Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,636,074	0	C	T	57.9%	‑5.8 / 17.6	19	E98E (GAG→GAA)	nohA	putative prophage DNA‑packaging protein NohA
Reads supporting (aligned to +/- strand):  ref base C (5/3);  new base T (3/8);  total (8/11)
Fisher's exact test for biased strand distribution p-value = 1.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGG‑ATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTTCGGCATACCATCTTATAACGGCGGCAGAGTCATAAAGCACCTCATTACCCTTGCCACCGCCTCGCAGAACGG  >  NC_000913/1635845‑1636285                                                                                                                                                                                                                                       |                                                                                                                                                                                                                    cACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGG‑ATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTGTCAGCTCCTGTGCGTCGGCCTgcgn                                                                                                                                                                                                 <  1:94446/250‑2 (MQ=14)                  aTCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCGGCACCGACAGGGGG‑AGCCCTGCGAGAATACTGGCAATGTCACCTGCGATCCGCGACATCACGAAAGTAGAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTCTTCAGTTCCTGTGCGt                                                                                                                                                                                                           <  1:154916/223‑1 (MQ=11)                                          ttGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGG‑AGCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTCTTCAGTTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCTTTCGTACGCAATAGTTCctggcg                                                                                                                                                        <  1:88920/250‑2 (MQ=11)                                               cATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGG‑AGCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTCTTCAGTTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTTCctggctgg                                                                                                                                                      >  1:13324/1‑247 (MQ=9)                                                           gatATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGG‑AGCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTCTTCAGTTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTTCCTGGCTGGAGATCTGCCTCGCTg                                                                                                                                       <  1:13431/250‑1 (MQ=9)                                                                   gTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGG‑AGCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTCTTCAGTTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTTCCTGGCTGGAGATCTGCCTCGCTGGCCTGCCGc                                                                                                                              <  1:264115/251‑1 (MQ=255)                                                                          gAAATCAACATGTCGGTTTTCCAGTTCCGGAACACGCCGCTGCACCGACAGGGGG‑ATCCCGTCGAGAATACTGGCAATTTAACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGttctt                                                                                                                       >  1:309410/1‑251 (MQ=18)                                                                                               cAGTTCCGGAAAACGCCGCTGCACCGACAGGGGG‑AGCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTCTTCAGTTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTTCCTGGCTGGAGATCTGCCTCGCTGGCCTGCCGCAGTTCTTCAACCTCCCGGCGCAGCtttt                                                                                                  >  1:68775/1‑251 (MQ=255)                                                                                                   tCCGGAAAACGCCGCTGCACCGACAGGGGGGAGCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTCTTCAGTTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGGTCGTACTCAATAGTTCCTGGCTGGAGATCTGCCTCGCTGGCCTGCCGCAGTTCTTCAACCTCCCGGCGCAGCTTTTCg                                                                                                <  1:130817/250‑1 (MQ=11)                                                                                                   tCCGGAAAACGCCGCTGCACCGACAGGGGG‑ATCCCGTCGAGAATACGGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCTGCGCAGCTTTTCgn                                                                                               <  1:81699/250‑2 (MQ=25)                                                                                                                            ggggg‑AGCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTCTTCAGTTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCTATGGCGGTCGTACTCAATAGTTCCTGGCTGGAGATCTGCCTCGCTGGCCTGCCGCAGTTCTTCAAcc                                                                                                                  <  1:214939/206‑2 (MQ=11)                                                                                                                             gggg‑AGCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCTCCACTTCAGCGGAGTCTCTGGCATTCTTCAGTTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTTCctggctgn                                                                                                                                                      <  1:58313/169‑2 (MQ=11)                                                                                                                                         cGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATa                                                                                                                                                                  >  1:166384/1‑146 (MQ=32)                                                                                                                                                        tttCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGcc                                                                                                                                    <  1:104853/161‑1 (MQ=32)                                                                                                                                                                          aCNGCANGNNANNACANAATGCGGTTTCCACCACTTCANNGGAGTCTCTNGCATTCTTCAGTTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCNTACTCAATANNGCNGGGCGNGNNNTNNNCCNCGCTGGCCTGCCGCAGTTCNTCNNCCTCCCNGCGCAGCTTTTCGTTCGCAATTTCAg                                                                                   <  2:68775/192‑1 (MQ=11)                                                                                                                                                                                  aaaGTACAAAATGCGGTTTCCAACACTTAAGCGGAGTCTCTGGCATTTTTAAGCGCCTGTCCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTATTCAATAGTCCCTGACTGGAGCTCGGTCTGGCTGGNCttnnnnngtnnnnnn                                                                                                                     >  2:204413/1‑136 (MQ=2)                                                                                                                                                                                                ggTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCACTTTCGGCATACCATCTTATAACGGCGGCAGAGTCATAAAGCACCTCATTACCCTTGCCACCGCCTCGCAGAACgg  >  1:160045/1‑251 (MQ=38)                                                                                                                                                                                                                ncGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGGACTCAATAGAACCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGATTTTCGTTCTCACTTTCAGCATCCCTTTCGGCATACCATCTTATAATGGCGGCAGAGTCATAAAGCACCTCATTACCCTTGCCACCGCCTc           >  1:27956/2‑226 (MQ=14)                                                                                                                                                                                                                       ctctGGCATTCTTCAGTTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGAAGACGTTCGTACTCAATAGTTCCTGGCTGGAGATCCGCCTCGCTAGCCTGc                                                                                                                                 >  1:143179/1‑101 (MQ=255)                                                                                                                                                                                                                                       |                                                                                                                                                                                                                    CACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGG‑ATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTTCGGCATACCATCTTATAACGGCGGCAGAGTCATAAAGCACCTCATTACCCTTGCCACCGCCTCGCAGAACGG  >  NC_000913/1635845‑1636285

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑