Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	573,394	0	A	C	53.6%	30.3 / 41.6	28	L8F (TTA→TTC)	rusA	DLP12 prophage; endonuclease RUS
Reads supporting (aligned to +/- strand):  ref base A (12/1);  new base C (0/15);  total (12/16)
Fisher's exact test for biased strand distribution p-value = 4.27e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.01e-06

ATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCG  >  NC_000913/573264‑573543                                                                                                                                   |                                                                                                                                                      aTCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCaataa                                                                                                                                   <  1:433467/151‑1 (MQ=255)                caTTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCa                                                                                                                    >  1:346215/1‑151 (MQ=255)                      tttgACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTCCCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATcg                                                                                                              <  2:144839/150‑1 (MQ=255)                          ccGCTGGATATACAAAAGAAGGCGCGCTGGAAGTTAGGGCGAAAACACAGTTTATCTGGCTGAAAGGGGGGTTTATAAAGGCGTAAATCCCAACAGCATCACATTCCCCTGGCCTCCGAGAAAAAATCGCTTTTACCGCCATAATCGCggg                                                                                                          <  1:376404/150‑1 (MQ=255)                           cGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCggg                                                                                                          >  1:285071/1‑150 (MQ=255)                                   atGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGcgcacgca                                                                                                  >  1:162649/1‑150 (MQ=255)                                           gAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAgcg                                                                                          >  1:379967/1‑150 (MQ=255)                                                      ggAAGGTAGGGCGAAAACACAGTTTATCTGGCTGAAAGGGGGGGTTATTAAGGCGTAAATCCCTACAGCATCACATTCCCCTGGCCCCCGAGAAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGggcag                                                                               <  2:215444/150‑1 (MQ=255)                                                             aTGGCGAAAACCCAGTTTTTCTGGCTGAAAGGGGGGTTTATTAAGGAGTGAATACCACAAGCATCACATCCCCCTGGCCCCCGAGAAAAAATCGCAATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACcg                                                                       <  1:292654/151‑1 (MQ=255)                                                                 cGAGAACACAGGTTATCGGGCTGAAAGAGGGGTTTATTAAGGCGTAAATACCTACAGCATCACATTCCCCTGGCCTCCGAGAAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGAt                                                                   <  2:376525/151‑1 (MQ=255)                                                                     aaCACAGGTTATCTGGCTGAAAGAGGGGGTTATAAGGGGGTGAATCCCTACAGCATCACATTCCCCTGGCCTCCGAGAAATAATCGTTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACg                                                               <  2:471805/151‑1 (MQ=255)                                                                      acacAGTTTATCGGGCTGAAAGGGGGGGTTATTAAGGCGTAAATCCCTACACCATCACATTCCCCTGGCCTCCGAGAAATAATCGTTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGt                                                              <  2:92626/151‑1 (MQ=255)                                                                                                     ttaAGGCGTAAATACCTACAGCATCACATTCCCCTGGCCCCCGAAAAAAAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGat                               <  1:348840/151‑1 (MQ=255)                                                                                                     taaaGGCGTGAATCCCAACAACATCACATTCCCCTGGCCCCAGAGAAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGat                               <  1:225192/149‑1 (MQ=255)                                                                                                     taaaGGCGTAAACACCTACAGCACCACATTCCCCTGCCCCCGGAGCAATACGCGTTATAACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGat                               <  1:266227/149‑1 (MQ=255)                                                                                                       aaGGCGTGAATACCTACAGCATCACATTCCCCTGCCCTCCGAGAAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGatat                             <  2:425292/151‑1 (MQ=255)                                                                                                       aaGGCGTAAATCCCTACAGCATCACATTCCCCTGGCCTCCGAGAAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAACGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGatat                             <  2:156877/151‑1 (MQ=255)                                                                                                         ggCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCg                           >  2:412381/1‑151 (MQ=255)                                                                                                             tGAATCCCTACAGCACCACATTCCCCTGCCCTCCGAGAAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGcc                        <  2:195998/150‑1 (MQ=255)                                                                                                               aaTACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTgg                     >  2:378365/1‑151 (MQ=255)                                                                                                                atcccacaaccATAACTTTCCCCTGCCCCCCGAGAAAAAATCGTTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGc                    <  2:284871/141‑1 (MQ=255)                                                                                                                aTACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTgg                     >  1:397484/1‑150 (MQ=255)                                                                                                                 tACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTgg                     >  2:402106/1‑149 (MQ=255)                                                                                                                  aCCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTa                  >  1:420236/1‑151 (MQ=255)                                                                                                                         gCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGc               >  2:308036/1‑147 (MQ=255)                                                                                                                         gCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGc               >  2:198714/1‑147 (MQ=255)                                                                                                                           aTCACATTCCCCTGCCCTCCGAGAAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGa         <  2:166722/151‑1 (MQ=255)                                                                                                                               caTTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAAt     >  1:4519/1‑151 (MQ=255)                                                                                                                                   aCCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCg  >  2:71708/1‑150 (MQ=255)                                                                                                                                   |                                                                                                                                                      ATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCACATTACCCTGGCCTCCGAGCAATAATCGCTATTACCGCCATAATCGCGGGCGCACGCACGTCAGCGCAGAGGGGCAGGCATACCGCGATAACGTCGCCCGAATCATTAAAAACGCAATGCTGGATATCGGCCTGGCTATGCCTGTGAAAATCCG  >  NC_000913/573264‑573543

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑