Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007790	717	C→A	T146T (ACC→ACA)	SAUSA300_RS14705 →	replication protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	717	0	C	A	97.5%	111.6 / ‑3.2	40	T146T (ACC→ACA)	SAUSA300_RS14705	replication protein
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base A (33/6);  total (34/6)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.66e-01

AAGAGCATTACAAGTTGACTATCGACCTGTTGCTAATGTTAAAGCGATCAAACCGAATAGAAAAGGCGATAAAGACATTGAATCGGCAATCAAAGAGACCTCAAAATATTCGGTTAAATCATCTGATTTTTTAACTGATGATGATG‑AAAAAAATCAAGAAATTGTAAGTGATTTAGAAAAAGGTTTGTATCGAAAAC  >  NC_007790/618‑814                                                                                                    |                                                                                                   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                       >  1:3523420/11‑100 (MQ=255)                                                                             gattttataacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAg                       <  1:3770622/90‑1 (MQ=255)                                                                               tgcgtctgctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGaa                     >  1:319734/11‑100 (MQ=255)                                                                                  gtctgctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑‑AAAAAATCAAGAAATTATCAGTGATCTTGAAAAAg                 >  1:3599873/8‑100 (MQ=255)                                                                                   ataacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACCTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAGaaaagg                 >  1:5050157/5‑98 (MQ=255)                                                                                   ataacAATCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACCTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAGaaaagg                 >  1:70271/5‑98 (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              >  1:115164/4‑100 (MQ=255)                                                                                      gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt              >  1:2319428/4‑100 (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           <  1:3111065/100‑1 (MQ=255)                                                                                        aaTCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGt           <  1:80129/100‑1 (MQ=255)                                                                                         aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGt           >  1:4325601/1‑100 (MQ=255)                                                                                         aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGt           >  1:218931/1‑100 (MQ=255)                                                                                         aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGt           >  1:3410430/1‑100 (MQ=255)                                                                                         aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTCGt           >  1:2647157/1‑100 (MQ=255)                                                                                           cAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGTAt         >  1:4367600/1‑100 (MQ=255)                                                                                            aaggagaCATCAAAATATTCCGTTAAATCATCTGACCTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGTATc        <  1:1621429/97‑1 (MQ=255)                                                                                             acgagaCATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATGAAAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGTATc        >  1:4012739/3‑100 (MQ=255)                                                                                              agagACATCAAAATATCCCTTTAAATCACCGGACTTTTTAACTGAGGACGCCG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGaa     <  1:2099493/100‑1 (MQ=255)                                                                                               cagaCATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGaaa    >  1:128674/2‑100 (MQ=255)                                                                                                agaCATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAGATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGaaaa   >  1:2375573/1‑100 (MQ=255)                                                                                                agaCATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGaaaa   >  1:1788173/1‑100 (MQ=255)                                                                                                agaCATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGaaaa   >  1:4610224/1‑100 (MQ=255)                                                                                                agaCATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGTATCGaaa    >  1:2027021/1‑100 (MQ=255)                                                                                                agaCATCAAAATATTCCGTTAAATCATCTGACCTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGaaaa   >  1:53122/1‑100 (MQ=255)                                                                                                 gaCATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAAc  >  1:1258944/1‑100 (MQ=255)                                                                                                    |                                                                                                   AAGAGCATTACAAGTTGACTATCGACCTGTTGCTAATGTTAAAGCGATCAAACCGAATAGAAAAGGCGATAAAGACATTGAATCGGCAATCAAAGAGACCTCAAAATATTCGGTTAAATCATCTGATTTTTTAACTGATGATGATG‑AAAAAAATCAAGAAATTGTAAGTGATTTAGAAAAAGGTTTGTATCGAAAAC  >  NC_007790/618‑814

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑