Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	525,622	(A)8→7	pseudogene (63/157 nt)	SAUSA300_RS02505 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	525,615	0	A	.	97.6%	153.6 / ‑2.5	42	pseudogene (70/157 nt)	SAUSA300_RS02505	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base . (41/0);  total (42/0)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

AAACGATTTTATAAACGCAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGATAAAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGATGACGA  >  NC_007793/525530‑525710                                                                                      |                                                                                                aaaCGATTTTATAAACGCAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACa                                                                                  >  1:3063097/1‑100 (MQ=255)          tataAACGCAAGCTGTAATTTTAACTGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGttt                                                                         >  1:5665024/1‑100 (MQ=255)          tataAACGCAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑‑AAAAAATGATGACATCGACGtttt                                                                        >  1:6580626/1‑100 (MQ=255)              aaCGCAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTa                                                                     >  1:6036987/1‑100 (MQ=255)                tgCAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAAt                                                                   >  1:4458685/2‑100 (MQ=255)                 gCAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGATAAAAAAAATGATGACATCGACGTTTTTTAAt                                                                   >  1:4408037/1‑100 (MQ=255)                  ctaGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGt                                                                 >  1:3942741/3‑100 (MQ=255)                  cAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGt                                                                 >  1:132317/1‑100 (MQ=255)                  ataGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGt                                                                 >  1:4527173/3‑100 (MQ=255)                   gcgCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTa                                                                >  1:1662406/3‑100 (MQ=255)                   aaGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTa                                                                >  1:3985209/1‑100 (MQ=255)                    aGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTaa                                                               >  1:4683942/1‑100 (MQ=255)                      cTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTaaaa                                                             >  1:277663/1‑100 (MQ=255)                        gTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAaaata                                                           >  1:2009570/1‑100 (MQ=255)                        gTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAaaata                                                           >  1:2582196/1‑100 (MQ=255)                         atataccaaaTGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAaaataa                                                          >  1:1389693/8‑100 (MQ=255)                                 caTGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTg                                                  >  1:491050/2‑100 (MQ=255)                                                  gtacATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCtt                                 >  1:5965680/4‑100 (MQ=255)                                                  gtGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCtt                                 >  1:5965780/2‑100 (MQ=255)                                                       tgcccccTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACAt                            >  1:1384266/7‑100 (MQ=255)                                                        tGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACAtt                           >  1:4440461/1‑100 (MQ=255)                                                        tGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACAtt                           >  1:5470952/1‑100 (MQ=255)                                                         gATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTg                          >  1:5135938/1‑100 (MQ=255)                                                              tGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATaa                     >  1:2365209/1‑100 (MQ=255)                                                               gATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAg                    >  1:816443/1‑100 (MQ=255)                                                               gATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAg                    >  1:4810646/1‑100 (MQ=255)                                                               gATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAg                    >  1:5589258/1‑100 (MQ=255)                                                               gATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAg                    >  1:1469841/1‑100 (MQ=255)                                                                      gcttgTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGaaaa             >  1:1386988/4‑100 (MQ=255)                                                                          atggACTATGAT‑‑AAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATgaga        >  1:6559984/4‑100 (MQ=255)                                                                           gtGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATgaga        >  1:4713500/2‑100 (MQ=255)                                                                           gtGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATgaga        >  1:592052/2‑100 (MQ=255)                                                                           ctGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATgaga        >  1:1649721/2‑100 (MQ=255)                                                                            tGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGAt       >  1:4308770/1‑100 (MQ=255)                                                                            tGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGAt       >  1:1591921/1‑100 (MQ=255)                                                                            tGACTATGAT‑‑AAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGTTg      >  1:5751418/1‑100 (MQ=255)                                                                             gACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGATg      >  1:5877365/1‑100 (MQ=255)                                                                             gACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGATg      >  1:1804285/1‑100 (MQ=255)                                                                             gACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGATg      >  1:2337756/1‑100 (MQ=255)                                                                             gACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGATg      >  1:2879689/1‑100 (MQ=255)                                                                                 aTGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGAtcggaa  >  1:6572309/1‑95 (MQ=255)                                                                                 aTGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGATGACga  >  1:5380834/1‑100 (MQ=255)                                                                                      |                                                                                                AAACGATTTTATAAACGCAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGATAAAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGATGACGA  >  NC_007793/525530‑525710

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑