Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	711	0	A	G	64.5%	17.2 / 19.8	31	K144K (AAA→AAG)	SAUSA300_RS14705	replication protein
Reads supporting (aligned to +/- strand):  ref base A (7/4);  new base G (19/1);  total (26/5)
Fisher's exact test for biased strand distribution p-value = 4.16e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.56e-01

AAGAGCATTACAAGTTGACTATCGACCTGTTGCTAATGTTAAAGCGATCAAACCGAATAGAAAAGGCGATAAAGACATTGAATCGGCAATCAAAGAGACCTCAAAATATTCGGTTAAATCATCTGATTTTTTAACTGATGATGATG‑AAAAAAATCAAGAAATTGTAAGTGATTTAGAAAAAGGTTTGTATCGAA  >  NC_007790/618‑811                                                                                              |                                                                                                      gcaagCATTAAAAGTAAATTATCGACCTGTCGTAAATATTAAAGCGATCAAACC‑‑‑‑A‑AAAAGGAGATAAAGATATTGCGTCTGCTATCAAGGAGACATCaaa                                                                                            >  1:3632583/4‑100 (MQ=255)          aaaagtaaattATCGACCTGTCGTAAATATTAAAGCGATCAAACC‑‑‑‑A‑AAAAGGAGATAAAGATATTGCGTCTGCTATCAAGGAGACATCAAAATATTCCGt                                                                                   >  1:3180128/11‑100 (MQ=255)                                                                         aGATATTGCGTCTGCTATCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGAt                        <  1:2343521/100‑1 (MQ=255)                                                                             gattttataacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAg                    <  1:3770622/90‑1 (MQ=255)                                                                             gattttataacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAg                    >  1:3523420/11‑100 (MQ=255)                                                                               tgcgtctgctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGaa                  >  1:319734/11‑100 (MQ=255)                                                                                  gtctgctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑‑AAAAAATCAAGAAATTATCAGTGATCTTGAAAAAg              >  1:3599873/8‑100 (MQ=255)                                                                                   ataacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACCTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAGaaaagg              >  1:70271/5‑98 (MQ=255)                                                                                   ataacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACCTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAGaaaagg              >  1:5050157/5‑98 (MQ=255)                                                                                    gtgctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAgg             >  1:3419989/6‑100 (MQ=255)                                                                                    ctgctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAgg             >  1:109937/6‑100 (MQ=255)                                                                                    cGGCAATCAAAGAGACCTCAAAATATTCGGTTAAATCATCTGATTTTTTAACTGATGATAATG‑AAAAAAATCAAGAAATTGTAAGTGATTTAGAAAAAgg             >  1:2591394/1‑100 (MQ=255)                                                                                     tgctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGt            >  1:2368030/5‑100 (MQ=255)                                                                                     aacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAGaaaaggtt            >  1:4474383/3‑96 (MQ=255)                                                                                     aacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAGaaaaggtc            >  1:3998324/3‑96 (MQ=255)                                                                                      gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTGACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt           >  1:2432412/4‑100 (MQ=255)                                                                                      gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt           >  1:1097812/4‑100 (MQ=255)                                                                                      gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt           >  1:4815684/4‑100 (MQ=255)                                                                                      gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt           >  1:2319428/4‑100 (MQ=255)                                                                                      gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt           >  1:115164/4‑100 (MQ=255)                                                                                      gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGA‑CTTTTAACTGATAGCGATGAAAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt           >  1:2738253/4‑100 (MQ=255)                                                                                      acAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGttt          <  1:1007062/99‑1 (MQ=255)                                                                                       attgcAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTg         >  1:4663603/5‑100 (MQ=255)                                                                                        taTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTg         >  1:3909731/2‑100 (MQ=255)                                                                                        aaTCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGt        <  1:80129/100‑1 (MQ=255)                                                                                        aaTCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGt        <  1:3111065/100‑1 (MQ=255)                                                                                         aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGt        >  1:4325601/1‑100 (MQ=255)                                                                                         aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGt        >  1:3410430/1‑100 (MQ=255)                                                                                         aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGt        >  1:218931/1‑100 (MQ=255)                                                                                         aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTCGt        >  1:2647157/1‑100 (MQ=255)                                                                                           cAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGTAt      >  1:4367600/1‑100 (MQ=255)                                                                                              agagACATCAAAATATCCCTTTAAATCACCGGACTTTTTAACTGAGGACGCCG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGaa  <  1:2099493/100‑1 (MQ=255)                                                                                              |                                                                                                      AAGAGCATTACAAGTTGACTATCGACCTGTTGCTAATGTTAAAGCGATCAAACCGAATAGAAAAGGCGATAAAGACATTGAATCGGCAATCAAAGAGACCTCAAAATATTCGGTTAAATCATCTGATTTTTTAACTGATGATGATG‑AAAAAAATCAAGAAATTGTAAGTGATTTAGAAAAAGGTTTGTATCGAA  >  NC_007790/618‑811

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑