Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,463,475 T→C 14.8% intergenic (+316/‑21) USA300HOU_RS12680 → / → gltS Putative 3‑methyladenine DNA glycosylase/Sodium/glutamate symporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,463,4750TC14.8% 52.9 / 4.3 28intergenic (+316/‑21)USA300HOU_RS12680/gltSPutative 3‑methyladenine DNA glycosylase/Sodium/glutamate symporter
Reads supporting (aligned to +/- strand):  ref base T (9/14);  new base C (2/2);  total (12/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.14e-01

TTATAATTATTAAATTTAGATGCATTAATATTATTGATATTATTTTCAAAAACTAGAAATATTGATTTGTTGCATGTATAATGTTAAAAGCGCCCTTTTATAACGCTTACATATAAAAGCTTATTTAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACGTTAATTTTTTAAAACGTATTTGTATACCAGCACCAGTGATT  >  USA300TCH1516_ALE/2463336‑2463615
                                                                                                                                           |                                                                                                                                            
ttatAATTATTAAATTTATATGCATTAATATTATTGATATTATTTTCAAAAACTAGAAATATTGATTTGTTGCATGTATAATGTTAAAAGCGCCCTTTTATAACGCTTACATATAAAAGCTTATTTAGGGAGAGGGATAtt                                                                                                                                             <  2:275779/141‑1 (MQ=255)
              tttAGATGCATTAATATTATTGATATTATTTTCAAAAACTAGAAATATTGATTTGTTGCATGTATAATGTTAAAAGCGCCCTTTTATAACGCTTACATATAAAAGCTTATTTAGGGAGAGGGATATTCAACAAGGGGGAtt                                                                                                                               <  2:307653/141‑1 (MQ=255)
                 aGATGCATTAATATTATTGATATTATTTTCAAAAACTAGAAATATTGATTTGTTGCATGTATAATGTTAAAAGCGCCCTTTTATAACGCTTACATATAAAAGCTTATTTAGGGAGAGGGATATTCAACAAGGGGGATTTGa                                                                                                                            <  2:253887/141‑1 (MQ=255)
                  gATGCATTAATATTATTGATATTATTTTCAAAAACTAGAAATATTGATTTGTTGCATGTATAATGTTAAAAGCGCCCTTTTATAACGCTTACATATAAAAGCTTATTTAGGGAGAGGGATACTCAACAAGGGGGATTTGaa                                                                                                                           >  1:211581/1‑141 (MQ=255)
                  gATGCATTAATATTATTGATATTATTTTCAAAAACTAGAAATATTGATTTGTTGCATGTATAATGTTAAAAGCGCCCTTTTATAACGCTTACATATAAAAGCTTATTTAGGGAGAGGGATACTCAACAAGGGGGATTTGaa                                                                                                                           >  1:53786/1‑141 (MQ=255)
                        ttAATATTATTGATATTATTTTCAAAAACTAGAAATATTGATTTGTTGCATGTATAATGTTAAAATCGCCCTTTTATAACGCTTACATATAAAAGCTTATTTAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGAt                                                                                                                     <  2:58322/141‑1 (MQ=255)
                         tAATATTATTGATATTATTTTCAAAAACTAGAAATATTGATTTGTTGCATGTATAATGTTAAAAGCGCCCTTTTATAACGCTTACATATAAAAGCTTATTTAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGATa                                                                                                                    >  1:193572/1‑141 (MQ=255)
                             attattGATCTTATTTTCAAAAACTAGAACTATTGATTTGTTGCATGTATAATGTTAAAAGCGCCCTTTTATAACGCTTACATATAAAAGCTTATTTAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGATAGAAc                                                                                                                <  1:89584/141‑1 (MQ=255)
                                 tggATATTATTTTCAAAAACTAGAAATATTGATTTGTTGCATGTATAATGTTAAAAGCGCCCTTTTATAACGCTTACATATAAAAGCTTATTTAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGATAGAACTTaa                                                                                                            <  2:54275/139‑1 (MQ=255)
                                  tGATATTATTTTCAAAAACTAGAAATATTGACTTGTTGCATGTATAATGTTAAAAGCGCCCTTTTATAACGCTTACATATAAAAGCTTATTTAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGATAGAACTTAAt                                                                                                           <  1:97081/141‑1 (MQ=255)
                                    atatTAATTTCAAAAACTAGAAATATTAATTTGTTGCAAGTAAAATGTTAAAAGCGCCCTTTTATAACGCTTACATATAAAAGCTTATTTAGGGAGAGGGATATTTAACAAGGGGGATTTGAAAATGATAGAACTTAATGc                                                                                                         <  2:250639/141‑1 (MQ=255)
                                                                                   ttAAATGCGCCCTTTTATAACGCTTACATATAAATGCTTTGTTAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGTTAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAgg                                                          <  2:157955/141‑1 (MQ=255)
                                                                                    tAAAAGCGCCCTTTTATAACGCTTACATAGAAAAGCTTATTTAGGGAGAGGGATATTCAACCAGGGGGATTTGAACATGATAGAACTTAATGCAATTACAACATTATGTTTGGCTTGTATCCTTTATTTAATTGGTTAGGc                                                         >  2:85464/1‑141 (MQ=255)
                                                                                          cgcCCTTTTATAACGCTTACATATAAAAGCTTAATTAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATAATAGAACTTAATGCAATTACAACATTATGTTTAACTTGTATCCTTTATTCAATTGCAAAGGCtttagt                                                   >  2:226805/1‑136 (MQ=255)
                                                                                           gcCCTTTTATAACGCTTACATATAAAAGCTTATTTAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGtt                                                  >  1:276952/1‑141 (MQ=255)
                                                                                                  tataACGCTTACAGATAAAAGCTTATTTAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACg                                           <  2:349674/141‑1 (MQ=255)
                                                                                                  tagaaCGCTTACATATAAATGCTTATTTAGGGAGAGGGATATTCAAAACGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACg                                           <  2:349773/138‑1 (MQ=255)
                                                                                                   ataACGCTTACATATAAAAGCTTATTTAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACGt                                          <  2:51411/141‑1 (MQ=255)
                                                                                                   ataACGCTTAAATATAAAAGCTTATTTAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACGt                                          <  2:51429/141‑1 (MQ=255)
                                                                                                   ataACGCTCACATATAAAAGCTTATTTAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACGt                                          <  2:5202/141‑1 (MQ=255)
                                                                                                                ataAAAGCTTATTTAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACGTTAATTTTTTaaac                             >  2:155368/1‑140 (MQ=255)
                                                                                                                         tATTTAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACGTTAATTTTTTAAAACGTATTTGt                    >  1:270590/1‑141 (MQ=255)
                                                                                                                            ttAGGGAGAGGGATACTCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACGTTAATTTTTTAAAACGTATTTGtata                 <  2:53786/141‑1 (MQ=255)
                                                                                                                            ttAGGGAGAGGGATACTCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACGTTAATTTTTTAAAACGTATTTGtata                 <  2:211581/141‑1 (MQ=255)
                                                                                                                             tAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACGTTAATTTTTTAAAACGTATTTGTATAc                >  2:97604/1‑141 (MQ=255)
                                                                                                                             tAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACGTTAATTTTTTAAAACGTATTTGTATAc                >  2:278003/1‑141 (MQ=255)
                                                                                                                               gggAGAGGGATATTCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACGTTAATTTTTTAAAACGTATTTGTATACCa              >  1:314283/1‑141 (MQ=255)
                                                                                                                                    agGGATATTCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACGTTAATTTTTTAAAACGTATTTGTATACCAGCAcc         <  2:26173/141‑1 (MQ=255)
                                                                                                                                     gggATAGTCAACAAGGGGTATTGGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTGGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACGTTAATTTTTTAAAACGTATTTATATACCAGCACCa        >  2:315176/1‑141 (MQ=255)
                                                                                                                                         tatTCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATAACTGTAATTTTTTAAAACGTATTTGTATACCAGCACCAGTGa    <  1:69449/141‑1 (MQ=255)
                                                                                                                                         tatGCACCATGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACGTTAATTTTGTAGAACGTATTTGTATACCAGCACCAGTGa    <  2:126434/141‑1 (MQ=255)
                                                                                                                                           ttCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATACTTTATTTACTTGGTAAGGCTATCGTTAATCACGTTAATTTTTTAAATAGTATTGATATACAAGCACGAGTGAtt  >  2:279907/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                            
TTATAATTATTAAATTTAGATGCATTAATATTATTGATATTATTTTCAAAAACTAGAAATATTGATTTGTTGCATGTATAATGTTAAAAGCGCCCTTTTATAACGCTTACATATAAAAGCTTATTTAGGGAGAGGGATATTCAACAAGGGGGATTTGAAAATGATAGAACTTAATGCAATTACAACATTATGTTTAGCTTGTATCCTTTATTTACTTGGTAAGGCTATCGTTAATCACGTTAATTTTTTAAAACGTATTTGTATACCAGCACCAGTGATT  >  USA300TCH1516_ALE/2463336‑2463615

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑