255)
                                         ttataaCCTTGTTTTTTACGTTCTTTCATTCGTTGGTCACGAGTAAGTAATCCAGTGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGt                                                                                   <  1:106924/135‑1 (MQ=255)
                                         ttAAGACCTTGTTGTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGt                                                                                   <  1:93024/140‑1 (MQ=255)
                                            aGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTgga                                                                                >  1:549706/1‑138 (MQ=255)
                                                  ggTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGATCCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccacc                                                                          <  1:384855/140‑1 (MQ=255)
                                                  ggTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccacc                                                                          <  1:503134/140‑1 (MQ=255)
                                                  ggTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccacc                                                                          <  1:347926/140‑1 (MQ=255)
                                                     tttttACGTTCTTTAATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAacaaccacc                                                                       >  1:409648/1‑140 (MQ=255)
                                                      ttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAAccaccacca                                                                      >  1:567926/1‑140 (MQ=255)
                                                        ttcctttCTTTCATACGGTGGTCACGAGTAATTAATACAGCGCTTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAACGCACGAGCGATTCCGTGACGGATAGCTTGATCTTGTCCAGTGAAACCACCACCATg                                                                    <  1:42888/135‑1 (MQ=255)
                                                        ttACGTTCTTTCATTCGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTCTTCGTCCTGGGTATTCAGGATCTACTTCTAAGAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATg                                                                    <  1:717138/140‑1 (MQ=255)
                                                                 ttCATGCGTGGGTCACGAGTAAGTAATCCAGTGCGTTTTAAAGAACCTCTGCATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAAc                                                           <  1:43189/140‑1 (MQ=255)
                                                                     tACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTaaa                                                       >  1:33931/1‑140 (MQ=255)
                                                                       cGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAGCCACCACCATGAACGTTAACTAAAAc                                                     >  1:3221/1‑140 (MQ=255)
                                                                         tGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcat                                                   >  1:221664/1‑140 (MQ=255)
                                                                         tGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACAATGAACGTTAACTAAAActt                                                   >  1:737647/1‑138 (MQ=255)
                                                                            gTCACGAGTAAGTAATCCAGCGCGTTTTTAACAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcataat                                                >  1:182001/1‑140 (MQ=255)
                                                                            gTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTCACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcatcat                                                >  1:3483/1‑140 (MQ=255)
                                                                                   gtaagtaaTCCAGTGTGTTTTAAAGGAACTCTGTATTAAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTAcc                                         <  1:346053/140‑1 (MQ=255)
                                                                                         gaTCCAGCGCGTTTTAAAGAACCTCCGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGt                                   <  1:561086/139‑1 (MQ=255)
                                                                                         aaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGt                                   <  1:386483/140‑1 (MQ=255)
                                                                                         aaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGt                                   >  1:51960/1‑140 (MQ=255)
                                                                                            ccAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGACCTTGTCCAGTGAAACCACCACCATGAACGTTAAATAAAACAACATAGTTACCTTTAGTTTc                                >  1:269722/1‑140 (MQ=255)
                                                                                                     tttAAAGCACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATCGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATc                       <  1:515652/140‑1 (MQ=255)
                                                                                                     tttAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAACACATCATAGTTACCTTTAGTTTCAGTTACATc                       <  1:548300/140‑1 (MQ=255)
                                                                                                     tttAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCAACACCATGAACGTTAACTAAAACATCATAGTCACTTTTAATTTAAGTTGCact                       >  1:102609/1‑138 (MQ=255)
                                                                                                      ttAAAGACCCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTACCTAAAACATCATAGTTACTTTAAGTTTCAGTTACATCa                      <  1:426659/140‑1 (MQ=255)
                                                                                                           gcaCCTCTTTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCTTGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAtgg                 <  1:403240/138‑1 (MQ=255)
                                                                                                           gAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCGAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAtgg                 >  1:633708/1‑140 (MQ=255)
                                                                                                           gAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAtgg                 >  1:112438/1‑140 (MQ=255)
                                                                                                           gAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTCTAGTTTCAGTTACATCAAAtgg                 >  1:461669/1‑140 (MQ=255)
                                                                                                                 ctGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTAAGTTTCAGTTACATCAAATggatggtt           >  1:319187/1‑140 (MQ=255)
                                                                                                                          ggATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTACAGTTACATCAAATGGTTGGTATAAGTCTaa  >  1:677120/1‑140 (MQ=255)
                                                                                                                                |                                                                                                                                     
ACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTAA  >  USA300TCH1516_ALE/2352687‑2352948

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: ‑