Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,429,692	0	T	A	28.6%	21.1 / 10.4	21	L215Q (CTA→CAA)	stfR	putative prophage side tail fiber protein StfR
Reads supporting (aligned to +/- strand):  ref base T (9/6);  new base A (2/4);  total (11/10)
Fisher's exact test for biased strand distribution p-value = 3.61e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.16e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GATGCCAGCACATCAGCCCGTGAGGCGGCAACCCATGCGGCTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACGTCCGAGACGAACGCCAGGTCTTCTGAAACGGC  >  NC_000913/1429445‑1429908                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                         gATGCCAGCACATCAGCCCGTGAGGCGGCAACCCATGCGGCTGATGCTGCGAACTCAGCACGCGCAGCCAGCACGTCCGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTAc                                                                                                                                                                                                                        >  1:66557/1‑250 (MQ=255)                         gcggcAACCCATGCGGCTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTTCCGCTTCAGAGTCCTCAAAAAGCGCGGCTGCGACCAGTGCCGGTGCGGCGAAAACTTCAGAAACGAATGCTTCAGCGGCACTATAATCAGCAGCCACATCTGCATCCAc                                                                                                                                                                                               <  1:49167/251‑1 (MQ=255)                                                 actgACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGagnc                                                                                                                                                                       <  1:126281/248‑4 (MQ=255)                                                    gACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGAATCAGCAAAGGCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGaggccgc                                                                                                                                                                    <  1:65631/251‑7 (MQ=255)                                                        cAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGAGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGCATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGAcc                                                                                                                                                                >  1:147397/1‑251 (MQ=255)                                                                                           gcgTCGTCGGCTCAGTCAGCTTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCTTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACAAAGGCATCAGAAGCCGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGc                                                                                                                             <  1:152277/251‑1 (MQ=255)                                                                                           gcgTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGCGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCCCATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGc                                                                                                                             >  1:77999/1‑251 (MQ=255)                                                                                                    gCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGAATAAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCCGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCCTCAGAAGCTGTGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAatcatc                                                                                                                    >  1:25330/1‑251 (MQ=255)                                                                                                                                                cACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACcncg                                                                                                                                                                                           >  2:98419/1‑136 (MQ=255)                                                                                                                                                cACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCtn                                                                                                                                                                     <  1:98419/158‑2 (MQ=255)                                                                                                                                                cACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAAGCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCgg                                                                        <  1:55387/251‑1 (MQ=255)                                                                                                                                                    gAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCAAACAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCAACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTACTCGGCAAc                                                                    >  1:80951/1‑251 (MQ=255)                                                                                                                                                                        ngCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAaacg                                                                                                             >  1:45680/2‑190 (MQ=255)                                                                                                                                                                          nnnnnnagNNNNNAAANAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGTATg                                                                                                                                                   <  2:100821/144‑1 (MQ=255)                                                                                                                                                                          ccgCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACcgcggc                                                                                                                                                                                         <  1:6910/110‑3 (MQ=255)                                                                                                                                                                                    cTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGca                                                                                                       >  1:122560/1‑184 (MQ=255)                                                                                                                                                                                                    gcCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGACACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGCCCTAGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGAGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACGTCCGAGACGAACGc                    >  1:75763/1‑251 (MQ=255)                                                                                                                                                                                                      caccaGTGCCGGTGCGGCGAAAACGGCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTCTGCCAGGGCGGCAAAAGCTTCCGAGACGAATGCCa                  <  1:58178/251‑1 (MQ=255)                                                                                                                                                                                                         caGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCGCCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGCTGCGGCGGCCTCAAAAGAAGCGGCAACATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTACAGCTTCCTCGGCAAAGGCGGCAGGAAATTCCGCGAAGGCGGCAAAACCGTCCGCGACGAACGCCAggg               >  1:162175/1‑250 (MQ=255)                                                                                                                                                                                                         caGTGCAGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCTCCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTCTGCCAGggcggc                                         >  1:136215/1‑225 (MQ=255)                                                                                                                                                                                                                      gcgAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTTCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAAGCATCATAAACGAACGGAGCATCAAGCGCCAGGGGTGCAGCTACCGCGGCAACGGCGGCATGAAATGCCGCGAAGGCGGCGAAAACGTCCGAGACGAACGCCAGGTCTTCTGAAACGGc  <  1:155862/251‑1 (MQ=255)                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                         GATGCCAGCACATCAGCCCGTGAGGCGGCAACCCATGCGGCTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCATCCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACGTCCGAGACGAACGCCAGGTCTTCTGAAACGGC  >  NC_000913/1429445‑1429908

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑