Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,347,403 G→T 12.3% G429G (GGC→GGA)  USA300HOU_RS11980 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,347,4030GT12.3% 93.8 / 5.2 41G429G (GGC→GGA) USA300HOU_RS11980hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (15/21);  new base T (3/2);  total (18/23)
Fisher's exact test for biased strand distribution p-value = 6.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.08e-01

GATTCAATAATTGATCTTATTTACTGTATTTGACTTCTATACTTTTGAAAAAATTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTATTTTCGAAGAAGATAAAGAATTAAACTCCTCATTCACATGTTGTTTATTATATTCTGG  >  USA300TCH1516_ALE/2347267‑2347543
                                                                                                                                        |                                                                                                                                            
gATTCAATAATTGATCTTATTTACTGTATTTGACTTCTATACTTTTGAAAAAATTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGTTTTTGTAGAAAAAAAAGTATTGCCtt                                                                                                                                          >  1:225084/1‑141 (MQ=255)
   tCAATAATTGATCTTATTTACTGTATTTGACTTCTATACTTTTGAAAAAATTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCAc                                                                                                                                       <  1:392485/141‑1 (MQ=255)
       aaatTAATCTTATTTACTGTATTTGACTTCTATACTTTTGAAAAAATTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAATACACAATGCAAATATGGTATTACAAAAAAAAAAGTATTGCCTTCACTTAt                                                                                                                                   <  2:571299/140‑1 (MQ=255)
            gATCTGATTTAATGTATTTGACTTCTATACTTTTGAAAAAATTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGtt                                                                                                                              <  2:344975/141‑1 (MQ=255)
              tCTTATTTACTGTATTTGACTTCTATACTTTTGAAAAAATTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGa                                                                                                                            >  1:229872/1‑141 (MQ=255)
                  aTTTACTGTATTTGACTTCTATACTTTTGAAAAAATTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAAt                                                                                                                        <  1:160963/141‑1 (MQ=255)
                            tttGACTTCTATACTTTTGAAAAAATTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCtt                                                                                                              >  1:75134/1‑141 (MQ=255)
                                 cTTCTATACTTTTGAAAAAATTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATACTTAACATCCTTAACAt                                                                                                         >  2:325712/1‑141 (MQ=255)
                                 cTTCTATACTTTTGAAAAAATTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGAAGTAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATTCTTAAAAt                                                                                                         >  2:481561/1‑141 (MQ=255)
                                   tCTATACTTTTGAAAAAATTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCCGTTGATAATTAACATCCTTAAAAttt                                                                                                       >  1:107042/1‑141 (MQ=255)
                                   tCTATACTTTTGAAAAAATTTTCTATATCAACTTTATACATATTTAAAATATCTTTATTGAAAACACAATGCAAATATGGTTTTGCAGAAAAAAAAATATTTCCTTTACTTATTAGTTTATAATTAAAATTCTTTAAAttt                                                                                                       >  2:392091/1‑141 (MQ=255)
                                          ttttGAAAAAATTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTtaaataaa                                                                                                <  1:477125/141‑1 (MQ=255)
                                           tttGAAAAAATTTTCTATATCAACTTTATCAATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCATAAAAATTTatataaat                                                                                               >  1:34858/1‑141 (MQ=255)
                                            ttGAAAAAATTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAaataaata                                                                                              >  2:576675/1‑141 (MQ=255)
                                              gAAAAAATTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTTCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAaataat                                                                                            >  1:180207/1‑141 (MQ=255)
                                              gAAAAAATTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTTCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAaataat                                                                                            >  1:414738/1‑141 (MQ=255)
                                                aaaaaTTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAaataataa                                                                                          <  1:6879/141‑1 (MQ=255)
                                                          tataTCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCAtt                                                                                <  2:527877/141‑1 (MQ=255)
                                                                   tttATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGc                                                                       <  1:514751/141‑1 (MQ=255)
                                                                    ttATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTTTTTGGCt                                                                      >  1:76054/1‑141 (MQ=255)
                                                                     tATCCATATTTAAAATATCTTTATTGAACACACGAGGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGACAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTa                                                                     <  1:57536/141‑1 (MQ=255)
                                                                     tATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGTCTa                                                                     >  2:379748/1‑141 (MQ=255)
                                                                                 aaaTATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTTCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTAttt                                                         <  2:180207/141‑1 (MQ=255)
                                                                                 aaaTATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTTCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTAttt                                                         <  2:414738/141‑1 (MQ=255)
                                                                                   atatCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTATTTTc                                                       <  1:568094/141‑1 (MQ=255)
                                                                                   atatCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTATTTTc                                                       <  1:455733/141‑1 (MQ=255)
                                                                                      tCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTATTTTCgaa                                                    <  1:217918/141‑1 (MQ=255)
                                                                                        tttATTGAACACACAATGCAAATATGGTTTTGAAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTATTTTCgaaga                                                  <  2:609021/141‑1 (MQ=255)
                                                                                          tATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTATTTTCGaagaag                                                <  1:583968/141‑1 (MQ=255)
                                                                                            ttGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTATTTTCGAAGAAGAt                                              >  1:558612/1‑141 (MQ=255)
                                                                                                    aaaaggtaaaTATTGAATTTCAAAAAAAAAATTATTGCCTTCACTTATCAGTTAATAATTAACATCCTTAAAAATTAAATAAATAATAATACCATAATTTTCTTTGACTAAATTTTTTATTTTCGAAGAAGATAAAGAAtt                                      <  2:144982/134‑1 (MQ=255)
                                                                                                       aTGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTATTTTCGAAGAAGATAAAGAATTaaa                                   >  1:232559/1‑141 (MQ=255)
                                                                                                                tGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTATTTTCGAAGAAGATAAAGAATTAAACTCCTCAtt                          <  1:133674/141‑1 (MQ=255)
                                                                                                                 ggTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATAATCTTCTTTGGCTAAATTCTTTATTTTCGAAGAAGATAAAGAATTAAACTCCTCATTc                         >  1:121403/1‑141 (MQ=255)
                                                                                                                     ttGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATGATGTTGCCAGGGGCTTTGGCTAAATTCTTTATTTTCGAAGAAGATAAAGAATTAAACTCCTCATTCACAt                     >  1:149234/1‑141 (MQ=255)
                                                                                                                      tGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTATTTTCGAAGAAGATAAAGAATTAAACTCCTCATTCACAtg                    <  1:280593/141‑1 (MQ=255)
                                                                                                                       gCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTATTTTCGAAGAAGATAAAGAATTAAACTCCTCATTCACAtgt                   <  1:109172/141‑1 (MQ=255)
                                                                                                                           aaaaaaaaGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTATTTTCGAAGAAGATAAAGAATTAAACTCCTCATTCACATgttgtt               <  1:591883/141‑1 (MQ=255)
                                                                                                                              aaaaaGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTATTTTCGAAGAAGATAAAGAATTAAACTCCTCATTCACATGTTGTttat            <  1:576675/141‑1 (MQ=255)
                                                                                                                                aaaGTATTGTCATCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTATTTTCGAAGAAGATAAAGAATTAAACTCCTCATTCACATGTTGTttatta          <  2:169002/141‑1 (MQ=255)
                                                                                                                                       tGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTATTTTCGAAGAAGATAAAGAATTAAACTCCTCATTCACATGTTGTTTATTATATTCTg   >  1:331556/1‑141 (MQ=255)
                                                                                                                                        gCCTTTACGTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAAGTCTGTATTTTCGAAGAAGATAAAGAATTAAACTCCTCATTCACATGTTGTTTATTATATTCTgg  <  2:229872/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                            
GATTCAATAATTGATCTTATTTACTGTATTTGACTTCTATACTTTTGAAAAAATTTTCTATATCAACTTTATCCATATTTAAAATATCTTTATTGAACACACAATGCAAATATGGTTTTGCAGAAAAAAAAGTATTGCCTTCACTTATCAGTTGATAATTAACATCCTTAAAATTTAAATAAATAATAATACCATCATTTTCTTTGGCTAAATTCTTTATTTTCGAAGAAGATAAAGAATTAAACTCCTCATTCACATGTTGTTTATTATATTCTGG  >  USA300TCH1516_ALE/2347267‑2347543

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑