Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	711	0	A	G	69.8%	66.3 / 36.4	63	K144K (AAA→AAG)	SAUSA300_RS14705	replication protein
Reads supporting (aligned to +/- strand):  ref base A (17/2);  new base G (43/1);  total (60/3)
Fisher's exact test for biased strand distribution p-value = 2.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATGGCAAAGAGCATTACAAGTTGACTATCGACCTGTTGCTAATGTTAAAGCGATCAAACCGAATAGAAAAGGCGATAAAGACATTGAATCGGCAATCAAAGAGACCTCAAAATATTCGGTTAAATCATCTGATTTTTTAACTGATGATGATG‑AAAAAAATCAAGAAATTGTAAGTGATTTAGAAAAAGGTTTGTATCGA  >  NC_007790/612‑810                                                                                                    |                                                                                                     aTGGCAACAAGCATTAAAAGTAAATTATCGACCTGTCGTAAATATTAAAGCGATCAAACC‑‑‑‑A‑AAAAGGAGATAAAGATATTGCGTCTGCTATCAAGGAGAc                                                                                                 >  1:5687566/1‑100 (MQ=255) aTGGCAACAAGCATTAAAAGTAAATTATCGACCTGTCGTAAATATTAAAGCGATCAAACC‑‑‑‑A‑AAAAGGAGATAAAGATATTGCGTCTGCTATCAAGGAGAc                                                                                                 >  1:3043883/1‑100 (MQ=255) aTGGCAACAAGCATTAAAAGTAAATTATCGACCTGTCGTAAATATTAAAGCGATCAAACC‑‑‑‑A‑AAAAGGAGATAAAGATATTGCGTCTGCTATCAAGGAGAc                                                                                                 >  1:1468365/1‑100 (MQ=255)   ggCAACAAGCATTAAAAGTAAATTATCGACCTGTCGTAAATATTAAAGCGATCAAACC‑‑‑‑A‑AAAAGGAGATAAAGATATTGCGTCTGCTATCAAGGAGAcat                                                                                               >  1:5963664/1‑98 (MQ=255)   ggCAACAAGCATTAAAAGTAAATTATCGACCTGTCGTAAATATTAAAGCGATCAAACC‑‑‑‑A‑AAAAGGAGATAAAGATATTGCGTCTGCTATCAAGGAGAcag                                                                                               >  1:1837706/1‑98 (MQ=255)                      tacttATCGACCTGTCGTAAATATTAAAGCGATCAAACC‑‑‑‑A‑AAAAGGAGATAAAGATATTGCGTCTGCTATCAAGGAGACATCAAAATATTCCGTTAAatc                                                                            >  1:2957014/5‑100 (MQ=255)                              gACCTGTCGTAAATATTAAAGCGATCAAACC‑‑‑‑A‑AAAAGGAGATAAAGATATTGCGTCTGCTATCAAGGAGACATCAAAATATTCCGTTAAATCATCTGact                                                                    >  1:1477282/1‑98 (MQ=255)                                                                  taaaaGGAGATAAAGATATTGCGTCTGCTATCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGa                                    >  1:5833852/2‑100 (MQ=255)                                                                   caaaGGAGATAAAGATATTGCGTCTGCTATCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGaa                                   >  1:104/2‑100 (MQ=255)                                                                         agATAAAGATATTGCGTCTGCTATCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAAttatc                             <  1:4542502/99‑4 (MQ=255)                                                                                        tataacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAGaaaag              >  1:221725/6‑99 (MQ=255)                                                                                         ataacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAGaaaagg             >  1:2862335/5‑98 (MQ=255)                                                                                         ataacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAGaaaagg             >  1:890634/5‑98 (MQ=255)                                                                                          taacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAGaaaaggt            >  1:2750975/4‑97 (MQ=255)                                                                                          gaccAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAGaaaaggt            >  1:3737961/4‑97 (MQ=255)                                                                                          gaacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAGaaaaggt            >  1:5576103/4‑97 (MQ=255)                                                                                          ctgctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAgg            >  1:3210335/6‑100 (MQ=255)                                                                                          ctgctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAgg            >  1:441617/6‑100 (MQ=255)                                                                                          ctgctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAgg            >  1:2943434/6‑100 (MQ=255)                                                                                          ctgctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAgg            >  1:1713272/6‑100 (MQ=255)                                                                                          ctgctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAgg            >  1:6018524/6‑100 (MQ=255)                                                                                           aacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAGaaaaggtt           >  1:435161/3‑96 (MQ=255)                                                                                           aacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAGaaaaggtt           >  1:2484140/3‑96 (MQ=255)                                                                                           aacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAGaaaaggtt           >  1:5702444/3‑96 (MQ=255)                                                                                            gctaTCAAGGTGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:5533489/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATGAAAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGt           >  1:1362130/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:426309/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:4370099/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:899092/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:4017731/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:5213278/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:5367808/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:5603125/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:629766/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:779373/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:3393980/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:1148623/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:1595894/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:2027631/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:3945046/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:3267193/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt          >  1:2945307/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACAGATAGCTATG‑AAAAAAATCAAGAAATTATCAGTGTCCTAGAAAAAGGtt          >  1:5883051/4‑100 (MQ=255)                                                                                            gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGA‑CTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGttt         >  1:2773697/4‑100 (MQ=255)                                                                                            ctgcccAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGttt         >  1:2356951/6‑100 (MQ=255)                                                                                            acAATCAAAGAGACATCAAAATATTCCTTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTTAGTGATCTAG‑AAAAGGttt         <  1:2712678/99‑1 (MQ=255)                                                                                             cccgcAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTg        >  1:4798793/5‑100 (MQ=255)                                                                                               ctCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGGGATCTAGAAAAAGGTTTGt       >  1:776831/2‑100 (MQ=255)                                                                                               cgcAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTa      >  1:5761228/3‑100 (MQ=255)                                                                                               cccAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTa      >  1:5887239/3‑100 (MQ=255)                                                                                               aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATGAAAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTg        >  1:2803011/1‑100 (MQ=255)                                                                                               aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGt       >  1:3072070/1‑100 (MQ=255)                                                                                               aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGt       >  1:2336604/1‑100 (MQ=255)                                                                                               aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGt       >  1:5415962/1‑100 (MQ=255)                                                                                               aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGt       >  1:681172/1‑100 (MQ=255)                                                                                               aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGt       >  1:1091563/1‑100 (MQ=255)                                                                                               aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGt       >  1:837156/1‑100 (MQ=255)                                                                                               aTCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTCTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTa      >  1:1087240/1‑100 (MQ=255)                                                                                                ccAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAGAAAAAgatgagat      >  1:771387/2‑93 (MQ=255)                                                                                                 cAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGTAt     >  1:2825272/1‑100 (MQ=255)                                                                                                 cAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATc    <  1:5588955/100‑1 (MQ=255)                                                                                                 cAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCCAGaaaagatcggaaga     >  1:5457938/1‑90 (MQ=255)                                                                                                 cAAAGAGACATCAAAATATTCCGTTAAATCATCTGACCTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGCTTGTATc    >  1:2826308/1‑100 (MQ=255)                                                                                                  ccagagACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCg   >  1:3232872/3‑100 (MQ=255)                                                                                                   aaGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACGAAAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCg   >  1:1048700/1‑100 (MQ=255)                                                                                                   aaGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACA‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGa  >  1:2701390/1‑100 (MQ=255)                                                                                                    |                                                                                                     ATGGCAAAGAGCATTACAAGTTGACTATCGACCTGTTGCTAATGTTAAAGCGATCAAACCGAATAGAAAAGGCGATAAAGACATTGAATCGGCAATCAAAGAGACCTCAAAATATTCGGTTAAATCATCTGATTTTTTAACTGATGATGATG‑AAAAAAATCAAGAAATTGTAAGTGATTTAGAAAAAGGTTTGTATCGA  >  NC_007790/612‑810

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑