Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,663,592	0	A	T	30.0%	26.6 / 14.2	20	P163P (CCT→CCA)	USA300HOU_RS13705	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (7/7);  new base T (3/3);  total (10/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.58e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TTGACTTCTGTAGCTACAAAGATTTTACGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTCCTACATCTGTAGGCTTAACATCTCTTATACTTGTCATTTTATACTTACGTGTTTCATTACCAACTTTAAAGTACACCATACTACCTTTTTTGGCTGCTTTAAGATTTGTAAATTGATAGTTCGGACGGTCAATGAAAGTGTGT  >  USA300TCH1516_ALE/2663464‑2663724                                                                                                                                 |                                                                                                                                     ttGACTTCTGTATCTACAAAGATTTTACGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTCCTACATCTGTAGGCTTAACAtct                                                                                                                          <  2:212230/141‑1 (MQ=255)       tCTGTAGCTACAAAGATTTTACGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTCCTACATCTGTAGGCTTAACATCTCTtata                                                                                                                    >  1:67138/1‑141 (MQ=255)                       ttttACGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTCCTACATCTGTAGGCTTAACATCTCTTATACTTGTCATTTTATACt                                                                                                    <  2:67138/141‑1 (MQ=255)                           aCGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTTCTACATCTGTTGGCTTAACATCTCTTATACTTGTCATTTTATACTTACg                                                                                                >  2:172534/1‑141 (MQ=255)                           aCGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTTCTACATCTGTTGGCTTAACATCTCTTATACTTGTCATTTTATACTTACg                                                                                                >  2:99495/1‑141 (MQ=255)                           aCGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTTCTACATCTGTTGGCTTAACATCTCTTATACTTGTCATTTTATACTTACg                                                                                                >  2:98423/1‑141 (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)                                                                                                                       cTACATCTGTAGGCTTAACATCTCTTATACTTGTCATTTTATACTTACGTGTTTCATTACCAACTTTAAAGTACACCATACTACCTTTTTTTTTTTTTTTTTTATTTGTAAATTGATAGTTCGGATGGTCAATGTAAgtgt    >  2:187713/1‑141 (MQ=255)                                                                                                                       cTACATCTGTAGGCTTAACATCTCTTATACTTGTCATTTTATACTTACGTGTTTCATTACCAACTTTAAAGTACACCATACTACCTTTTTTGGCTGCTTTAAGATTTGTAAATTGATAGTTCGGACGGTCAATGAAAgtgt    >  2:213577/1‑141 (MQ=255)                                                                                                                         aCATCTGTAGGATTAACATCTCTTATACTTGTCATTTTATACTTACGTGTTTCATTACCAACTTTAAAGTACACCATACTACCTTTTTTGGCTGCTTTAAGATTTGTAAATTGCTAGTTCGGACGGTCAATGAAAgtgtgt  <  2:440/141‑1 (MQ=255)                                                                                                                                 |                                                                                                                                     TTGACTTCTGTAGCTACAAAGATTTTACGTTTTTCCCAAACGCCTGTCTTTTCATTGTAATCATCACAAGTAATTAATGTTAATTGTTTATCTTTACCTTTTTGTTCATCTAGAACTCCTACATCTGTAGGCTTAACATCTCTTATACTTGTCATTTTATACTTACGTGTTTCATTACCAACTTTAAAGTACACCATACTACCTTTTTTGGCTGCTTTAAGATTTGTAAATTGATAGTTCGGACGGTCAATGAAAGTGTGT  >  USA300TCH1516_ALE/2663464‑2663724

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