Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007790	729	G→C	S150S (TCG→TCC)	SAUSA300_RS14705 →	replication protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	729	0	G	C	98.0%	135.5 / ‑3.7	50	S150S (TCG→TCC)	SAUSA300_RS14705	replication protein
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base C (43/6);  total (44/6)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.49e-01

ACAAGTTGACTATCGACCTGTTGCTAATGTTAAAGCGATCAAACCGAATAGAAAAGGCGATAAAGACATTGAATCGGCAATCAAAGAGACCTCAAAATATTCGGTTAAATCATCTGATTTTTTAACTGATGATGATG‑AAAAAAATCAAGAAATTGTAAGTGATTTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGT  >  NC_007790/627‑825                                                                                                       |                                                                                                  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                         >  1:2319428/4‑100 (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                      >  1:218931/1‑100 (MQ=255)                                                                                aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGt                      >  1:3410430/1‑100 (MQ=255)                                                                                aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGt                      >  1:4325601/1‑100 (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)                                                                                         acatCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACg            >  1:1561031/4‑100 (MQ=255)                                                                                          catCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGt           >  1:5021494/3‑100 (MQ=255)                                                                                           atCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTa          >  1:4280628/2‑100 (MQ=255)                                                                                             ccaaaTATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATg        >  1:4338221/3‑100 (MQ=255)                                                                                             cAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATg        >  1:1711521/1‑100 (MQ=255)                                                                                             cAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATg        >  1:567754/1‑100 (MQ=255)                                                                                             cAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATg        >  1:2056005/1‑100 (MQ=255)                                                                                                   atTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGt  >  1:3534441/1‑100 (MQ=25)                                                                                                   atTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGt  >  1:1246074/1‑100 (MQ=37)                                                                                                   atTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGt  >  1:3217137/1‑100 (MQ=25)                                                                                                   atTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGCTTGTATCGAAAACGTATGTTAAGt  >  1:3360514/1‑100 (MQ=255)                                                                                                       |                                                                                                  ACAAGTTGACTATCGACCTGTTGCTAATGTTAAAGCGATCAAACCGAATAGAAAAGGCGATAAAGACATTGAATCGGCAATCAAAGAGACCTCAAAATATTCGGTTAAATCATCTGATTTTTTAACTGATGATGATG‑AAAAAAATCAAGAAATTGTAAGTGATTTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGT  >  NC_007790/627‑825

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: ‑