Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,108,728 A→G 9.8% Y419Y (TAT→TAC)  USA300HOU_RS10675 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,108,7280AG 9.8% 106.5 / 3.9 41Y419Y (TAT→TAC) USA300HOU_RS10675hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (14/23);  new base G (2/2);  total (16/25)
Fisher's exact test for biased strand distribution p-value = 6.37e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.52e-01

TTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACAAACGAATGTCCTAACCAAATGTAATCATCGTT  >  USA300TCH1516_ALE/2108589‑2108868
                                                                                                                                           |                                                                                                                                            
ttGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACtatat                                                                                                                                             <  1:84378/141‑1 (MQ=255)
         gATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATAttcaattt                                                                                                                                    >  1:4218/1‑141 (MQ=255)
             tCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATAttcaatttcaat                                                                                                                                >  1:536832/1‑141 (MQ=255)
                 aGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGAca                                                                                                                            <  2:98191/141‑1 (MQ=255)
                         aaGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACatcatcatc                                                                                                                    >  1:209909/1‑141 (MQ=255)
                           gTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGa                                                                                                                  <  1:620362/141‑1 (MQ=255)
                           gTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTAAAAAAAAAAAAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGa                                                                                                                  <  2:279998/141‑1 (MQ=255)
                            ttttATGCCAGCATCCGCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGaa                                                                                                                 >  2:660376/1‑140 (MQ=255)
                             tttATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACa                                                                                                                <  1:20587/141‑1 (MQ=255)
                               tATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATGTATTCAATTTCAATTACATCATCATCGACAAt                                                                                                              >  1:152216/1‑141 (MQ=255)
                               tATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATGTATTCAATTTCAATGACATCATCATCGACAAt                                                                                                              >  1:181118/1‑141 (MQ=255)
                                     aGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTaaa                                                                                                        >  2:247590/1‑141 (MQ=255)
                                          ccTCAAACGCACGTTTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATc                                                                                                   <  1:264370/141‑1 (MQ=255)
                                          ccTCAAACGCACGTCTTACAATATCATTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATc                                                                                                   <  1:618481/141‑1 (MQ=255)
                                             cAAACGCACGTCTTACAATTTCAGTTCTATATTTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCa                                                                                                <  1:217066/141‑1 (MQ=255)
                                             cAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCa                                                                                                <  1:66899/141‑1 (MQ=255)
                                                           aCAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCt                                                                                  >  2:587389/1‑141 (MQ=255)
                                                            cAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCtt                                                                                 <  1:492451/141‑1 (MQ=255)
                                                                 tCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTGTTTCCCATTCTTTAATa                                                                            <  1:171186/141‑1 (MQ=255)
                                                                 tCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTATAGTGATTTTTTACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATa                                                                            <  1:454024/141‑1 (MQ=255)
                                                                    gTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATagga                                                                         <  2:112309/141‑1 (MQ=255)
                                                                        tataATTATCAGCTATGACTTTTTCAAGCCCATATTTTGCTCTAGCCTTTAAAAACCAATTAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGtt                                                                     <  1:324789/141‑1 (MQ=255)
                                                                              tATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAAtt                                                               <  1:566703/141‑1 (MQ=255)
                                                                                 cAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCTCATTTTTTCCTATTTTTTATTAGAAGGTTATCATTTgt                                                            >  2:411737/1‑140 (MQ=255)
                                                                                 cAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTATACtttat                                                            >  2:164553/1‑139 (MQ=255)
                                                                                  aGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGTCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTACCATTCTTTAATAGGTGGTTCTTATTTGAc                                                           >  2:546059/1‑141 (MQ=255)
                                                                                    cTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCCTCATCGACAATGGTCAATAACCCCATTTTTTCCCTTTCTTTCATAGTAGGTTCTACATTTAcat                                                         >  2:194927/1‑141 (MQ=255)
                                                                                      aTGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGAcatca                                                       <  2:536832/141‑1 (MQ=255)
                                                                                       tGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGAcatcat                                                      <  2:463258/141‑1 (MQ=255)
                                                                                         aCTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATcc                                                    <  2:209909/141‑1 (MQ=255)
                                                                                                cAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCATTGACATCATCATCGACACTGGTCAATAATCCCATTTTTTCCCAATCTTTAATGGGAGGTCTAAAGTTGACATCATCCACAAAcc                                             <  1:490659/141‑1 (MQ=255)
                                                                                                    cccATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTg                                         >  1:76055/1‑141 (MQ=255)
                                                                                                       atatTTTTCCCTAGCCTTTATAACCCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGCCATCATCCAAAAACCCTTGTCt                                      <  1:390478/141‑1 (MQ=255)
                                                                                                          tttttCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTAc                                   >  1:381389/1‑141 (MQ=255)
                                                                                                            tttCTCTAGCCTTTAAAAACCAATCAACTATGTATTCAATTTCAATGACTTCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACaa                                 <  2:152216/141‑1 (MQ=255)
                                                                                                            tttCTCTAGCCTTTAAAAACCAATCAACTATGTATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACaa                                 <  2:181118/141‑1 (MQ=255)
                                                                                                            tgtctcTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGATAATGGTCAATAATCCCATTTTTTCCCCTTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACaa                                 <  2:7737/139‑1 (MQ=255)
                                                                                                                 ctAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACAAACGaa                            <  2:208603/141‑1 (MQ=255)
                                                                                                                    gCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCTTTTTTTTTAATACGAGGTTCTTATTTGGAGTGTTCCAAAGACACTTTTCTTACAAACGaagtt                         >  2:201727/1‑138 (MQ=255)
                                                                                                                        ttAAAAACCATTGAACTATATAGTCAATTTCAATGACATCCTCATCGACAATTGTCGATAATCCCATTTTTTCCCATTCTTTAATAGGATGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACAAACGAATGTCCTa                     <  2:125816/141‑1 (MQ=255)
                                                                                                                        ttAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACAAACGAATGTCCTa                     >  2:422908/1‑141 (MQ=255)
                                                                                                                                   tccaCTATATATACAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACAAACGAATGTCCTAACCAAATGTaa          <  2:373950/138‑1 (MQ=255)
                                                                                                                                           atatTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCTATTTTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACAAACGAATGTCCTAACCAAATGTAATCATCGtt  >  2:529545/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                            
TTGCTTTTGGATTTCTAAGTACTTCAAGTTTTATGCCAGCATCCTCAAACGCACGTCTTACAATATCAGTTCTATAATTATCAGCTATGACTTTTTCAAGCCCATATTTTTCTCTAGCCTTTAAAAACCAATCAACTATATATTCAATTTCAATGACATCATCATCGACAATGGTCAATAATCCCATTTTTTCCCATTCTTTAATAGGAGGTTCTAATTTGACATCATCCAAAAACCCTTGTCTTACAAACGAATGTCCTAACCAAATGTAATCATCGTT  >  USA300TCH1516_ALE/2108589‑2108868

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: ‑