Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,168,350	Δ1 bp	coding (483/633 nt)	ycfQ ←	repressor for bhsA(ycfR)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,168,348	0	G	.	100.0%	161.4 / NA	39	coding (485/633 nt)	ycfQ	repressor for bhsA(ycfR)
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (24/15);  total (24/15)

TTCGGGCCATAAACGCAAAGTCGTTCCGGCAATCTGCATCAGTTTTTCCAGCGATGCACCTTCGCGTGCGCTGATCGACATCCCCTGAATAATACAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGCGGGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCTGAATCTGGGGAGAGGGTGGTGCAGTTGTTGATC  >  NC_000913/1168212‑1168476                                                                                                                                         |                                                                                                                                 ttCGGGCCATAAACGCAAAGTCGTTCCGGCAATCTGCATCAGTTTTTCC‑GCGATGCACCTTCGCGTGCGCTGATCGACATCCCCTGAATAATACAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGCggat                                                                                                                               >  2:1194846/1‑137 (MQ=255)                      cGTTCCGGCAATCTGCATCAGTTTTTCCAGCGATGCACCTTCGCGTGCGCTGATCGACATCCCCTGAATAATACAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGtt                                                                                                          <  1:364697/139‑1 (MQ=255)                        ttCCGGCAATCTGCATCAGTTTTTCCAGCGATGCACCTTCGCGTGCGCTGATCGACATCCCCTGAATAATACAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGa                                                                                                        >  1:550735/1‑139 (MQ=255)                                                                 cgTGCGCTGATCGACATCCCCTGAATAATACAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCg                                                               >  1:1117616/1‑139 (MQ=255)                                                                   tGCGCTGATCGACATCCCCTGAATAATACAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTg                                                                                   <  1:1189772/117‑1 (MQ=255)                                                                   tGCGCTGATCGACATCCCCTGAATAATACAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTg                                                                                   >  2:1189772/1‑117 (MQ=255)                                                                   tGCGCTGATCGACATCCCCTGAATAATACAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTg                                                             >  1:378736/1‑139 (MQ=255)                                                                          aTCGACATCCCCTGAATAATACAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGtt                                                                                                          >  2:42759/1‑87 (MQ=255)                                                                          aTCGACATCCCCTGAATAATACAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGtt                                                                                                          <  1:42759/87‑1 (MQ=255)                                                                          aTCGACATCCCCTGAATAATACAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCaa                                                      >  2:1147645/1‑139 (MQ=255)                                                                                  ccccTGAATAATACAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGctc                                                                              <  2:879205/107‑1 (MQ=255)                                                                                  ccccTGAATAATACAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGctc                                                                              >  1:879205/1‑107 (MQ=255)                                                                                    ccTGAATAATACAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCg                                            >  1:635681/1‑139 (MQ=255)                                                                                      tGAATAATACAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGat                                          <  1:1194846/139‑1 (MQ=255)                                                                                            ataCAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTcc                                    >  1:977375/1‑139 (MQ=255)                                                                                             taCAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCg                                                                      <  1:281374/104‑1 (MQ=255)                                                                                             taCAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCg                                                                      >  2:281374/1‑104 (MQ=255)                                                                                             taCAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCt                                   >  1:1060452/1‑139 (MQ=255)                                                                                             taCAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCt                                   >  1:335763/1‑139 (MQ=255)                                                                                             taCAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCt                                   >  1:1163707/1‑139 (MQ=255)                                                                                                  ttAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCTGAATc                              >  2:294704/1‑139 (MQ=255)                                                                                                  ttAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCTGAATc                              >  2:1216221/1‑139 (MQ=255)                                                                                                  ttAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGA‑TTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCTGAATCt                             >  2:867115/1‑139 (MQ=255)                                                                                                       gAATTCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCTGAATCTgggg                         >  2:807204/1‑139 (MQ=255)                                                                                                          ttCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTg                                                                                                         >  1:353798/1‑56 (MQ=255)                                                                                                          ttCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTg                                                                                                         <  2:353798/56‑1 (MQ=255)                                                                                                          ttCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGt                                                              >  1:803421/1‑99 (MQ=255)                                                                                                          ttCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGt                                                              <  2:803421/99‑1 (MQ=255)                                                                                                          ttCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCTGAATCTGGGgaga                      <  1:807204/139‑1 (MQ=255)                                                                                                          ttCTGCCAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCTGAATCTGGGgaga                      >  1:805700/1‑139 (MQ=255)                                                                                                               ccAGATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCTGAATCTGGGGAGAGggtg                 >  1:358903/1‑139 (MQ=255)                                                                                                                  ggtgtgtgATGTTACGGTGGGGC‑GGAGGTCTCCGCGCGCTTGTCGTCGACATAAGATCTTCTCCAACGTGCGCTCTTGCCTCGGATGCCGTGATTTCAACGTATTGGCGATATCTCCTGATTCTGGGGAGAGGgttgtg              <  1:592918/137‑1 (MQ=255)                                                                                                                  gATGTGTCACGTCACAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCTGAATCTGGGGAGAGGgtggtg              <  2:358903/139‑1 (MQ=255)                                                                                                                       gtcacgtcacAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCTGAATCTggg                          >  2:650824/1‑122 (MQ=255)                                                                                                                       gtcacgtcacAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCTGAATCTggg                          <  1:650824/122‑1 (MQ=255)                                                                                                                          acgtcacAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCTGAATCTGGGGAGAGGGTGGTGCAgttgtt      <  2:378736/139‑1 (MQ=255)                                                                                                                           cgtcacAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCa                                                                                        <  2:244866/56‑1 (MQ=255)                                                                                                                           cgtcacAGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCa                                                                                        >  1:244866/1‑56 (MQ=255)                                                                                                                              cacaGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCTGAATCTGGGGAGAGGGTGGTGCAGTTGTTGATc  <  2:550735/139‑1 (MQ=255)                                                                                                                                caGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATaaaaa                                                                                                <  2:1212847/43‑1 (MQ=255)                                                                                                                                caGTGGGGC‑GGATTTCCCCGCGCGCTTGTCGTTGACATaaaaa                                                                                                >  1:1212847/1‑43 (MQ=255)                                                                                                                                         |                                                                                                                                 TTCGGGCCATAAACGCAAAGTCGTTCCGGCAATCTGCATCAGTTTTTCCAGCGATGCACCTTCGCGTGCGCTGATCGACATCCCCTGAATAATACAATTAAGGAATTCTGCCAGATGTGTCACGTCACAGTGGGGCGGGATTTCCCCGCGCGCTTGTCGTTGACATAAAAACTGCTGCAAAGTGCGCTCTTGCATCGCATGGCGTGATTTCAACGTATTGGCGATATCTCCTGAATCTGGGGAGAGGGTGGTGCAGTTGTTGATC  >  NC_000913/1168212‑1168476

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑