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	.	100.0%	161.4 / NA	42	pseudogene (70/157 nt)	SAUSA300_RS02505	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (42/0);  total (42/0)

TATAAACGCAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGATAAAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGATGACGAG  >  NC_007793/525539‑525711                                                                             |                                                                                                 tataAACGCAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGttt                                                                          >  1:789541/1‑100 (MQ=255) tataAACGCAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGttt                                                                          >  1:1473836/1‑100 (MQ=255)  ataAACGCAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGtttt                                                                         >  1:4024105/1‑100 (MQ=255)     aaCGCAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTa                                                                      >  1:3347325/1‑100 (MQ=255)      aCGCAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTaa                                                                     >  1:1280856/1‑100 (MQ=255)       cGCAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑‑AAAAAATGATGACATCGACGTTTTTTAATg                                                                   >  1:583552/1‑100 (MQ=255)         cAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGt                                                                  >  1:5673120/1‑100 (MQ=255)         cAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGt                                                                  >  1:3264891/1‑100 (MQ=255)            gCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTaaa                                                               >  1:5581260/1‑100 (MQ=255)             cTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTaaaa                                                              >  1:2789012/1‑100 (MQ=255)               gTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑‑AAAAAATGATGACATCGACGTTTTTTAATGTAaaataa                                                           >  1:2127093/1‑100 (MQ=255)               gTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑‑AAAAAATGATGACATCGACGTTTTTTAATGTAaaataa                                                           >  1:3478856/1‑100 (MQ=255)               gTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTACGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAaaata                                                            >  1:4603651/1‑100 (MQ=255)                          tGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGaa                                                 >  1:4346712/1‑100 (MQ=255)                           ggTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGaaa                                                >  1:1752012/1‑100 (MQ=255)                                        tttGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGGCATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCt                                   >  1:3687596/1‑100 (MQ=255)                                         ttGCATTGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCtt                                  >  1:1328165/1‑100 (MQ=255)                                           gCATTGATACTGATAAAATGATGTTGACTATGAT‑‑AAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAAc                               >  1:1476803/1‑100 (MQ=255)                                               tGATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACAtt                            >  1:5649097/1‑100 (MQ=255)                                                gATACTGATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTg                           >  1:4587882/1‑100 (MQ=255)                                                      gATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAg                     >  1:3083645/1‑100 (MQ=255)                                                      gATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAg                     >  1:536151/1‑100 (MQ=255)                                                      gATAAAATGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAg                     >  1:3810674/1‑100 (MQ=255)                                                      gATAAAATGATGTTGACTATGAT‑‑AAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGa                    >  1:5745518/1‑100 (MQ=255)                                                         aaagTGATGTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATg                  >  1:4088276/1‑100 (MQ=255)                                                           aaTGATGTTGACTATGAT‑AAGAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGaa                >  1:4596338/1‑100 (MQ=255)                                                            atgatgTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGaaa               >  1:3531159/1‑100 (MQ=255)                                                             tgatgTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGaaaa              >  1:4840146/1‑100 (MQ=255)                                                              gatgTTGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAAt             >  1:3732142/1‑100 (MQ=255)                                                                atctGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATga           >  1:4758841/4‑100 (MQ=255)                                                                  ctGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATgaga         >  1:5339484/2‑100 (MQ=255)                                                                   tGACTATGAT‑AACAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTACTAAATACCTTAACATTGAATAAGATGAAAATgagac        >  1:5019210/1‑99 (MQ=255)                                                                   tGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGAt        >  1:4250387/1‑100 (MQ=255)                                                                   tGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGAt        >  1:1300757/1‑100 (MQ=255)                                                                   tGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGAt        >  1:151152/1‑100 (MQ=255)                                                                   tGACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGAt        >  1:1208164/1‑100 (MQ=255)                                                                    gACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGGTg       >  1:4337458/1‑100 (MQ=255)                                                                    gACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGATg       >  1:5248429/1‑100 (MQ=255)                                                                    gACTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGATg       >  1:1623350/1‑100 (MQ=255)                                                                     aCTATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGATGa      >  1:658262/1‑100 (MQ=255)                                                                      atATGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGATGAc     >  1:3483093/2‑100 (MQ=255)                                                                        aTGAT‑AAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATG‑AAATGAGAtcggaag  >  1:1441987/1‑94 (MQ=255)                                                                             |                                                                                                 TATAAACGCAAGCTGTAATTTTAAATGGTAAGTTATCATTTTGCATTGATACTGATAAAATGATGTTGACTATGATAAAAAAAATGATGACATCGACGTTTTTTAATGTAAAATAAATACATTGAAAGTAATAAATACCTTAACATTGAATAAGATGAAAATGAGATGACGAG  >  NC_007793/525539‑525711

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑