Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	320,653	G→A	A143T (GCA→ACA)	rclR →	DNA‑binding transcriptional activator RclR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	320,653	0	G	A	90.9%	18.1 / ‑3.1	11	A143T (GCA→ACA)	rclR	DNA‑binding transcriptional activator RclR
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (4/6);  total (5/6)
Fisher's exact test for biased strand distribution p-value = 4.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.20e-01

GTCCTGCTACCACAAAATTCAGCTCATCGCCTGAGTCATGTCGATAATGAATCGACCTGTATTGTCTGCGGCACTCTTCGGTTGCAACATTCGGCGCGTTATTTTTTAACGTCTTTGCCGGAAACGCTGTTTTTAGCACCGGTTAACCACAGCGTGGAATATAACTGGCTGAGGGAGGCGATCCCGTTTTTACAACAGGAATCCAGATCGGCAATGCCGGGAGTGGATGCACTGTGTAGCCAGATCTGCGCTACATTCTTTACCCTCGCGGTGCGTGAGTGGATTGCACAGGTTAATACTGAGAAAAACATTCTCAGTTTGCTTCTGCATCCACGTCTTGGTGCGGTAATACAGCAAATGCTGGAAATGCCAGGACACGCCTGGACCGTCGAATCGCTGGCCAGCATCGCTCACATGTCCCGGGCAAGTTTTGCCCAGCTTTTCCGTGATGTTTC  >  NC_000913/320425‑320879                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                   gTCCTGCTACCACAAAATTCAGCTCATCGCCTGAGTCATGTCGATAATGAATCGACCTGTATTGTCTGCGGCACTCTTCGGTTGCAACATTCGGCGCGTTATTTTTTAACGTCTTTGCCGGAAACGCTGTTTTTAGCACCGGTTAACCACAGCGTGGAATATAACTGGCTGAGGGAGGCGATCCCGTTTTTACAACAGGAATCCAGATCGGCAATGCCGGGAGTGGATACACTGTGTAGCCAGATCTgcgc                                                                                                                                                                                                              >  1:99648/1‑251 (MQ=255)      gCTACCACAAAATTCAGCTCATCGCCTGAGTCATGTCGATAATGAATCGACCTGTATTGTCTGCGGCACTCTTCGGTTGCAACATTCGGCGCGTTATTTTTTAACGTCTTTGCCGGAAACGCTGTTTTTAGCACCGGTTAACCACAGCGTGGAATATAACTGGCTGAGGGAGGCGATCCCGTTTTTACAACAGGAATCCAGATCGGCAATGCCGGGAGTGGATGCACTGTGTAGCCAGATCTGCGCTACAt                                                                                                                                                                                                         >  1:258008/1‑251 (MQ=255)                  ttCAGCTCATCGCCTGAGTCATGTCGATAATGAATCGACCTGTATTGTCTGCGGCACTCTTCGGTTGCAACATTCGGCGCGTTATTTTTTAACGTCTTTGCCGGAAACGCTGTTTTTAGCACCGGTTAACCACAGCGTGGAATATAACTGGCTGAGGGAGGCGATCCCGTTTTTACAACAGGAATCCAGATCGGCAATGCCGGGAGTGGATACACTGTGTAgn                                                                                                                                                                                                                         <  1:96843/223‑2 (MQ=255)                                                                                ggTTGCAACATTCGGCGCGTTATTTTTTAACGTCTTTGCCGGAAACGCTGTTTTTAGCACCGGTTAACCACAGCGTGGAATATAACTGGCTGAGGGAGGCGATCCCGTTTTTACAACAGGAATCCAGATCGGCAATGCCGGGAGTGGATACACGGTGTAGCCAGATCTGCGCTACATTCTTTACCCTCGCGGTGCGTGAGtn                                                                                                                                                                                <  1:206030/202‑2 (MQ=255)                                                                                                              cGTCTTTGCCGGAAACGCTGTTTTTAGCACCGGTTACCCACAGCGTGGAATATAACTGGCTGAGGGAGGCGATCCCGTTTTTACAACAGGAATCCAGATCGGCAATGCCGGGAGTGGATACACTGTGTAGCCAGATCTGCGCTACATTATTTACCCTCGCGGTGCGTGAGTGGATTGCACAGGTTAATACTGAGAAAAACATTCTCAGTTTGCTTCTGCATCCACGTCTTGGTGCGGTAATACAGCAAATg                                                                                                 >  1:253107/1‑251 (MQ=255)                                                                                                                      cnGGAACCGCTGTTTTTAGCACCGGTTAACCACAGCGTGGAATATAACTGGCTGAGGGAGGCGATCCCGTTTTTACAACAGGAATCCAGATCGGCAATGCCGGGAGTGGATACACTGTGTAGCCAGATCTGCGCTACATTCTTTACCCTCGCGGTGCGTGAGTGGATTGCACAGGTTAATACTGAGAAAAACATTCTCAGTTTGCTTCTGCATCCACGTCTTGGTGCGGTAATACAGCAAATGCTGGAAAt                                                                                         >  1:254063/1‑251 (MQ=255)                                                                                                                                                   ccACAGCCTGGAATATAACTGGCTGAGGGAGGCGATCCCGTTTTTACAACAGGAATCCAGATCGGCAATGCCGGGAGTGGATACACTGNNTAGcc                                                                                                                                                                                                                        >  2:8802/1‑95 (MQ=255)                                                                                                                                                                       ggCTGAGGGAGGCGATCCCGTTTTTACAACAGGAATCCAGATCGGCAATGCCGGGAGTGGATACACTGTGTAGCCAGATCTGCGCTACATTCTTTACCCTCGCGGTGCGTGAGTGGATTGCACAGGTTAATACTGAGAAAAACATTCTCAGTTTGCTTCTGCATCCACGTCTTGGTGCGGTAATAc                                                                                                         <  1:885/186‑1 (MQ=255)                                                                                                                                                                              ggaggCGATCCCGTTTTTACAACAGGAATCCAGATCGGCAATGCCGGGAGTGGATACTCTGTGTAGCCAGATCTGCGCTACATTCTTTACCCTCGCGGTGCGTGAGTGGATTGCACAGGTTAATACGGAGAAAAACATTCTCAGTTTGCTTCTGCATCCACGTCTTGGTGCGGTAATACAGCAAATGCTGGAAATGCCAGGACACGCCTGGACCGTCGAATCGCTGGCCAGCATCGCTCACATGTCCCggg                                 <  1:264169/251‑1 (MQ=255)                                                                                                                                                                                                      ggAATCCAAATCGGCAATGCCGGGAGTGGATACACTGTGTAGCCAGATCTGCGCTACATTCTTTCCCCTCGCGGTGCGTGAGTGGATTGCACAGGTTAATACTGAGAAAAACATTCTCAGTTTGCTTCTGCATCCACGTCTTGGTGCGGTAATACAGCAAATGCTGGAAATGCCAGGACACGCCTGGACCGTCGAATCGCTGGCCAGc                                                    <  1:108567/208‑1 (MQ=255)                                                                                                                                                                                                             aGATCGGCAATGCCGGGAGTGGATACACGGTGTAGCCAGATCTGCGCTACATTCTTTACCCTCGCGGTGCGTGAGTGGACTGCACAGGTTAATACTGAGAAAAACATTCTCAGTTTGCTTCTGCATCCACGTCTTGGTGCGGTAATACAGCAAATGCTGGAAATGCCAGGACACGCCTGGACCGTCGAATCGCTGGCCAGCATCGCTCACATGTCCCGGGCAAGTTTTGCCCAGCTTTTCCGTGATGTTTc  <  1:247227/251‑1 (MQ=255)                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                   GTCCTGCTACCACAAAATTCAGCTCATCGCCTGAGTCATGTCGATAATGAATCGACCTGTATTGTCTGCGGCACTCTTCGGTTGCAACATTCGGCGCGTTATTTTTTAACGTCTTTGCCGGAAACGCTGTTTTTAGCACCGGTTAACCACAGCGTGGAATATAACTGGCTGAGGGAGGCGATCCCGTTTTTACAACAGGAATCCAGATCGGCAATGCCGGGAGTGGATGCACTGTGTAGCCAGATCTGCGCTACATTCTTTACCCTCGCGGTGCGTGAGTGGATTGCACAGGTTAATACTGAGAAAAACATTCTCAGTTTGCTTCTGCATCCACGTCTTGGTGCGGTAATACAGCAAATGCTGGAAATGCCAGGACACGCCTGGACCGTCGAATCGCTGGCCAGCATCGCTCACATGTCCCGGGCAAGTTTTGCCCAGCTTTTCCGTGATGTTTC  >  NC_000913/320425‑320879

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑