Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	1,593,380	T→C	pseudogene (628/2027 nt)	SAUSA300_RS07860 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	1,593,380	0	T	C	100.0%	55.8 / NA	22	pseudogene (628/2027 nt)	SAUSA300_RS07860	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (6/16);  total (6/16)

TCTAACCTGGGCACACCATCATTAATGTTAACGCGTTTTCCTGGCATATCTTTGATGAATGGATCTTGTAACCATGTTAATAAATCGTTGGTACTATTAAAACTAATCATATTATCAAAGCGTGGTCTAGCAAATTTCTGCCAAGCAGCATAAGGAATCATTGCTGAGTCAGT  >  NC_007793/1593289‑1593461                                                                                            |                                                                                  tCTAACCTGGGCACACCATCATTAATGTTAACGCGTTTTCCTGGCATATCTTTGATGAATGGATCTTGTAACCATGTTAATAAATCGTTGGCACTATTaa                                                                           <  1:3979586/100‑1 (MQ=255)    aaCCTGGGCACACCATCATTAATGTTAACGCGTTTTCCTGGCATATCTTTGATGAATGGATCTTGTAACCATGTTAATAAATCGTTGGCACTATTAAAAc                                                                        >  1:1994760/1‑100 (MQ=255)                          tGTTATCGCGTTTTCCTGGCATATCTTGGATGAATGGATCTTGTAACCATGTTAATAAAGCGTTGGCACTATTAAAACTAATCATATTATCAAAGCGTgg                                                  <  1:6087247/100‑1 (MQ=255)                           gTTAACGCGTTTTCCTGGCATATCTTTGATGAATGGATCTTGTAACCATGTTAATAAATCGTTGGCACTATTAAAACTAATCATATTATCAAAGCGTGGt                                                 <  1:2044754/100‑1 (MQ=255)                             tcttccgatctCCTGGTATATCTTTGAGGAATGGATCTTGTAACCATGTTAATAAATCGTTGGCACTATTAAAACTAATCATATTATCAAAGCGTGGTCt                                               <  1:873244/90‑1 (MQ=255)                             tAACGCGTTTTCCTGGCATATCTTTGATGAATGGATCTTGTAACCATGTTAATAAATCGTTGGCACTATTAAAACTAATCATATTATCAAAGCGTGGTCt                                               <  1:1566030/100‑1 (MQ=255)                              aaCGCGTTTTCCTGGCATATCTTTGATGAATGGATCTTGTAACCATGTTAATAAATCGTTGGCACTATTAAAACTAATCATATTATCAAAGCGTGGTCTa                                              >  1:1878729/1‑100 (MQ=255)                                  cgTTTTCCTGGCATATCCTTGATGAATGGATCTTGTAACCATGTTAATAAATCGTTGGCACTATTAAAACTAATCATATTATCAAAGCGTGGTCTAGCaa                                          <  1:5836217/100‑1 (MQ=255)                                    tcttCCTGGTATATCTTTGATGAATGGATCTTGTAACCATGTTAATAAATCGTTGGCACTATTAAAACTAATCATATTATCAAAGCGTGGTCTAgggcta                                        <  1:6225621/98‑6 (MQ=255)                                        gcTGGCATATCTTTGATGAATGGATCTTGTAACCATGTTAATAAATCGTTGGCACTATTAAAACTAATGATATTATCAAAGCGTGGTCTAGCAAATTTCt                                    >  1:285480/2‑100 (MQ=255)                                               tatCTTTGATGAATGGATCTTGTAACCATGTTAATAAATCGTTGGCACTATTAAAACTAATCATATTATCAAAGCGTGGTCTAGCAAATTTCTGCCAagc                             <  1:3700980/100‑1 (MQ=255)                                               tatCTTTGATGAATGGATCTTGTAACCATGTTAATAAATCGTTGGCACTATTAAAACTAATCATATTATCAAAGCGTGGTCTAGCAAATTTCTGCCAagc                             <  1:87594/100‑1 (MQ=255)                                               tagcTTTGATGAATGGATCTTGTAACCATGTTAATAAATCGTTGGCACTATTAAAACTAATCATATTATCAAAGCGTGGTCTAGCAAATTTCTGCCAagc                             <  1:6553118/97‑1 (MQ=255)                                                    ttGATGAATGGATCTTGTAACCATGTTAATAAATCGTTGGCACTATTAAAACTAATCATATTATCAAAGCGTGGTCTAGCAAATTTCTGCCAAGCAGCAt                        <  1:246834/100‑1 (MQ=255)                                                    ttGATGAATGGATCTTGTAACCATGTTAATAAATCGTTGGCACTATTAAAACTAATCATATTATCAAAGCGTGGTCTAGCAAATTTCTGCCAAGCAGCAt                        <  1:6262533/100‑1 (MQ=255)                                                    ttGATGAATGGATCTTGTAACCATGTTAATAAATCGTTGGCACGATTAAAACTAATCATATTATCAAAGCGTGGTCTAGCAAATTTCTGCCAAGCAGCAt                        <  1:6506470/100‑1 (MQ=255)                                                         gaATGGATCTTGTAACCATGTTAATAAATCGTTGGCACTATTAAAACTAATCATATTATCAAAGCGTGGTCTAGCAAATTTCTGCCAAGCAGCATAAGGa                   <  1:6333498/100‑1 (MQ=255)                                                                   tGTAACCATGTTAATAAATCGTTGGCACTATTAAAGCTAATCATATTATCAAAGCGTGGTCTAGCAAATTTCTGCCAAGCAGCATAAGGAATCATTGCTg         >  1:1148834/1‑100 (MQ=255)                                                                   tGTAACCATGTTAATAAATCGTTGGCACTATTAAAACTAATCATATTATCAAAGCGTGGTCTAGCAAATTTCTGCCAAGCAGCATAAGGAATCATTGCTg         >  1:3163815/1‑100 (MQ=255)                                                                   tGTAACCATGTTAATAAATCGTTGGCACTACTAAAACTAATCATATTATCAAAGCGTGGTCTAGCAAATTTCTGCCAAGCAGCATAAGGAATCATGGCTg         >  1:2183796/1‑100 (MQ=255)                                                                       aCCATGTTAATAAATCGTTGGCACTATTAAAACTAATCATATTATCAAAGCGTGGTCTAGCAAATTTCTGCCAAGCAGCATAAGGAATCATTGCTGAGTc     <  1:6234554/100‑1 (MQ=255)                                                                          aTGTTAATAAATCGTTGGCACTATTAAAACTAATCATATTATCAAAGCGTGGTCTAGCAAATTTCTGCCAAGCAGCATAAGGAATCATTGCTGAGTCAGt  <  1:6118426/100‑1 (MQ=255)                                                                                            |                                                                                  TCTAACCTGGGCACACCATCATTAATGTTAACGCGTTTTCCTGGCATATCTTTGATGAATGGATCTTGTAACCATGTTAATAAATCGTTGGTACTATTAAAACTAATCATATTATCAAAGCGTGGTCTAGCAAATTTCTGCCAAGCAGCATAAGGAATCATTGCTGAGTCAGT  >  NC_007793/1593289‑1593461

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑