Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,636,074	0	C	T	47.1%	2.2 / 17.3	17	E98E (GAG→GAA)	nohA	putative prophage DNA‑packaging protein NohA
Reads supporting (aligned to +/- strand):  ref base C (4/5);  new base T (4/4);  total (8/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.33e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTTCGGCATACCATCTTATAACGGCGGCAGAGTCATAAAGCACCTCATTACCCTTGCCACCGCCTCGCAGAACGGGCATTCCCTGTTCCTGCCAGT  >  NC_000913/1635840‑1636306                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                         atatTCACTCAGCAACCCCGGTAGCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCGCCGACAGGGGGAGCCCGTCGAGAATACTGGCAATTTCACCTGCGAGCCGCGTCAGCACGAAAGTACAGAATGCGGTTTCCACCACTGCATCGGAGTCTCTGGCATTCTTCAGTTCCTGTGCGTCggac                                                                                                                                                                                                                           <  1:149655/250‑3 (MQ=11)   atTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTGTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGGCGGCCTgn                                                                                                                                                                                                                        <  1:46703/251‑2 (MQ=14)        cTCAGCAACCCAGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGAGCCCGTCGAGAATACTGGCAATTCCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTCTTCAGTTCCTGTGCGTCGGCCTGCGCAcg                                                                                                                                                                                                                   >  1:124219/1‑251 (MQ=9)                    ggTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGTGGAGCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTCTTCAGTTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATg                                                                                                                                                                                                       <  1:117823/251‑1 (MQ=9)                                            gctTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACCTGCAATTTCACCGGCGATCCGCGACAGCACGAAAGTACAGAATGCGGGGTCCACCACTTCAGCGGAGTCTCTGGCAGTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAAGAGTCCctgg                                                                                                                                                                               <  1:164903/251‑1 (MQ=11)                                                 gTTCATGGCTTTGATGATATCCCGTTTCCGGAAATCACCATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGCCGAGAATACTGGCAATTTCACCTGCGATCCGCGACCGCACGAACGTACAGAATGCGGTTTCCACCACTTCGGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCctggctgg                                                                                                                                                                           >  1:49474/1‑250 (MQ=255)                                                             gatgatATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGc                                                                                                                                                              >  1:5160/1‑251 (MQ=31)                                                                               gAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGAAATTTTACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTGCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGttctt                                                                                                                                            <  1:6020/251‑1 (MQ=18)                                                                                    cAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGAGCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTCTTCAGTTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTTCCTGGCTGGAGATCTGCCTCGCTGGCCTGCCGCAGTTCTTCAAc                                                                                                                                        <  1:7626/250‑1 (MQ=255)                                                                                                         ccGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTGCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGTAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTtc                                                                                                                  <  1:70692/251‑1 (MQ=21)                                                                                                             aaaaCGCCGCTGCACCGACAGGGGGAGCCCGTCGAGAATAATGGCAATTTCACCTGCGACCCGAGACAGCACGAAAGCACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGAATTCTTCAGTTCCTGTGCGTCGGCCTGCGCATGCGTAAGTCGATGGCGTTCGTACTCAATAGTTCCTGGCTGGAGATCTGCCTCGCTGGcc                                                                                                                                                         >  1:161907/1‑208 (MQ=11)                                                                                                                 cgccgcTGCACCGACAGGGGGAGCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTCTTCAGTTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTTCCTGGCTGGAGATCTGCCTCGCTGGCCTGCCGCAGTTCTTCAACCTCCCGGCGCAGCTTTTCGTTCTCAATTTc                                                                                                          >  1:35418/1‑251 (MQ=255)                                                                                                                                                       ggCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGTGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTTCGGCATACCATCTTATAACggcggc                                                                      <  1:8877/249‑1 (MQ=39)                                                                                                                                                                                                                    gCGGAGTCTCTGGCATTCTTCAGTTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTTCCTGGCTGGAGATCTGCCTCGCTGGCCTGCCGCAGTTCTTCAACCTCCCGGCGCAGCTTTTCGTTCTCAATTTCAg                                                                                                        >  1:58313/1‑154 (MQ=11)                                                                                                                                                                                                                         gTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTACCTGGCTGGAGCTCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCCATTTCAGCATCCCTTTCGGCATACCATCTTATAACGGCGGCCGAGTCATAACGCACCTCATTCCCCTTGCCACCGCCTCGCAGAACGGGCATTCCCTGTTCCTGCCAGt  >  1:164421/1‑251 (MQ=255)                                                                                                                                                                                                                                     cttCAGTTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTTCCTGGCTGGAGATCTGCCTCGCTGGCCTGCCGCAGTTCTTCAACCTCCCGGCTCAGCTTTTCGTtctc                                                                                                                <  1:123941/128‑1 (MQ=11)                                                                                                                                                                                                                                        cAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTACCTGGCTAGAGATCTGTCTCGCTAGCCTGCCGCCGTTCTTCAACTTCCCGGCGCAGCtttt                                                                                                                       >  1:143485/1‑119 (MQ=14)                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                         ATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTTCGGCATACCATCTTATAACGGCGGCAGAGTCATAAAGCACCTCATTACCCTTGCCACCGCCTCGCAGAACGGGCATTCCCTGTTCCTGCCAGT  >  NC_000913/1635840‑1636306

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑