Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,663,5810CT35.3% 13.3 / 12.5 17G167E (GGA→GAA) USA300HOU_RS13705hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (3/8);  new base T (3/3);  total (6/11)
Fisher's exact test for biased strand distribution p-value = 6.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.61e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CATCCATTAGCGTAATAGATTATTTGACTTCTGTAGCTACAAAGATTTTACGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTCCTACATCTGTAGGCTTAACATCTCTTATACTTGTCATTTTATACTTACGTGTTTCATTACCAACTTTAAAGTACACCATACTACCTTTTTTGGCTGCTTTAAGATTTGTAAATTGATAGTTCGGACGGTCAATGAAAGTG  >  USA300TCH1516_ALE/2663441‑2663721
                                                                                                                                            |                                                                                                                                            
cATCCATTAGCGTAATAGATTATTTGACTTCTGTAGCTACAAAGATTTTACGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTCATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTc                                                                                                                                              <  1:6184/141‑1 (MQ=255)
cATCCATTAGCGTAATAGATTATTTGACTTCTGTAGCTACAAAGATTTTACGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTc                                                                                                                                              <  1:189901/141‑1 (MQ=255)
cATCCATTAGCGTAATAGATTATTTGACTTCTGTAGCTACAAAGATTTTACGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTc                                                                                                                                              <  1:217207/141‑1 (MQ=255)
   ccATTAGCGTAATATATTATTTGACTTCTGGAGCTACAAAGATTTTACGTTTTTCCCCAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTCCTa                                                                                                                                           <  2:203431/141‑1 (MQ=255)
   ccATTAGCGTAATAGATTATTTGACTTCTGTAGCTACAAAGATTTTACGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTCCTa                                                                                                                                           <  1:75667/141‑1 (MQ=255)
                       ttGACTTCTGTATCTACAAAGATTTTACGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTCCTACATCTGTAGGCTTAACAtct                                                                                                                       <  2:212230/141‑1 (MQ=255)
                             tCTGTAGCTACAAAGATTTTACGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTCCTACATCTGTAGGCTTAACATCTCTtata                                                                                                                 >  1:67138/1‑141 (MQ=255)
                                             ttttACGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTCCTACATCTGTAGGCTTAACATCTCTTATACTTGTCATTTTATACt                                                                                                 <  2:67138/141‑1 (MQ=255)
                                                 aCGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTTCTACATCTGTTGGCTTAACATCTCTTATACTTGTCATTTTATACTTACg                                                                                             >  2:99495/1‑141 (MQ=255)
                                                 aCGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTTCTACATCTGTTGGCTTAACATCTCTTATACTTGTCATTTTATACTTACg                                                                                             >  2:98423/1‑141 (MQ=255)
                                                 aCGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTTCTACATCTGTTGGCTTAACATCTCTTATACTTGTCATTTTATACTTACg                                                                                             >  2:172534/1‑141 (MQ=255)
                                                  cGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTCCTACATCTGTAGGCTTAACATCTCTTATACTTGTCATTTTATACTTACgt                                                                                            <  1:69851/141‑1 (MQ=255)
                                                           cAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTCCTACATCTGTAGGCTTAACATCTCTTATACTTGTCATTTTATACTTACGTGTTTCATTa                                                                                   >  1:216825/1‑141 (MQ=255)
                                                                                           aGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGATCTCCTACATCTGTAGGCTTAACATCTCTTATACTTGTCATTTTATACTTACGTGTTTCATTACCAACTTTAAAGTACACCATACTACCtttttt                                                   <  2:189626/141‑1 (MQ=255)
                                                                                                 taatGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTCCTACATCTGTAGGCTTAACATCTCTTATACTTGTCATTTTATACTTACGTGTTTCATTACCAACTTTAAAGTACACCATACTACCTTTTTTGgctgc                                             <  1:85062/141‑1 (MQ=255)
                                                                                                        aaTTGTTTATCTTTACCTTTTTGTTCATCTAGAACTTCTACATCTGTTGGCTTAACATCTCTTATACTTGTCATTTTATACTTACGTGTTTCATTACCAACTTTAAAGTACACCATACTACCTTTTTTGGCTGCTTTAAGa                                      <  1:98423/141‑1 (MQ=255)
                                                                                                        aaTTGTTTATCTTTACCTTTTTGTTCATCTAGAACTTCTACATCTGTTGGCTTAACATCTCTTATACTTGTCATTTTATACTTACGTGTTTCATTACCAACTTTAAAGTACACCATACTACCTTTTTTGGCTGCTTTAAGa                                      <  1:99495/141‑1 (MQ=255)
                                                                                                        aaTTGTTTATCTTTACCTTTTTGTTCATCTAGAACTTCTACATCTGTTGGCTTAACATCTCTTATACTTGTCATTTTATACTTACGTGTTTCATTACCAACTTTAAAGTACACCATACTACCTTTTTTGGCTGCTTTAAGa                                      <  1:172534/141‑1 (MQ=255)
                                                                                                        aaTTGTTTATCTTTACCTTTTTGTTCATCTAGAACTCCTACATCTGTAGGCTTAACATCTCTTATACTTGTCATTTTATACTTACGTGTTTCATTACCAACTTTAAAGTACACCATACTACCTTTTTTGGCTGCTTTAAGa                                      <  2:78738/141‑1 (MQ=255)
                                                                                                                 tCTTTACCTTTTTGTTCATCTAGAACTCCTACATCTGTAGGCTTAACATCTCTTATACTTGTCATTTTATACTTACGTGTTTCATTACCAACTTTAAAGTACACCATACTACCTTTTTTGGCTGCTTTAAGATTTGTAAAt                             >  1:164587/1‑141 (MQ=255)
                                                                                                                                            ccTACATCTGTAGGCTTAACATCTCTTATACTTGTCATTTTATACTTACGTGTTTCATTACCAACTTTAAAGTACACCATACTACCTTTTTTGGCTGCTTTAAGATTTGTAAATTGATAGTTCGGACGGTCAATGAAAgtg  >  2:125150/1‑141 (MQ=255)
                                                                                                                                            ccTACATCTGTAGGCTTAACATCTCTTATACTTGTCATTTTATACTTACGTATTTCATTACCAACTTTAAAGTACACCATACTACCTTTTTTGGCTGCTTTAAGATTTGTAAATTGATAGTTCGGACGGTCAATGAAAgtg  >  1:107766/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                            
CATCCATTAGCGTAATAGATTATTTGACTTCTGTAGCTACAAAGATTTTACGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTCCTACATCTGTAGGCTTAACATCTCTTATACTTGTCATTTTATACTTACGTGTTTCATTACCAACTTTAAAGTACACCATACTACCTTTTTTGGCTGCTTTAAGATTTGTAAATTGATAGTTCGGACGGTCAATGAAAGTG  >  USA300TCH1516_ALE/2663441‑2663721

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑