Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 984,788 C→T 10.0% A50T (GCT→ACT)  USA300HOU_RS04870 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE984,7880CT10.0% 119.2 / 4.9 40A50T (GCT→ACT) USA300HOU_RS04870hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (15/21);  new base T (2/2);  total (17/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.11e-01

AAATATTCAAAATACAAAACATTAATGGCCAAAAATAAAAGCCGCCTTTATCTGGGCAGCTTCAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCATTTGCATTAATAATAATGCCCAAAAGAATGTTACGAG  >  USA300TCH1516_ALE/984649‑984926
                                                                                                                                           |                                                                                                                                          
aaaTATTCAAAATACAAAACATTAATGGCCAAAAATAAAAGCCGCCTTTATCTGGGCAGCTTCAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTgcagca                                                                                                                                           <  1:457207/141‑1 (MQ=255)
      tCAAAATACAAAACATTAATGGCCAAAAATAAAAGCCGCCTTTATCTGGGCAGCTTCAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAAtt                                                                                                                                     <  1:100164/141‑1 (MQ=255)
         aaaTACAAAACATTAATGGCCAAAAATAAAAGCCGCCTTTATCTGGGCAGCTTCAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCt                                                                                                                                  >  2:39520/1‑141 (MQ=255)
               aaaaCATTAATGGCCAAAAATAAAAGCCGCCTTTATCTGGGCAGCTTCAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGaaa                                                                                                                            >  1:356252/1‑141 (MQ=255)
                     ttAATGGCCAAAAATAAAAGCCGCCTTTATCTGGGCAGCTTCAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTg                                                                                                                      >  1:296246/1‑141 (MQ=255)
                        aTGGCCAAAAATAAAAGCCGCCTTTATCTGGGCAGCTTCAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAAc                                                                                                                   <  2:455874/141‑1 (MQ=255)
                        aTGGCCAAAAATAAAAGCCGCCTTTATCTGGGCAGCTTCAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAAc                                                                                                                   <  2:393240/141‑1 (MQ=255)
                                 aaTAAAAGCCGCCTTTATCTGGGCAGCTTCAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGcc                                                                                                          >  2:291767/1‑141 (MQ=255)
                                                    tGGGCAGCTTCAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTa                                                                                       >  1:424669/1‑141 (MQ=255)
                                                            ttCAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGTAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAg                                                                               >  1:403204/1‑141 (MQ=255)
                                                            ttCAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGTAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAg                                                                               >  1:403337/1‑141 (MQ=255)
                                                            ttCAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAg                                                                               >  2:403973/1‑141 (MQ=255)
                                                            ttCAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAg                                                                               >  2:253466/1‑141 (MQ=255)
                                                            ttCAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAg                                                                               >  1:426211/1‑141 (MQ=255)
                                                              cAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCt                                                                             <  2:59307/141‑1 (MQ=255)
                                                              cAATAATAAGAAAGACATATTTCATTTTATACTAAAGAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCCCTACATTTAAGCt                                                                             <  2:43052/141‑1 (MQ=255)
                                                                ataataAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGt                                                                           <  2:86375/141‑1 (MQ=255)
                                                                 taataaGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGtc                                                                          <  2:296246/141‑1 (MQ=255)
                                                                            aCATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACctacta                                                               <  1:173005/141‑1 (MQ=255)
                                                                            aCATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACctacta                                                               <  1:446866/141‑1 (MQ=255)
                                                                                atTTCATTTTATACTAAATCGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCt                                                           >  1:224119/1‑141 (MQ=255)
                                                                                 tttCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTCCTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTa                                                          >  2:50433/1‑141 (MQ=255)
                                                                                 tttCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTa                                                          >  2:60378/1‑141 (MQ=255)
                                                                                                   aGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAAcc                                        <  1:394177/141‑1 (MQ=255)
                                                                                                   aGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAAcc                                        <  1:224112/141‑1 (MQ=255)
                                                                                                     ttATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCAt                                      >  2:429732/1‑141 (MQ=255)
                                                                                                       aTTGTGATGCATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCAttt                                    >  2:20080/1‑141 (MQ=255)
                                                                                                       aTTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCAttt                                    >  1:19529/1‑141 (MQ=255)
                                                                                                          gtgATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCATTTGCa                                 >  2:158241/1‑141 (MQ=255)
                                                                                                            gatgaATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCATTTGCAtt                               <  1:445383/141‑1 (MQ=255)
                                                                                                                   cTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCATTTGCATtaataata                        <  1:39520/141‑1 (MQ=255)
                                                                                                                        ggcggTTTAATTACTGCAGCAGAAACTGCTGTGAACTTCGTGAACAATACTGCCCTGATAATTCGATTCACTACACTTAAGCAGGCTCCACCTACTAGGCTATAAAGTACAAAGTTACCCCTTTGCATtaataaaacggcc                   <  2:9004/141‑8 (MQ=255)
                                                                                                                        ggcggTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCATTTGCATTAATAATAATGcc                   <  1:414597/141‑1 (MQ=255)
                                                                                                                        ggcggTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCATTTGCATTAATAATAATGcc                   <  1:305300/141‑1 (MQ=255)
                                                                                                                        ggcggTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCATTTGCATTAATAATAATGcc                   <  1:178510/141‑1 (MQ=255)
                                                                                                                            gTTTAATTACTGCAGTAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCATTTGCATTAATAATAATGCCCaaa               <  2:403337/141‑1 (MQ=255)
                                                                                                                            gTTTAATTACTGCAGTAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCATTTGCATTAATAATAATGCCCaaa               <  2:403204/141‑1 (MQ=255)
                                                                                                                            gTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCATTTGCATTAATAATAATGCCCaaa               <  2:426211/141‑1 (MQ=255)
                                                                                                                            gTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCATTTGCATTAATAATAATGCCCaaa               <  1:403973/141‑1 (MQ=255)
                                                                                                                            gTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCATTTGCATTAATAATAATGCCCaaa               <  1:253466/141‑1 (MQ=255)
                                                                                                                                    aCTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCATTTGCATTAATAATAATGCCCAAAAGAATGtt       <  2:424669/141‑1 (MQ=255)
                                                                                                                                        cagcaAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCATTTGCATTAATAATAATGCCCAAAAGAATGTTACGa   >  1:141067/1‑141 (MQ=255)
                                                                                                                                         agcaAAAATTACTGTGAAAATCTTGAACAATACTGCCATGATAATTGTATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCCTATGATTTAAGAATAATGCCCAAAAGAATGTTACGAg  <  2:20398/141‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                          
AAATATTCAAAATACAAAACATTAATGGCCAAAAATAAAAGCCGCCTTTATCTGGGCAGCTTCAATAATAAGAAAGACATATTTCATTTTATACTAAATAGTTATTGTGATGAATCTTTCGGCGGTTTAATTACTGCAGCAAAAATTGCTGTGAAAATCGTGAACAATACTGCCATGATAATTGGATTCACTACATTTAAGCTGTCTCCACCTACTAGGCTATTAAGTACAAAGTTAACCATTTGCATTAATAATAATGCCCAAAAGAATGTTACGAG  >  USA300TCH1516_ALE/984649‑984926

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑