Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,406	0	C	G	29.6%	87.3 / 43.2	54	intergenic (+410/‑173)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base C (35/3);  new base G (9/7);  total (44/10)
Fisher's exact test for biased strand distribution p-value = 4.43e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TGTAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTA‑AAAACCTATATGA‑TA‑CCCCCTAAACCTTTAAAATACCCCCT  >  NC_007790/1311‑1504                                                                                                  |                                                                                                      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)                                                            aGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAg‑aaaa                                         >  1:3147610/1‑100 (MQ=255)                                                               ctcTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAG‑AAAActa                                      >  1:851766/3‑98 (MQ=255)                                                               cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGtagcagatcg                                       >  1:721293/1‑91 (MQ=255)                                                               cACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAG‑AAAActa                                      >  1:2684367/1‑98 (MQ=255)                                                                ccTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAG‑AAAActat                                     >  1:3752757/2‑97 (MQ=255)                                                                aCTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAG‑AAAActat                                     >  1:4878765/1‑97 (MQ=255)                                                                 cTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAG‑AAAActata                                    >  1:1094682/1‑96 (MQ=255)                                                                   ggTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAG‑AAAActataag                                  >  1:5239713/1‑94 (MQ=255)                                                                   ggTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAG‑AAAActataag                                  >  1:1192359/1‑94 (MQ=255)                                                                   ggTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAG‑AAAActataag                                  >  1:4222215/1‑94 (MQ=255)                                                                   ggTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAG‑AAAActataag                                  >  1:1208509/1‑94 (MQ=255)                                                                   ggTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAG‑AAAActataag                                  >  1:2697160/1‑94 (MQ=255)                                                                   ggTTCTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAG‑AAAActataag                                  >  1:3394140/1‑94 (MQ=255)                                                                     ccttGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑t                              >  1:3668955/3‑100 (MQ=255)                                                                       ttGCTGAAA‑TTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑ttta                           >  1:2203626/1‑97 (MQ=255)                                                                        tGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑ttta                           >  1:1809959/1‑97 (MQ=255)                                                                         gCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑tttac                          >  1:2000266/1‑96 (MQ=255)                                                                         gCTAAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑tttac                          >  1:1398334/1‑96 (MQ=255)                                                                         acggAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑tttac                          >  1:52174/4‑96 (MQ=255)                                                                                       ttgtGAAATTAGCATATATGTATTTGGCTCATATTTTCGTTTTAAAAGC‑‑GTATATAAGTTTTGGATAGAAAAAATATATGATTT‑ACCCCTAAACCTTTaa            >  1:4013432/1‑100 (MQ=255)                                                                                         gtgAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGATTT‑ACCTCTAAATCTTTaaaa          >  1:4084218/1‑100 (MQ=255)                                                                                               ttAGCATATATGTATTTGGCTCATATTTTCGTTTTAAAAGC‑‑GTATATAAGTTTTGGATAGAAAAAATATATGATTT‑ACCCCTAAACCTTTAAAATGcccc    >  1:1853242/1‑100 (MQ=255)                                                                                                tACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑TTTACCTCTAAATCTTTAAAATAccctc   >  1:3535992/1‑98 (MQ=255)                                                                                                gaCCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGGTTTTTAAGTAG‑AAAA‑CTATAAGATTT‑ACCTCTAAATCTTTAAAATAccctc   >  1:4359420/2‑98 (MQ=255)                                                                                                 aCCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGATTT‑ACCTCTAAATCTTTAAAATACCctct  >  1:1405439/1‑100 (MQ=255)                                                                                                  |                                                                                                      TTAAAGGATTTTATGCTAATTTTTAATTTGCA‑TGTAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTA‑AAAACCTATATGA‑TA‑CCCCCTAAACCTTTAAAATACCCCCT  >  NC_007790/1311‑1504

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑