Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007790	744	T→C	D155D (GAT→GAC)	SAUSA300_RS14705 →	replication protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007790	744	0	T	C	98.7%	198.8 / ‑4.9	77	D155D (GAT→GAC)	SAUSA300_RS14705	replication protein
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (48/27);  total (50/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.35e-01

AGACATTGAATCGGCAATCAAAGAGACCTCAAAATATTCGGTTAAATCATCTGATTTTTTAACTGATGATGATG‑AAAAAAATCAAGAAATTGTAAGTGATTTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGTTATGGTGGATTGCTT  >  NC_007790/690‑840                                                       |                                                                                                  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                                           >  1:70271/5‑98 (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                                        >  1:2319428/4‑100 (MQ=255)              gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt                                        >  1:4815684/4‑100 (MQ=255)              gctaTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGtt                                        >  1:1097812/4‑100 (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                                     <  1:3111065/100‑1 (MQ=255)                aaTCAAAGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGt                                     <  1:80129/100‑1 (MQ=255)                 aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGt                                     >  1:218931/1‑100 (MQ=255)                 aTCAAGGAGACATCAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGt                                     >  1:4325601/1‑100 (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)                          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                       >  1:567754/1‑100 (MQ=255)                              cAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATg                       >  1:1711521/1‑100 (MQ=255)                              cAAAATATTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATg                       >  1:2056005/1‑100 (MQ=255)                                    atTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGt                 >  1:3217137/1‑100 (MQ=25)                                    atTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGt                 >  1:3534441/1‑100 (MQ=25)                                    atTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGt                 >  1:1246074/1‑100 (MQ=37)                                    atTCCGTTAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGCTTGTATCGAAAACGTATGTTAAGt                 >  1:3360514/1‑100 (MQ=255)                                          ttAAATCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtggt           <  1:2944042/100‑1 (MQ=37)                                           tAAGTCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtggt           <  1:2939967/100‑1 (MQ=25)                                           tAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtggt           <  1:4624538/100‑1 (MQ=25)                                           tAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtggt           <  1:2507888/100‑1 (MQ=37)                                           tAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtggg           <  1:4513717/100‑2 (MQ=25)                                           tAAATCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTAGTATCGAAAACGTATGTTAAGTTAtggt           <  1:3974056/100‑1 (MQ=37)                                           gaaaTCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtggtg          >  1:1292568/2‑100 (MQ=25)                                            aaaTCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtggtgg         <  1:3505570/100‑1 (MQ=37)                                            aaaTCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtggtgg         <  1:1614606/100‑1 (MQ=37)                                            aaaTCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtggtgg         <  1:5158940/100‑1 (MQ=37)                                            aaaTCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtggtgg         <  1:2139921/100‑1 (MQ=25)                                            aaaTCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtggtgg         <  1:4508363/100‑1 (MQ=37)                                            aaaTCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtggtgg         <  1:3857916/100‑1 (MQ=37)                                            aaaTCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtgggtg         <  1:2247896/100‑4 (MQ=37)                                            aaaTCATCTGACTTTTTAACTGATAGCGATGAAAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtggt           <  1:2431521/100‑1 (MQ=25)                                             aaTCATCTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTATGGTGGa        <  1:3064175/100‑1 (MQ=37)                                             aaTCATCTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtggtat         <  1:4240592/100‑3 (MQ=25)                                              atcatcTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTATGGTGGag       <  1:909288/100‑2 (MQ=37)                                              atcatcTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTATGGTGGAt       <  1:1822403/100‑1 (MQ=37)                                              atcatcTGACTTTTTAACTGATAGCGATGAAAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtggtat         <  1:190300/100‑3 (MQ=21)                                              atcatcTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGTTAtggtagg        <  1:3404133/100‑4 (MQ=25)                                                catcTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTATGGTGGAtta     >  1:2344796/1‑99 (MQ=37)                                                catcTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTATGGTGGAtta     >  1:758475/1‑99 (MQ=25)                                                catcTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGTTATGGTAGAtt      >  1:1660966/1‑100 (MQ=25)                                                 cgcTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTATGGTGGAttac    >  1:3910361/3‑98 (MQ=25)                                                  tcTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTATGGTGGATTACt   >  1:3350510/1‑100 (MQ=25)                                                   cTGACTTTTTAACTGATGACGACG‑AAAAAAATCAAGAAATTTTAAGTGATCTAG‑AAAAGGTTTGTATCGAAAACGTATGTTAAGTTATGGTGGATTACtt  >  1:4554415/1‑100 (MQ=25)                                                   cTGACTTTTTAACTGATAGCGATG‑AAAAAAATCAAGAAATTATCAGTGATCTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGTTATGGTAGATTGCt   <  1:1537373/100‑1 (MQ=25)                                                       |                                                                                                  AGACATTGAATCGGCAATCAAAGAGACCTCAAAATATTCGGTTAAATCATCTGATTTTTTAACTGATGATGATG‑AAAAAAATCAAGAAATTGTAAGTGATTTAGAAAAAGGTTTGTATCGAAAACGTATGTTAAGTTATGGTGGATTGCTT  >  NC_007790/690‑840

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: ‑