Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,373	0	C	T	52.5%	3.4 / 37.5	41	intergenic (+377/‑206)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base C (16/3);  new base T (11/10);  total (27/14)
Fisher's exact test for biased strand distribution p-value = 4.55e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.70e-01

CCTGCAGGAATTTAGAAAAACAT‑GTGGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TGTAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTAAAAACCTAT  >  NC_007790/1279‑1472                                                                                                  |                                                                                                    tcTGCAGGAATTTAGAAAAACAC‑GGGAAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TGTAAATGGACAGTG‑TTACAAAA‑TAGTCATTGtttt                                                                                               <  1:4090303/99‑1 (MQ=255) cttGCAGGAATTTAGAAAAACATGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TGTAAATGGGCAGTGTTTAAAAAAATAGTCATTgg                                                                                                  <  1:4479990/98‑1 (MQ=255)  ttGCAGGAATTTAGAAAAACATGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TGTAAATGGGCAGTGTTTAAAAAAATAGTCATTgag                                                                                                 <  1:629625/99‑3 (MQ=255)   tGCAGGAATTTAGAAAAACATGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TGTAAATGGGCAGTGTTTAAAAAAATAGTCATTGGtt                                                                                                >  1:4525441/1‑100 (MQ=255)    gCAGGAATTTAGAAAAACATGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TGTAAATGGGCAGTGTTTAAAAAAATAGTCATTGGttt                                                                                               <  1:1487178/100‑1 (MQ=255)    gCAGGAATTTAGAAAAACAC‑GGGAAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TGTAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGc                                                                                            >  1:4919110/1‑100 (MQ=255)    gCAGGAATTTAGAAAAACAC‑GGGAAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TGTAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGc                                                                                            >  1:25383/1‑100 (MQ=255)     cAGGAATTTAGAAAAACATGGGGGAAGTTTTAAAGGATTTTATGCTAACTTTTAATTTGCA‑TGTAAATGGGCAGTGTTTAAAAAAATAGTCATTGGtttt                                                                                              >  1:18624/1‑100 (MQ=255)                                  ttAAAGGATTTTATGCTAACTTTTAATTTGCA‑TGTAAATGGGCAGTGTTTAAAAAAATAGTCATTGGTTTTATTTAAAATTTTGTTTTTGAAAATAGCac                                                                 <  1:4992463/100‑2 (MQ=255)                                            ttATGCTAATTTTTAATTTGCA‑TGTAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTTTGTTTGTGAAATTAGCATAtatgtattcct                                                     <  1:3675651/100‑4 (MQ=255)                                               tGCTAATTTTTAATTTGCA‑TGTAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATGTATTTGGCTc                                                  <  1:2728162/100‑1 (MQ=255)                                                 atcgttccgaaTTTGCATTTTAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGTAATTACCATATATTTATTTGGCtg                                                  <  1:2805640/91‑2 (MQ=255)                                                          taTTTGCATTTTAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCg                                         >  1:4105158/2‑100 (MQ=255)                                                            attgcattttAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGtt                                       >  1:117674/10‑100 (MQ=255)                                                             ttGCA‑TGTAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTTTGTTTGTGAAGTTAGCATATATGTATTTGGCTCATATTTTCGTTTTa                                    >  1:2731533/1‑100 (MQ=255)                                                              tgcattttAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAGATTACCATATATTTATTTGGCTCATATTTGCGtttt                                     >  1:1710372/8‑100 (MQ=255)                                                              tgcattttAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGttta                                     <  1:959513/93‑2 (MQ=255)                                                              tGCA‑TGTAAATGGGCAGTGTTTAAAAAAATAGTCATTGGTTTTATTTAAAATTTTGTTTTTGAAAATAGCATATATGTATTTGGCTCATATTTGCGtttt                                     >  1:4899697/1‑100 (MQ=255)                                                              tGCA‑TGTAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATGTATTTGGCTCATATTTTCGTTTTaa                                   >  1:1434112/1‑100 (MQ=255)                                                               gcattttAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTa                                    >  1:3071450/7‑100 (MQ=255)                                                               gCA‑TGTAAATGGACAGTG‑TTACAAAA‑TAGTCATTGTTTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATGTATTTGGCTCATATTTTCGTTTTaaa                                  >  1:3421417/1‑99 (MQ=255)                                                                 a‑TGTAAATGGGCAGTGTTTAAAAAAATAGTCATTGGTTTTATTTAAAATTTTGTTTTTGAAAATAGCATATATGTATTTGGCTCATATTTGCGTTTTAag                                  <  1:3137676/100‑1 (MQ=255)                                                                    gTAAATGGGCAGTGTTTAAAAAAATAGTCATTGGTTTTATTTAAAATTTTGTTTTTGAAAATAGCATATATGTATTTGGCTCATATTTGCGTTTTAagag                                >  1:2592826/1‑100 (MQ=255)                                                                    gTAAATGGACAGTG‑TTACAAAA‑TAGTCA‑TTGTTTTGCTGAAATTTTTGTTTGTGAAATTAGCATATATGTATTTGGCTCATATTTTCGTTTTAAAAGcgt                             <  1:5225335/100‑3 (MQ=255)                                                                      acaTGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCtt                             >  1:2331597/3‑100 (MQ=255)                                                                      aaaTGGGCAGTGTTTAAAAAAATAGTCATTGGTTTTATTTAAAATTTTGTTTTTGAAAATAGCATATATGTATTTGGCTCATATTTGCGTTTTAagagat                              >  1:858166/1‑98 (MQ=255)                                                                      aaaTGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGcct                             >  1:280320/1‑98 (MQ=255)                                                                       caTGGGCAGTGTTTAAAAAAATAGTCATTGGTTTTATTTAAAATTTTGTTTTTGAAAATAGCATATATGTATTTGGCTCATATTGGCGTTTTAAGAGAtt                             >  1:2193710/2‑100 (MQ=255)                                                                       aaTGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTg                            >  1:3054722/1‑100 (MQ=255)                                                                       aaTGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTg                            >  1:1913085/1‑100 (MQ=255)                                                                        aTGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGt                           >  1:1114517/1‑100 (MQ=255)                                                                          gggCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGtat                         <  1:3707766/100‑1 (MQ=255)                                                                           ggCAGTGTTTAAAAAAATAGTCATTGGTTTTATTTAAAATTTTGTTTTTGAAAATAGCATATATGTATTTGGCTCATATTTGCGTTTTAAGAGAttatgt                         <  1:4515818/100‑5 (MQ=255)                                                                            gCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGtatag                       >  1:2984861/1‑99 (MQ=255)                                                                             cAGTGTTTAAAAAAATAGTCATTGGTTTTATTTAAAATTTTGTTTTTGAAAATAGCATATATGTATTTGGCTCATATTTGCGTTTTAAGAGAttatgtag                       <  1:2673155/100‑7 (MQ=255)                                                                                            tAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGtagaaa        >  1:358997/1‑95 (MQ=255)                                                                                             aGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGtagagaa       >  1:4989752/1‑94 (MQ=255)                                                                                             aGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAgaaaa       >  1:3147610/1‑100 (MQ=255)                                                                                                ctcTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa    >  1:851766/3‑98 (MQ=255)                                                                                                cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGtagcagatcg    >  1:721293/1‑91 (MQ=255)                                                                                                cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActa    >  1:2684367/1‑98 (MQ=255)                                                                                                 ccTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActat   >  1:3752757/2‑97 (MQ=255)                                                                                                 aCTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActat   >  1:4878765/1‑97 (MQ=255)                                                                                                  cTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAGAAAActata  >  1:1094682/1‑96 (MQ=255)                                                                                                  |                                                                                                    CCTGCAGGAATTTAGAAAAACAT‑GTGGAAGTTTTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TGTAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTAAAAACCTAT  >  NC_007790/1279‑1472

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑