Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,289,252 C→A 100% A80S (GCT→TCT)  cdaA ← Cyclic di‑AMP synthase CdaA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,289,2520CA100.0% 86.1 / NA 32A80S (GCT→TCT) cdaACyclic di‑AMP synthase CdaA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (15/17);  total (15/17)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAG  >  USA300TCH1516_ALE/2289119‑2289385
                                                                                                                                     |                                                                                                                                     
gCCTTTGAAACCGATTGAATCAATTTATCTTCAACTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATAc                                                                                                                                 <  1:143042/140‑1 (MQ=255)
 ccTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATAcc                                                                                                                                >  2:256291/1‑140 (MQ=255)
  cTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCCAATTTCTGGTTGGAATATTACTATTAAAGATAATAccc                                                                                                                               <  2:309643/140‑1 (MQ=255)
               tGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAAc                                                                                                                  <  1:303363/140‑1 (MQ=255)
                   tCAATTTCTCTTCATTTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGata                                                                                                              <  1:87526/140‑1 (MQ=255)
                       tgtctcTTCATCTTTACTATACTTATTATAAGTATAGCTTTTTAAAAAGCTACCTCTACCAAGTTTTTCTAACGCACGTATAATTTCTTGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGa                                                                                                          <  1:105938/138‑1 (MQ=255)
                            ctTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGaataat                                                                                                     >  1:150877/1‑140 (MQ=255)
                            ctTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGaataat                                                                                                     >  2:208731/1‑140 (MQ=255)
                                   tttACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTGCCTCTACCACGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATGCCCCCCATTAAATCACGATATCGAATAATATAAATg                                                                                              >  1:147213/1‑140 (MQ=255)
                                      aCTATACGTATGAGAAGTATAGCGGTTTATAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATCTTACTATAACACATTATACACCGCATGGAATAATGATATCGAGTAATTTAGATGTTg                                                                                           >  2:250215/1‑140 (MQ=255)
                                            cGTATTAGAAGGATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATCCCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCa                                                                                     <  2:102755/140‑1 (MQ=255)
                                                 tAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTc                                                                                >  2:274957/1‑140 (MQ=255)
                                                  aGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCa                                                                               >  2:43899/1‑140 (MQ=255)
                                                     aGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGATCAata                                                                            >  1:68588/1‑140 (MQ=255)
                                                      gTATAGCGTCTTAAACAGCTACCTCTACCCAGCGGTTCTAACGCACGTCTAATTTCTCGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTATATGTTTCAGTCAAGTTCAatat                                                                           <  2:296012/140‑1 (MQ=255)
                                                             gatttAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTAGTTGGAATATTACTATTAAAGATAATACCCCCCATAGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACtt                                                                    >  2:263353/3‑140 (MQ=255)
                                                             gTTTTAAAAAGCTACCTCTTCCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACtt                                                                    <  2:339713/140‑1 (MQ=255)
                                                              ttttAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTa                                                                   <  2:149124/140‑1 (MQ=255)
                                                                    aaaGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCTTACTTATctgct                                                             >  2:237076/1‑140 (MQ=255)
                                                                       gCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATCATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGAc                                                          >  2:64669/1‑140 (MQ=255)
                                                                                aCCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCCTTGAACAACGATATCGAAAACTTTAGATCTTGCAGTCAAATTCAATATCACAAATCTCTCCTGACCCAGAAccc                                                 >  2:349852/1‑138 (MQ=255)
                                                                                     ggcttgcTAAAGAACGTCTAATTTCCGGTTGGAATATCACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAAAAATTTAGATGTTCCAGTCAAGTTCAACATCATACTTATCTGCTGACCAATAACAATTACt                                            <  2:139678/134‑1 (MQ=255)
                                                                                          tCTAACGCACGTATAATTTTTGGTTGAAATATTAATAATAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAatat                                       <  1:322904/140‑1 (MQ=255)
                                                                                             aacgaacgTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGAACAATAACAATTACTAATATccc                                    <  2:236544/140‑1 (MQ=255)
                                                                                                  aCGTCTAATTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTaa                               >  1:108173/1‑140 (MQ=255)
                                                                                                       tAATGTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATATTTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTTACCATTATCAATTACTTATATCCCTTTAAGTTAt                          <  2:115833/140‑1 (MQ=255)
                                                                                                        aaTTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTAAAGTTCAAAAGTATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTAAAATAAtt                         >  1:276445/1‑140 (MQ=255)
                                                                                                         aTTTCTGGTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTg                        <  2:61374/140‑1 (MQ=255)
                                                                                                               ggTTGGCATATCACTATTAAAGATAATACCCCCCATTGAATATCGACATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGc                  <  2:137656/140‑1 (MQ=255)
                                                                                                               ggTTGGAATATTACTATTAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGc                  <  2:108173/140‑1 (MQ=255)
                                                                                                                     tatatTACTATTAACGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGt            <  2:187013/139‑1 (MQ=255)
                                                                                                                               ttAAAGATAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAg  >  2:184137/1‑140 (MQ=255)
                                                                                                                                     |                                                                                                                                     
GCCTTTGAAACCGATTGAATCAATTTCTCTTCATCTTTACTATACGTATTAGAAGTATAGCGTTTTAAAAAGCTACCTCTACCAAGTTGTTCTAACGCACGTCTAATTTCTGGTTGGAATATTACTATTAAAGCTAATACCCCCCATTGAATAACGATATCGAATAATTTAGATGTTGCAGTCAAGTTCAATATCATACTTATCTGCTGACCAATAACAATTACTAATATCCCTTTAAGTAATTGTATCGCTTTAGTTCCCTTAAAG  >  USA300TCH1516_ALE/2289119‑2289385

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: ‑