Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 256,718 C→T 13.0% E219K (GAA→AAA)  USA300HOU_RS01135 ← putative response regulatory protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE256,7180CT13.0% 114.4 / 8.4 46E219K (GAA→AAA) USA300HOU_RS01135putative response regulatory protein
Reads supporting (aligned to +/- strand):  ref base C (11/29);  new base T (3/3);  total (14/32)
Fisher's exact test for biased strand distribution p-value = 3.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.26e-01

AATGGAGGCGCCATAATCATTAGTTATGTGCTAATCTATTTTGCTTGCTTACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGATCTTTAAATGTTCGCATCGCATACGATTCACTAACATCGATATGTTGAATTA  >  USA300TCH1516_ALE/256579‑256858
                                                                                                                                           |                                                                                                                                            
aaTGTAGGCGCCATAATCATTAGTTATGTGCTAATCTATTTTGCTTGCTTACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCa                                                                                                                                             <  1:179991/141‑1 (MQ=255)
 aTGGAGGCGCCATAATCATTAGTTATGTGCGAATCTATTTTGCTTGCTTACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCAt                                                                                                                                            <  2:250527/141‑1 (MQ=255)
    gAGGCGCCATAATCATTAGTTATGTGCTAATCTATTTTGCTTGCTTACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTCCTTTGTCTGCAATTTCATAgt                                                                                                                                         >  2:155155/1‑141 (MQ=255)
          ccATAATCATTAGTTATGTGCTAATCTATTTTGCTTGCTTACAATAATCACTTGGCGCCATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTTATAGTGTTTGt                                                                                                                                   >  1:72083/1‑141 (MQ=255)
          ccATAATCATTAGTTATGTGCTAATCTATTTTGCTTGCTTACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTTATAGTGTTTGt                                                                                                                                   >  1:382086/1‑141 (MQ=255)
          ccATAATCATTAGTTATGTGCTAATCTATTTTGCTTGCTTACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGt                                                                                                                                   <  1:347537/141‑1 (MQ=255)
          ccATAATCATTAGTTATGTGCTAATCTATTTTGCTTGCTTACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGt                                                                                                                                   <  1:295553/141‑1 (MQ=255)
          ccATAATCATTAGTTATGTGCTAATCTATTTTGCTTGCTTACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTGTATAGTGTTTGt                                                                                                                                   >  1:148653/1‑141 (MQ=255)
                      gTTATGTGCTATTCTATTTGGCTTGCTTACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTa                                                                                                                       <  1:233517/141‑1 (MQ=255)
                      gTTATGTGCTAATCCATTTTGCTTGCTTACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTa                                                                                                                       <  1:377814/141‑1 (MQ=255)
                      gTTATGTGCTAATCCATTTTGCTTGCTTACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTa                                                                                                                       <  1:377810/141‑1 (MQ=255)
                       ttATGTGCTAATCTATTTTGCTTGCTTACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTaa                                                                                                                      <  1:122085/141‑1 (MQ=255)
                               tAATCTATTTTGCTTGCTTACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCa                                                                                                              <  2:366075/141‑1 (MQ=255)
                                   cTATTTTGCTTGCTTACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTCTTCTCAGAGAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAgaga                                                                                                          >  1:388916/1‑141 (MQ=255)
                                   cTATTTTGCTTGCTTACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAgaga                                                                                                          <  1:8576/141‑1 (MQ=255)
                                              gcttACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATAc                                                                                               <  2:215268/141‑1 (MQ=255)
                                              gcttACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATAc                                                                                               >  1:387806/1‑141 (MQ=255)
                                              gcttAAAATAATCACTTGGCGACATTGATAAATGTTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATAc                                                                                               <  2:178236/141‑1 (MQ=255)
                                               cttACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAGTACg                                                                                              >  2:125003/1‑141 (MQ=255)
                                                     ataatCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCg                                                                                        >  1:175171/1‑141 (MQ=255)
                                                           aCTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTCAAATACGATAGCGATTTaa                                                                                  >  2:210305/1‑141 (MQ=255)
                                                           aCTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTaa                                                                                  <  2:91834/141‑1 (MQ=255)
                                                            cTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTaaa                                                                                 <  2:154407/141‑1 (MQ=255)
                                                                ccgcaacttGTGATTATTTTTTTGAATGGCGTCTAAACATTTTTTACTCTGAAAAGCTTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAaataat                                                                             <  2:271818/134‑1 (MQ=255)
                                                                    cATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGAc                                                                         <  1:181881/141‑1 (MQ=255)
                                                                          tAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGt                                                                   <  2:387806/141‑1 (MQ=255)
                                                                          tAAATATGTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGt                                                                   <  1:24083/141‑1 (MQ=255)
                                                                            aaTACTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTaa                                                                 <  1:234620/141‑1 (MQ=255)
                                                                                ttttttAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATAcc                                                             <  2:200351/141‑1 (MQ=255)
                                                                                       aaaTGATAGCTAAACATTTTATACTCTGAAAAGCCTGCTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGCGTTAAATAATCGACAATTGTAATACCAACATGa                                                      >  2:167584/1‑141 (MQ=255)
                                                                                        aaTGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGAt                                                     <  1:306004/141‑1 (MQ=255)
                                                                                        aaTGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGAt                                                     <  2:136438/141‑1 (MQ=255)
                                                                                           gATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGATCtt                                                  <  2:367909/141‑1 (MQ=255)
                                                                                           gATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGATCtt                                                  <  1:363187/141‑1 (MQ=255)
                                                                                                   aaCATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTTATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGATCTTTAAATGtt                                          <  2:148653/141‑1 (MQ=255)
                                                                                                   aaCATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTTATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGATCTTTAAATGtt                                          <  2:72083/141‑1 (MQ=255)
                                                                                                   aaCATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTTATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAAGACCAACATGATCTTTAAATGtt                                          <  2:382086/141‑1 (MQ=255)
                                                                                                   aaCATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGATCTTTAAATGtt                                          >  2:128809/1‑141 (MQ=255)
                                                                                                            taCTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGATCTTTAAATGTtcgcatcgca                                 >  2:13162/1‑141 (MQ=255)
                                                                                                             aCTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGATCTTTAAATGTTcgcattgcat                                <  1:270210/141‑1 (MQ=255)
                                                                                                                    aaaGCCTACTTTGTTTGCAATTTCATAGTGTTTGGAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGATCTTTAAATGTTCGCATCGCATACGATTc                         <  1:146693/141‑1 (MQ=255)
                                                                                                                     aaGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGATCTTTAAATGTTCGCATCGCATACGATTCa                        <  2:203400/141‑1 (MQ=255)
                                                                                                                     aaGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGATCTTTAAATGTTCGCATCGCATACGATTCa                        <  2:58825/141‑1 (MQ=255)
                                                                                                                      aGCCTAGCTTGGTTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGATAATTGTAATACGAACATGGTCTTTAGATGTGCGCATCGCTTACGATTCAc                       <  2:124397/141‑1 (MQ=255)
                                                                                                                        ccTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGATCTTTAAATGTTCGAATCGCACACGATTCACTa                     >  1:302252/1‑141 (MQ=255)
                                                                                                                                          tCATAGTGTTTGTAAAGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGATCTTTAAATGTTCGCATCGCATACGATTCACTAACATCGATATGTTGAAtt   >  1:294370/1‑141 (MQ=255)
                                                                                                                                           cATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGATCTTTAAATGTTCGCATCGCATACGATTCACTAACATCGATATGTTGAATTa  <  1:13162/141‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                            
AATGGAGGCGCCATAATCATTAGTTATGTGCTAATCTATTTTGCTTGCTTACAATAATCACTTGGCGACATTTGTAAATATTTTTTAAAATGATAGCTAAACATTTTATACTCTGAAAAGCCTACTTTGTCTGCAATTTCATAGTGTTTGTAATGTCGATCTAACAATTGCAGAGATTGTAAAATACGATAGCGATTTAAATAATCGACAATTGTAATACCAACATGATCTTTAAATGTTCGCATCGCATACGATTCACTAACATCGATATGTTGAATTA  >  USA300TCH1516_ALE/256579‑256858

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: ‑