Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	1,414	0	T	G	30.9%	69.8 / 49.0	55	intergenic (+418/‑165)	SAUSA300_RS14705/SAUSA300_RS14710	replication protein/membrane protein
Reads supporting (aligned to +/- strand):  ref base T (35/3);  new base G (12/5);  total (47/8)
Fisher's exact test for biased strand distribution p-value = 9.08e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTATGCTAATTTTTAATTTGCA‑TGTAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTA‑AAAACCTATATGA‑TA‑CCCCCTAAACCTTTAAAATACCCCCTTAAAACTCA  >  NC_007790/1321‑1513                                                                                                |                                                                                                       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                                                                        >  1:1913085/1‑100 (MQ=255)                            aaTGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTg                                                                        >  1:3054722/1‑100 (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                                           >  1:2697160/1‑94 (MQ=255)                                                         ggTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAG‑AAAActataag                                           >  1:1192359/1‑94 (MQ=255)                                                         ggTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAG‑AAAActataag                                           >  1:5239713/1‑94 (MQ=255)                                                         ggTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAG‑AAAActataag                                           >  1:1208509/1‑94 (MQ=255)                                                         ggTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAGTAG‑AAAActataag                                           >  1:4222215/1‑94 (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)                                                                                      tagcATATATGTATTTGGCTCATATTTTCGTTTTAAAAGC‑‑GTATATAAGTTTTGGATAGAAAAAATATATGATTT‑ACCCCTAAACCTTTAAAATGcccct            >  1:3610816/4‑99 (MQ=255)                                                                                      tACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑TTTACCTCTAAATCTTTAAAATAccctc            >  1:3535992/1‑98 (MQ=255)                                                                                      gaCCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGGTTTTTAAGTAG‑AAAA‑CTATAAGATTT‑ACCTCTAAATCTTTAAAATAccctc            >  1:4359420/2‑98 (MQ=255)                                                                                       agcATATATGTATTTGGCTCATATTTTCGTTTTAAAAGC‑‑GTATATAAGTTTTGGATAGAAAAAATATATGATTT‑ACCCCTAAACCTTTAAAATGcccctt           >  1:3315975/3‑98 (MQ=255)                                                                                       agcATATATGTATTTGGCTCATATTTTCGTTTTAAAAGC‑‑GTATATAAGTTTTGGATAGAAAAAATATATGATTT‑ACCCCTAAACCTTTAAAATGcccctt           >  1:3831423/3‑98 (MQ=255)                                                                                       aCCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGATTT‑ACCTCTAAATCTTTAAAATACCctct           >  1:1405439/1‑100 (MQ=255)                                                                                              atttatttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGATTT‑ACCTCTAAATCTTTAAAATACCCTCTTaaaatt    >  1:4629165/1‑98 (MQ=255)                                                                                                ttatttGGCTCATATTTGCGTTTTAAGAGCTTGTATAGATTTTTAAG‑TA‑GAAAACTATAAGA‑TTTACCTCTAAATCTTTAAAATACCCTCTTAAAATTCa  >  1:203965/1‑100 (MQ=255)                                                                                                |                                                                                                       TTATGCTAATTTTTAATTTGCA‑TGTAAATGGGCAGTG‑TTAAAAAATTAGTCACTGGTTTTGCTGAAATTTTTGTTTGTGAAATTACCATATATTTATTTGGCTCATATTTGCGTTTTAAGAGCTTGTATATATTTTTAAGTTA‑AAAACCTATATGA‑TA‑CCCCCTAAACCTTTAAAATACCCCCTTAAAACTCA  >  NC_007790/1321‑1513

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: ‑