Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	2,113,235	0	C	A	76.5%	61.8 / 17.0	34	E44* (GAG→TAG)	SAUSA300_RS10710	acetyltransferase
Reads supporting (aligned to +/- strand):  ref base C (2/6);  new base A (14/12);  total (16/18)
Fisher's exact test for biased strand distribution p-value = 2.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

ATCTGTAGTTCGCTAAGTCTAAAACGGTAAAATTCGTATCTTCCAAACAATTCATTTTTAAGCGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTCTCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACGTTGTTTTCTCATCTTCTTCAACCTAGCTTCCATTACGCCT  >  NC_007793/2113138‑2113332                                                                                                  |                                                                                                  tggtGTAGTTCTCTAAATTTAAAACAGTAATGTTCGTATCTTCCAAGCAATTCATTTTTGACTGTGCGCCACATGTTCTCCAGCTCTTCGTTACGctatc                                                                                                 >  1:4858793/4‑100 (MQ=255)   gtGTAGTTCTCTAAATTTAAAACAGTAATGTTCGTATCTTCCAAGCAATTCATTTTTGACTGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCtt                                                                                               <  1:2964632/99‑1 (MQ=255)       aGTTCTCTAAATTTAAAACAGTAATGTTCGTATCTTCCAAGCAATTCATTTTTGACTGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACt                                                                                           >  1:3038638/1‑100 (MQ=255)         ttCGCTAAGTCTAAAACGGTAAAATTCGTATCTTCCAAACAATTCACTTTTAAGCGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTCTCTTAACTTa                                                                                         <  1:5226265/100‑1 (MQ=255)             cTAAATTTAAAACAGTAATGTTCGTATCTTCCAAGCAATTCATTTTTGACTGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCta                                                                                     >  1:460325/1‑100 (MQ=255)             cTAAATTTAAAACAGTAATGTTCGTATCTTCCAAGCAATTCATTTTTGACTGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCta                                                                                     >  1:3455713/1‑100 (MQ=255)              taaatttAAAACAGTAATGTTCGTATCTTCCAAGCAATTCATTTTTGACTGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCtat                                                                                    <  1:2256481/94‑1 (MQ=255)               aaatttAAAACAGTAATGTTCGTATCTTCCAAGCAATTCATTTTTGACTGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCtatg                                                                                   <  1:205003/95‑2 (MQ=255)                    tAAAACAGTAATGTTCGTATCTTCCAAGCAATTCATTTTTGACTGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCTATATccct                                                                              <  1:4565642/100‑2 (MQ=255)                        aCGGTAAAATTCGTATCTTCCAAACAATTCATTTTTAAGCGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTCTCTTAACTTAGCTATATCCCCAATa                                                                          <  1:318589/100‑1 (MQ=255)                         cagtaatgttCGTATCTTCCAAGCAATTCATTTTTGACTGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCTATATCCCCAATaa                                                                         >  1:4341592/9‑100 (MQ=255)                            taatgttCGTATCTTCCAAGCAATTCATTTTTGACTGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCTATATCCCCAATAGGCt                                                                      <  1:2077472/95‑1 (MQ=255)                                cttccgaTCTTCCAAGCAATTCATTTTTGACTGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCTATATCCCCAATAAGCTCGTc                                                                  <  1:4321560/94‑1 (MQ=255)                                       tCTTCCGATCTATTCATTTTTAAGCGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTCTCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGc                                                           <  1:3943430/100‑1 (MQ=255)                                         ttCCAAGCAATTCATTTTTGACTGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGctt                                                         <  1:880033/100‑1 (MQ=255)                                          tCCAAGCAATTCATTTTTGACTGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGcttc                                                        >  1:2891234/1‑100 (MQ=255)                                          cccAAACAATTCATTTTTAAGCGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTCTCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGcttc                                                        >  1:983401/2‑100 (MQ=255)                                           ccAAGCAATTCATTTTTGACTGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGcttct                                                       >  1:598432/1‑100 (MQ=255)                                            cAAGCAATTCATTTTTGACTGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGcttctt                                                      >  1:745713/1‑100 (MQ=255)                                                           tgactgTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACgttg                                       <  1:6025669/95‑1 (MQ=255)                                                           tgactgTGCGCCACATGTTCTCCAGCTCTTCGTT‑CGCTATCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACgttgt                                      >  1:3965651/6‑100 (MQ=255)                                                             actgTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACgttgtt                                     <  1:1488644/97‑1 (MQ=255)                                                              gCGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTCTCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACGTTGttt                                    <  1:2592604/100‑1 (MQ=255)                                                               tgTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACgtcccaca                                   <  1:666545/99‑7 (MQ=255)                                                                  gcgcCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACGTTGTTTtctc                                >  1:751801/1‑100 (MQ=255)                                                                   tgcCACATGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACGTTGTTTTCTCa                               >  1:935236/2‑100 (MQ=255)                                                                    gcCACATGTTCTCCAGCTCTTCGTTACGCTCTCTTAACTTAGCTATATCCCCAATAAGCTCGTCATGTTGCTTCTTGTACTCATCACGTTGTTTTCTCAt                              >  1:4501227/1‑100 (MQ=255)                                                                      cacaTGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACGTTGTTTTCTCAtct                            >  1:1977560/1‑100 (MQ=255)                                                                      cacaTGTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACGTTGTTTTCTCAtct                            >  1:753839/1‑100 (MQ=255)                                                                           gTTCTCCAGCTCTTCGTTACGCTATCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACGTTGTTTTCTCATCttcttc                       >  1:3396538/1‑100 (MQ=255)                                                                                     tctTCGTTACGCTCTCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACGTTGTTTTCTCATCTTCTTCAACCTAGCtt             <  1:5131825/100‑1 (MQ=255)                                                                                      ctTCGTTACGGGATCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACGTTGTTTTCTCATCTTCTTCAACCTAGCTTc            >  1:2168124/1‑100 (MQ=255)                                                                                      ctTCGTTACGCTATCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACGTTGTTTTCTCATCTTCTTCAACCTAGCtta            <  1:3735226/100‑2 (MQ=255)                                                                                         cGTTACGCTATCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACGTTGTTTTCTCATCTTCTTCAACCTAGCTTCCac         <  1:5704174/100‑2 (MQ=255)                                                                                           ctACGCTCTCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACGTTGTTTTCTCATCTTCTTCAACCTAGCTTCCATTa       <  1:2845207/99‑1 (MQ=255)                                                                                                ctctctTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACGTTGTTTTCTCATCTTCTTCAACCTAGCTTCCATTACGcac  <  1:5452772/100‑3 (MQ=255)                                                                                                ctctctTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACGTTGTTTTCTCATCTTCTTCAACCTAGCTTCCATTACGCCt  <  1:3005645/100‑1 (MQ=255)                                                                                                  |                                                                                                  ATCTGTAGTTCGCTAAGTCTAAAACGGTAAAATTCGTATCTTCCAAACAATTCATTTTTAAGCGTGCGCCACATGTTCTCCAGCTCTTCGTTACGCTCTCTTAACTTAGCTATATCCCCAATAAGCTCGTCACGTTGCTTCTTGTACTCATCACGTTGTTTTCTCATCTTCTTCAACCTAGCTTCCATTACGCCT  >  NC_007793/2113138‑2113332

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑