Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,932,853 T→C 100% I799V (ATT→GTT)  USA300HOU_1798 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,932,8530TC97.0% 79.9 / ‑5.5 28I799V (ATT→GTT) USA300HOU_1798hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (13/14);  minor base A (0/1);  total (13/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.09e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CTTTTGATAAACTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAATGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAATTTTA  >  CP000730/1932724‑1932978
                                                                                                                                 |                                                                                                                             
cTTTTGATAAACTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAATCGTCGATTCGaa                                                                                                                    >  1:344347/1‑141 (MQ=255)
      aTAAACTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACACAAGTCGATCCGAAGTGTCg                                                                                                              <  2:199467/141‑1 (MQ=255)
          aCTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGcccc                                                                                                          <  1:115533/141‑1 (MQ=255)
          aCTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCCCTATCTGTTTACGCCAAACGTCGATTCGAACTGTCGcccc                                                                                                          <  1:290751/141‑1 (MQ=255)
                ctatTCATTTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAAc                                                                                                    <  2:80436/140‑1 (MQ=255)
                atatTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAAc                                                                                                    <  2:387245/141‑1 (MQ=255)
                atatTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAAc                                                                                                    <  1:193432/141‑1 (MQ=255)
                     cAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTCTATATATATCTCAATCTTCGATTCGAAGTGTCGCCCCTAAAACAGAAg                                                                                               >  1:205089/1‑141 (MQ=255)
                     cAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGaaa                                                                                               >  2:302138/1‑140 (MQ=255)
                     cAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAg                                                                                               >  1:227842/1‑141 (MQ=255)
                       aTTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGACGTGTCGCCCCTAAAACAGAATCa                                                                                             >  2:233431/1‑141 (MQ=255)
                          gTTTGCCGAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCatat                                                                                          <  1:242339/141‑1 (MQ=255)
                           tttGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCAtata                                                                                         <  2:91730/141‑1 (MQ=255)
                             tGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTATTCATAAATATAATTAGCAATCTCTATATGTATTTCAACAACGTCGATTCGAAGTGTGGCACCTAAAACAGAAACATATAAt                                                                                       >  2:8097/1‑141 (MQ=255)
                              gCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATc                                                                                      <  1:365386/141‑1 (MQ=255)
                              gCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATc                                                                                      <  1:328927/141‑1 (MQ=255)
                               ccTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATCAATATAATTAGCAATCTCCATATGTATTTCCCAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAATCATATAATCt                                                                                     >  2:119180/1‑141 (MQ=255)
                                           tctcATTAAAATATGAGTATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACtatata                                                                         <  2:147683/141‑1 (MQ=255)
                                           tctcATTAAAATATGAGTATATACCAGTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACtatata                                                                         <  2:147680/141‑1 (MQ=255)
                                                    aaTATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCAtt                                                                >  2:111161/1‑141 (MQ=255)
                                                                           tATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTtaata                                         >  1:4016/1‑141 (MQ=255)
                                                                                aaTATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTTACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCa                                    <  1:31172/141‑1 (MQ=255)
                                                                                       cttcATAAATATAATTAGCAATCTCTATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAAttt                             >  1:137284/1‑141 (MQ=255)
                                                                                        ttcATAAATATAATTAGCAAGCTCTATAGGTATTTCACAAACGTCGATTCGAAGAGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAAtttt                            >  1:256431/1‑141 (MQ=255)
                                                                                                          aaTCTCTATATGTATTTCACAAACGTCGATTCGATGTGTCTTCCCTAAATTAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTTATATAATTTTATTAAACTAATAATTTTAGTTGGATATGTTTTGat          >  2:94006/1‑140 (MQ=255)
                                                                                                              tctATATGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGaataat      >  1:65671/1‑141 (MQ=255)
                                                                                                                tataTGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAAttt    <  1:381165/141‑1 (MQ=255)
                                                                                                                  aatGTATTTCACAAACGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAATTTTa  <  1:8203/140‑1 (MQ=255)
                                                                                                                                 |                                                                                                                             
CTTTTGATAAACTAATATATTCAATTGTTTGCCTAGCATAATCTCTCATTAAAATATGAGGATATACCATTTCTTTATCAAATATTTCTTCATAAATATAATTAGCAATCTCTATATGTATTTCACAAATGTCGATTCGAAGTGTCGCCCCTAAAACAGAAGCATATAATCTTTCGACTATATATGGATCATTGTTATTTTCAAATAATTTTAATAAACCAATAATTTTAGTTGGAAATGTTTTGAATAATTTTA  >  CP000730/1932724‑1932978

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: