Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,170,027	C→T	pseudogene (141/475 nt)	gatR ←	DNA‑binding transcriptional repressor GatR, N‑terminal fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,170,027	0	C	T	100.0%	35.2 / NA	14	pseudogene (141/475 nt)	gatR	DNA‑binding transcriptional repressor GatR, N‑terminal fragment
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (8/6);  total (8/6)

CGGCAATCACTTTATTAGCGGCTGTGACCATCGCACCGCTAATAGAATAACCTTCATTAAAGGTCGTAATACCATTAACCGCATCAATACCATCAGCACCGACAAACATTAAATCGGCATTAATATCCTGTAATGAACGCTCGGCAATGGAACCATGCATCGAGCGCGTTTTATGGCGGACCGTGCCACCACAGACGACCAGAGTAATGTCTTTATTTTCGGAAAGGGCAAACGCTGCCGGGAGACTGTTGGTAATCACCGTGATATTTTTGGCGGTCATTAATCCTTCGGCGATAAGCATTGTCGTACTTCCGCTGTCGAGAATAACGGTCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTC  >  NC_000913/2169839‑2170233                                                                                                                                                                                             |                                                                                                                                                                                                               cGGCAATCACTTTATTAGCGGCTGTGACCATCGCACCGCTAATAGAATAACCTTCATTAAATGTCGTAATACCATTAACCGCATCAATACCATCAGCACCGACAAACATTAAAGCGGCATTAATATCCTGTAATGAACGCTCGGCAATGGAACCATGCATCGAGCGCGTTTTATGGCGGACCGTGCCATCACAGACGACCAGAGTAATGTCTTTATTTTCGGAAAGGGCAAACGCTGCCGGGAGACTGTTg                                                                                                                                                  <  1:109387/251‑1 (MQ=255)    naaTCACTTTATTAGCGGCTGTGACCATCGCACCGCTAATAGAATAACCTTCATTAAAGGTCGTAATACCATTAACCGCATCAATACCATCAGCACCGACAAACATTAAATCGGCATTAATATCCTGTAATGAACGCTCGGCAATGGAACCATGCATCGAGCGCGTTTTATGGCGGACCGTGCCATCACAGACGACCAGAGTAATGTCTTTATTTTCGGAAAGGGCAAACGCTGCCGGGAGACTGTTGGt                                                                                                                                                >  1:100650/2‑250 (MQ=255)          cTTTATTAGCGGCTGTGACCATCGCACCGCTAATAGAATAACCTTCATTCAAGGTCGTCATACCCTTAACCGCATCAATACCATCAGCACCGACAAACATTAAATCGGCATTAATATCCTGTAATGAACGCTCGGCAATGGAACCATGCATCGAGCGCGTTTTATGGCGGACCGTGCCATCACAGACGACCAGAGTAATGTCTTTATTTTCGGAAAGGGCAAACGCTGCCGGGAGACTGTTGGTAATCAcc                                                                                                                                         >  1:160602/1‑251 (MQ=255)                        gtgACCATCGCACCGCTAATAGAATAACCTTCATTAAAGGTCGTAATACCATTAACCGCATCAATACCATCAGCACTGACAAACATTAAATCGGCATTAATATCCTGTAATGAACGCTCGGCAATGGAACCATGCATCGAGCGCGTTTTATGGCGGACCGTGCCATCACAGACGACCAGAGTAATGTCTTTATTTTCGGAAAGGGCAAACGCTGCCGGGAGACTGTTGGTAATCACCGTGATAtttttn                                                                                                                             <  1:101185/249‑2 (MQ=255)                                 ncACCGCTAATAGAATAACCTTCATTAAAGGTCGTAATACCATTAACCGCATCAATACCATCAGCACCGACAAACATTAAATCGGCATTAATATCCTGTAATGAACGCTCGGCAATGGAACCATGCATCGAGCGCGTTTTATGGCGGACCGTGCCATCACAGACGACCAGAGTAATGTCTTTATTTTCGGAAAGGGCAAACGCTGCCGGGAGACTGTTGGTAATCACCGTGATATTTTTGGCGGTCATTa                                                                                                                   >  1:14846/2‑250 (MQ=255)                                                                 cGTAATACCATTAACCGCATCAATACCATCAGCACCGACAAACATTAAATCGGCATTAATATCCTGTAATGAACGCTCGGCAATGGAACCATGCATCGAGCGCGTTTTATGGCGGACCGTGACATCACAGACGACCAGAGTAATGTCTTTATTTTCGGCAAGGGCAAACGCTGCCGGGAGACTGTTGGTAATCACCGTGATATTTTTGGCGGTCATTAATCCTTCGGCGATAAGCATTGTCGTACTTCCGc                                                                                  >  1:64965/1‑251 (MQ=255)                                                                                           cATCAGCACCGACAAACATTAAATCGGCATTAATATCCTGTAATGAACGCTCGGCAATGGAACCATGCATCGAGCGCGTTTTATGGCGGACCGTGCCATCACAGACGACCAGAGTAATGTCTTTATTTTCGGAAAGGGCAAACGCTGCCGGGAGACTGTTGGTAATCACCGTGATATTTTTGGCGGTCATTAATCCTTCGGCGATAAGCATTGTCGTACTTCCGCTGTCGAGAATAACGGTCTGATCTTAc                                                        <  1:78216/251‑1 (MQ=255)                                                                                                                                       naaCGCTCGGCAATGGAACCATGCATCGAGCGCGTTTTATGGCGGACCGTGCCATCACAGACGACCAGAGTAATGTCTTTATTTTCGGAAAGGGCAACCGCTGCCGGGAGACTGTTGGTAATCACCGTGATATTTTTGGCGGTCATTACTCCTTCGGCGATAAGCATTGCCGTACTTCCGCTGTCGAGAATAACGGTCTGATCTTACCCAGCAATAGTGGCCACGCGGCTAAGAGAGTAAACTCtcagta             >  1:20255/2‑249 (MQ=255)                                                                                                                                                 cAATGGAACCATGCATCGAGCGCGTTTTATGGCGGACCGTGCCATCACAGACGACCAGAGTAATGTCTTTATTTTCGGAAAGGGCAAACGCTGCCGGGAGACTGTTGGTAATCACCGTGATATTTTTGGCGGTCATTAATCCTTCGGCGATAAGCATTGTCGTACTTCCGCTGTCGAGAATAACGGTCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTc  >  1:91912/1‑251 (MQ=255)                                                                                                                                                                      nnnnnntANNNNNGACNGTGCCATCACAGACGACCAGAGTAATGTCTTTATTTTCGGAAAGGGCAAACGCTGCCGGGAGACTGTTGGTAATCACCGTGATATTTTTGGCGGTCATTAATCCTTCGGCGATAAGCATTGTCGTACTTCCGc                                                                                  <  2:100650/144‑1 (MQ=255)                                                                                                                                                                        gTTTTATGGCGGACCGTGCCATCACAGACGACCAGAGTAATGTCTTTATTTTCGGAAAGGGCAAACGCTGCCgg                                                                                                                                                            <  1:10585/74‑1 (MQ=255)                                                                                                                                                                        gTTTTATGGCGGACCGTGCCATCACAGACGACCAGAGTAATGTCTTTATTTTCGGAAAGGGCAAACGCTGCCgg                                                                                                                                                            >  2:10585/1‑74 (MQ=255)                                                                                                                                                                                gCGGACCGTGCCATGACAGACTACCAGAGTAATGGCTGTATTTTCGGAAAGGGCAAACGCTGCCGGGAGACTGTGGGGAAGCGCCGGGATATTTGTGCCGGGCAGGAATCCTTCGGGGATAAGCATTGTCGTACTTCCGCTGTCGAGAATAACgg                                                                   <  1:79826/155‑1 (MQ=255)                                                                                                                                                                                       gTGCCATCACAGACGACCAGAGTAATGTCTTTATTTTCGGACAGGGCAAACGCTGCCGGGAGAATGTTGGTCATCACCGTGATATTTTTGGCGGTCATTAATCCTTCGGCGATAAGCATTGTCGTACTTCCGCTGTCGAGAATAACGGTc                                                                 >  1:92560/1‑150 (MQ=255)                                                                                                                                                                                             |                                                                                                                                                                                                               CGGCAATCACTTTATTAGCGGCTGTGACCATCGCACCGCTAATAGAATAACCTTCATTAAAGGTCGTAATACCATTAACCGCATCAATACCATCAGCACCGACAAACATTAAATCGGCATTAATATCCTGTAATGAACGCTCGGCAATGGAACCATGCATCGAGCGCGTTTTATGGCGGACCGTGCCACCACAGACGACCAGAGTAATGTCTTTATTTTCGGAAAGGGCAAACGCTGCCGGGAGACTGTTGGTAATCACCGTGATATTTTTGGCGGTCATTAATCCTTCGGCGATAAGCATTGTCGTACTTCCGCTGTCGAGAATAACGGTCTGATCTTACCCAGCAATAGTGGACACGCGGCTAAGTGAGTAAACTCTCAGTCAGAGGTGACTC  >  NC_000913/2169839‑2170233

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑