Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	1,959,221	1	.	A	72.7%	19.8 / 4.0	11	pseudogene (632/788 nt)	SAUSA300_RS09695	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (3/0);  new base A (3/5);  total (6/5)
Fisher's exact test for biased strand distribution p-value = 1.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.69e-01

TTAGCGCTAAGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATGCAAGC‑‑‑‑AAAAAAATAAAAAGACACAGGCAAAATGAGTTTATTTTTATTTTAAATGACTCAAAAAAAGAAATAAATGAACATAATAAAA  >  NC_007793/1959122‑1959303                                                                                                     |                                                                                      ttaGCGCTAAGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATgcaagc                                                                                        >  1:59830/1‑100 (MQ=255) ttaGCGCTAAGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATgcaagc                                                                                        >  1:5029448/1‑100 (MQ=255) ttaGCGCTAAGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATgcaagc                                                                                        >  1:3427947/1‑100 (MQ=255) gtaGCGCTAAGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATgcaagc                                                                                        >  1:4477223/2‑100 (MQ=255)  taGCGCTAAGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTCAGTCGAAAATAACGGATGCTATgcaagc‑‑‑‑a                                                                                   >  1:3326340/1‑100 (MQ=255)  taGCGCTAAGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATgcaagc‑‑‑‑a                                                                                   >  1:5592404/1‑100 (MQ=255)  taGCGCTAAGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATgcaagc‑‑‑‑a                                                                                   <  1:459010/100‑1 (MQ=255)  taGCGCTAAGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATgcaagc‑‑‑‑a                                                                                   >  1:2310174/1‑100 (MQ=255)   aGCGCTAAGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATgcaagc‑‑‑‑aa                                                                                  <  1:3637382/100‑1 (MQ=255)   aGCGCTAAGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATgcaagc‑‑‑‑aa                                                                                  >  1:3535383/1‑100 (MQ=255)    gcgcTAAGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATGCAAGC‑‑‑‑aaa                                                                                 >  1:1192207/1‑100 (MQ=255)    gcgcTAAGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATGCAAGC‑‑‑‑aaa                                                                                 >  1:4002673/1‑100 (MQ=255)         aaGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATGCAAGC‑‑‑‑aaaaaaaa                                                                            >  1:2621757/1‑99 (MQ=255)         aaGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATGCAAGC‑‑‑‑aaaaaaaa                                                                            >  1:127828/1‑99 (MQ=255)         aaGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATGCAAGC‑‑‑‑aaaaaaaa                                                                            >  1:875101/1‑99 (MQ=255)         aaGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAAACCGAATAATTCTATGATTAGTAAGTCGAAAATAACGGATGCTATGCAAGC‑‑‑‑aaaaaaaa                                                                            >  1:5795581/1‑99 (MQ=255)              aaaTCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATGCAAGC‑‑‑‑AAAAAAAAataaa                                                                       >  1:3098122/1‑100 (MQ=255)               caTCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATGCAAGC‑‑‑‑AAAAAAAAataaaa                                                                      >  1:4040971/2‑99 (MQ=255)               aaTCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATGCAAGC‑‑‑‑AAAAAAAAataaaa                                                                      >  1:5654846/1‑99 (MQ=255)                       aGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATGCAAGCAA‑‑AAAAAAATAAAAAGACACAg                                                                >  1:5246441/1‑100 (MQ=255)                          aaaaTTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATGCAAGCAAA‑AAAAAAATAAAAAGACACAGGc                                                              <  1:1420026/100‑1 (MQ=255)                              tttATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATGCAAGCAAAAAAAAAAATAAAAAGACACAGGCaaa                                                           <  1:5589209/100‑1 (MQ=255)                               ttATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATGCAAGCAA‑‑AAAAAAATAAAAAGACACAGGCAAAATg                                                        <  1:4478020/100‑1 (MQ=255)                                tATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATGCAAGCAAA‑AAAAAAATAAAAAGACACAGGCAAAATg                                                        <  1:1422934/100‑1 (MQ=255)                                       ttccgatCTAGCCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATGCAAGCAAA‑AAAAAAATAAAAAGACACAGGCAAAATGAGtttaa                                                 <  1:1103656/94‑2 (MQ=255)                                                               aTGATTATTAAGTCGAAAATAACGGATGCTATGCAAGCAAA‑AAAAAAATAAAAAGACACAGGCAAAATGAGTTTATTTTTATTTTAAATGACTCaaaaaa                         >  1:4330240/1‑100 (MQ=255)                                                                                     aggATGCTATGCAAGCAA‑‑AAAAAAATAAAAAGACACAGGCAAAATGAGTTTATTTTTATTTTAAATGACTCAAAAAAAGAAATAAATGAACATAATaaaa  >  1:3179631/2‑100 (MQ=255)                                                                                                     |                                                                                      TTAGCGCTAAGAAAAATCAAAAAGAAAAATTTATCAATGCTATTTCTAACCCTAATAATTCTATGATTATTAAGTCGAAAATAACGGATGCTATGCAAGC‑‑‑‑AAAAAAATAAAAAGACACAGGCAAAATGAGTTTATTTTTATTTTAAATGACTCAAAAAAAGAAATAAATGAACATAATAAAA  >  NC_007793/1959122‑1959303

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: ‑