Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,856,087 T→A 100% P80P (CCT→CCA)  rpoA_2 → DNA‑directed RNA polymerase subunit alpha

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,856,0870TA100.0% 157.7 / NA 52P80P (CCT→CCA) rpoA_2DNA‑directed RNA polymerase subunit alpha
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (22/30);  total (22/30)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAA  >  USA300TCH1516_ALE/2855954‑2856220
                                                                                                                                     |                                                                                                                                     
tGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACggc                                                                                                                                >  1:102678/1‑139 (MQ=255)
  cATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTcaa                                                                                                                              >  2:377980/1‑141 (MQ=255)
  cATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACATTTTCAGTTATCAGTTGATGTGTCATGCAATCATGCGCCAAAACGTcaa                                                                                                                              >  2:134575/1‑141 (MQ=255)
    gggCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTcaaca                                                                                                                            <  2:40301/140‑1 (MQ=255)
     ggCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTcaacaa                                                                                                                           >  2:255733/1‑141 (MQ=255)
           tgTCCTAAAGCTAAATCAATATTGGAACAAGCTTTATTTCAGCAACAAATACATTTTAAAACTGATGTTCAGTCATCATTACCTTTTAAGTTAAAAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATa                                                                                                                     <  2:80169/140‑1 (MQ=255)
                 aaaGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGAtttt                                                                                                               >  1:381560/1‑141 (MQ=255)
                 aaaGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAAGGTTAGAtttt                                                                                                               >  2:56474/1‑141 (MQ=255)
                 aaaGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGACAACAAATGCTCGCtttt                                                                                                               >  1:68984/1‑141 (MQ=255)
                     cTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAg                                                                                                           <  2:131325/141‑1 (MQ=255)
                     cTAAATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGGCATCATTACCTGTGAAGTTATCCGGAGATGTGTTATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAg                                                                                                           <  1:358854/141‑1 (MQ=255)
                        tatCAATTTTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAgttg                                                                                                        <  2:9720/141‑1 (MQ=255)
                                 tGGAGCAAGCTTTATTTCAGCACGAACTTCATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAATTTCACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTAAAAAAATGACAGATATTATAGTTGTCAcagcag                                                                                               >  2:231267/1‑141 (MQ=255)
                                   gAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAgcagca                                                                                             >  1:237512/1‑141 (MQ=255)
                                   gAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAgcagca                                                                                             >  1:236075/1‑141 (MQ=255)
                                      cAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTa                                                                                          <  2:320865/141‑1 (MQ=255)
                                        aGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGa                                                                                        >  1:33507/1‑141 (MQ=255)
                                         gCTTTATTTCATCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGat                                                                                       <  1:7441/141‑1 (MQ=255)
                                           tttATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAACCGTCAGCAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGatat                                                                                     <  1:262226/141‑1 (MQ=255)
                                           tttATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCATCATTAGatat                                                                                     <  2:258669/141‑1 (MQ=255)
                                            ttATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTACCAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATCTTATAGTTGTTACAGCAGCATTAGATAtt                                                                                    >  2:73647/1‑141 (MQ=255)
                                              tattCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGa                                                                                  <  1:148172/139‑1 (MQ=255)
                                               tttCAGCACCAACTACATTATAAAACGGAAGTTAAATCCTCATTACCGTTGAAGTTAACATGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGTTAGATTTTATAGTTGTTACAGCAGCATTAGATATTGaa                                                                                 <  2:39676/141‑1 (MQ=255)
                                                   aGCACCAACTACATTTTAAACCGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGATACAGCAGCATTAGATATTGAattat                                                                             >  1:231374/1‑141 (MQ=255)
                                                   aGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAattat                                                                             >  2:41675/1‑141 (MQ=255)
                                                   aGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAattat                                                                             >  1:50541/1‑141 (MQ=255)
                                                   aGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATATTATAGTTGTTACAGCAGCATTAGATATTGAattat                                                                             >  1:355756/1‑141 (MQ=255)
                                                    gCACCAACTACGTTTTGAAGCGGGAGTTCAGTCAGCATTGCCTTTCAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAGACGTCAACAAATGATTGTTTTTATAGTTGTTACAGCAGCATTAGATATTGAattatt                                                                            <  1:291776/141‑1 (MQ=255)
                                                       ccAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACg                                                                         >  2:336820/1‑141 (MQ=255)
                                                          aCTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTc                                                                      <  1:44321/141‑1 (MQ=255)
                                                           cTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCa                                                                     <  1:266493/141‑1 (MQ=255)
                                                              cATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTg                                                                  >  1:241195/1‑141 (MQ=255)
                                                               aTTTTAAAACGGAAGTTCAGTCACCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTgg                                                                 <  1:364183/141‑1 (MQ=255)
                                                               aTTTTAAAACGCAAGTTCATTCATCATTACCTTTTGAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTgg                                                                 <  1:66010/141‑1 (MQ=255)
                                                                ttttAAAACGGAAGTTCAGTCATCTTTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGt                                                                <  1:172822/141‑1 (MQ=255)
                                                                ttttAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGt                                                                <  1:193413/141‑1 (MQ=255)
                                                                 tttAAAACGGAAGTTCAGTCATCATTACTGTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGCTTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGtt                                                               <  2:306062/141‑1 (MQ=255)
                                                                 tttAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGtt                                                               >  1:361392/1‑141 (MQ=255)
                                                                  ttAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGATATGTGTCATGCAATCATGCGCCAAAACGTCAAAAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTa                                                              <  2:304802/141‑1 (MQ=255)
                                                                         ggAAGTTCAGTCTTCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGa                                                       <  2:170784/141‑1 (MQ=255)
                                                                         ggAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGa                                                       >  2:231541/1‑141 (MQ=255)
                                                                          gAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGaa                                                      <  2:102678/141‑1 (MQ=255)
                                                                                  gTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTg                                              <  1:187314/141‑1 (MQ=255)
                                                                                               tttAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGGCTGTCCCTGGc                                 <  2:83895/141‑1 (MQ=255)
                                                                                                         cAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACa                       <  2:237512/141‑1 (MQ=255)
                                                                                                         cAGGAGATGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACa                       <  2:236075/141‑1 (MQ=255)
                                                                                                            gagaTGTGTCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACatat                    <  2:241195/141‑1 (MQ=255)
                                                                                                                tttctCATGCAATCATGGCCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACgg                <  2:345132/137‑1 (MQ=255)
                                                                                                                  ggtCATGCAATCATGCGCCAAAACGTCAACAAAGGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGAc              <  1:24889/140‑1 (MQ=255)
                                                                                                                    tCATGCAATCATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACGGGTTAAAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGAcgt            >  2:366133/1‑139 (MQ=255)
                                                                                                                             cATGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGCATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCGAATGttt   >  2:162930/1‑140 (MQ=255)
                                                                                                                              aTGCGCCAAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTaa  <  1:156425/141‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                     
TGCATGGCGTTGGTCCTAAAGCTATATCAATATTGGAACAAGCTTTATTTCAGCACCAACTACATTTTAAAACGGAAGTTCAGTCATCATTACCTTTTAAGTTAACAGGAGATGTGTCATGCAATCATGCGCCTAAACGTCAACAAATGATAGATTTTATAGTTGTTACAGCAGCATTAGATATTGAATTATTACGTTCACTGGTTACAACAGAATTTATTTGGTCTGTCCCTGGCCGCTTTGACATATACGGACCTCAAATATTAA  >  USA300TCH1516_ALE/2855954‑2856220

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: ‑