Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	725,902	0	G	A	75.0%	30.6 / 6.5	24	intergenic (+28/+560)	SAUSA300_RS03485/SAUSA300_RS03490	inorganic phosphate transporter/peptidase M23
Reads supporting (aligned to +/- strand):  ref base G (3/3);  new base A (0/18);  total (3/21)
Fisher's exact test for biased strand distribution p-value = 9.88e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.05e-01

TGATTACATTACCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAGTATCACAAACATATGGTGGTATTGAAGTTCAGTTTTTTATGTAAGTAGATAACAT  >  NC_007793/725807‑725957                                                                                                |                                                        tGATTACATTACCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAGTAtt                                                     <  1:5552826/100‑2 (MQ=255) tGATTACATTACCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAATacc                                                     <  1:991135/100‑3 (MQ=255) tGATTACATTACCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAATacc                                                     <  1:327142/100‑3 (MQ=255) tGATTACATTACCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAATATc                                                     <  1:3074303/100‑1 (MQ=255)    ttacattacCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAATACcacc                                                  <  1:938571/100‑2 (MQ=255)    ttacattacCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAATACcacc                                                  <  1:377543/100‑2 (MQ=255)    ttacattacCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACAAAACTGAACTTCAATACcacc                                                  <  1:395492/100‑2 (MQ=255)     tacgttacCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAAAAAAACTGAACTTCAATACcacca                                                 <  1:809884/100‑3 (MQ=255)     tacattacCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAATACcacca                                                 <  1:1531011/100‑3 (MQ=255)     tacattacCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAATACcacca                                                 <  1:5327372/100‑3 (MQ=255)     tacattacCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAATACcacca                                                 <  1:4520959/100‑3 (MQ=255)     tacattacCTATCTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAGACTAAACTGAACTTCAATACcacca                                                 <  1:893781/100‑3 (MQ=255)      acattacCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAGCTAAACTGAACTTCAATACcaccat                                                <  1:4805702/100‑4 (MQ=255)      acattacCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAGTATCACaat                                                <  1:5395875/100‑2 (MQ=255)      acattacCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAATACcaccat                                                <  1:2149104/100‑4 (MQ=255)      acattacCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAATACcaccag                                                <  1:4478633/100‑4 (MQ=255)      acattacCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAATACcaccag                                                <  1:5748908/100‑4 (MQ=255)       cattacCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAATACcaccaca                                               <  1:5460612/100‑5 (MQ=255)        attacCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAATACcaccacag                                              <  1:971486/100‑6 (MQ=255)        attacCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAATACcaccacag                                              <  1:1193165/100‑6 (MQ=255)               aTTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAGTATCACAAACATAtgggg                                       <  1:4433486/100‑3 (MQ=255)                   cAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAGTATCACAAACATATGGTGGTag                                   >  1:4783653/1‑99 (MQ=255)                            tAGCAGGTTTACTATTCTATATACTTAATTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAGTATCACAAACATATGGCGGTATTGAAGTTCa                          >  1:5465233/1‑100 (MQ=255)                                                    ttaacttaTTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAGTATCACAAACATATGGTGGTATTGAAGTTCAGTTTTTTATGTAAGTAGATAACat  >  1:408443/1‑100 (MQ=255)                                                                                                |                                                        TGATTACATTACCTATTTCAGCATTGTTAGCAGGTTTACTATTCTATATACTTAACTTATTTTTCTAATTGAAAATAAAACTAAACTGAACTTCAGTATCACAAACATATGGTGGTATTGAAGTTCAGTTTTTTATGTAAGTAGATAACAT  >  NC_007793/725807‑725957

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑