Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,682,694	A→T	Q179L (CAA→CTA)	rstA →	DNA‑binding transcriptional regulator RstA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,682,694	0	A	T	92.9%	72.6 / ‑1.8	28	Q179L (CAA→CTA)	rstA	DNA‑binding transcriptional regulator RstA
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base T (10/16);  total (11/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.21e-01

GACTATATTCTCAAAACGACGCCCCCTGCTGTTTTGCTAGCGCGTTTACGTTTGCATTTGCGTCAGAATGAGCAAGCCACACTGACCAAAGGTCTTCAGGAAACGTCTCTGACTCCCTACAAAGCCCTGCATTTCGGCACGTTGACCATCGATCCCATCAACCGCGTAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCAAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGACGTGGCTATTTCGCGGTTAAGAAAAAAACTGCTCGATAACGCCGCAGAACCTTATCGCATTAAAACTGTGCGTAACAAAGGCTATCTTTTTGCGCCTCATGCATGGGAATAAGCGATGAAAAAACTGTTTATCCAGTTTTACCTGTTATTGTTTGTCTGCTTCCTT  >  NC_000913/1682447‑1682932                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                               gACTATATTCTCAAAACGACGCCCCCTGCTGTTTTGCTAGCGCGTTTACGTTTGCATTTGCGTCAGAATGAGCAAGCCACACTGACCAAAGGTCTTCAGGAAACGTCTCTGACTCCCTACAAAGCCCTGCATTTCGGCACGTTGACCATCGATCCCATCAACCGCGTAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCTAAt                                                                                                                                                                                                                                             <  1:71818/251‑1 (MQ=255)                    cgCCCCCTGCTGTTTTGCTAGCGCGTTTACGTTTGCATTTGCGTCAGAATGAGCAAGCCACACTGACCAAAGGTCTTCAGGAAACGTCTCTGACTCCCTACAAAGCCCTGCATTTCGGCACGTTGACCATCGATCCCATCAACCGCGTAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCTAATCATGGACCGCGATGCATTg                                                                                                                                                                                                                          >  1:122355/1‑251 (MQ=255)                    cgCCCCCTGCTGTTTTGCTAGCGCGTTTACGTTTGCATTTGCGTCAGAATGAGCAAGCCACACTGACCAAAGGTCTTCAGGAAACGTCTCTGACTCCCTACAAAGCCCTGCATTTCGGCACGTTGACCATCGATCCCATCAACCGCGGAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGCATTATTGTGGGAATTAGCTACCCATGCCGGGCTAATCATGGACCGCGATGCATTg                                                                                                                                                                                                                          >  2:134721/1‑251 (MQ=255)                                      tAGCGCGTTTACGTTTGCATTTGCGTCAGAATGAGCAAGCCACACTGACCAAAGGTCTTCAGGAAACGTCTCTGACTCCCTACAAAGCCCTGCATTTCGGCACGTTGACCATCGATCCCATCAACCGCGTAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCTAATCATGTACCGCGTTGCATTGCTGCAAAATTTACgcggc                                                                                                                                                                                                        >  2:64308/1‑251 (MQ=255)                                                  gTTTGCATTTGCGTCAGAATGAGCAAGCCACACTGACCAAAGGTCTTCAGGAAACGTCTCTGACTCCCTACAAAGCCCTGCATTTCGGCACGTTGACCATCGATCCCATCAACCGCGTAGTCACCCAGGCTAACACTGAAATCTCGCTCTCGACAGCTGCTTTCGAATTATTGAGGGAATTAGCTACCCATGCCGGGCTAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGAc                                                                                                                                                                                            >  1:189554/1‑251 (MQ=255)                                                   tttGCATTTGCGTCAGAATGAGCAAGCCACACTGACCAAAGGTCTTCAGGAAACGTCTCTGACTCCCTACAAAGCCCTGCATTTCGGCACGTTGACCATCGATCCCATCAACCGCGTAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCTAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACg                                                                                                                                                                                           >  1:328624/1‑251 (MQ=255)                                                                cAGAATGAGCAAGCCACACTGACCAAAGGTCTTCAGGAAACGTCTCTGACTCCCTACAAAGCCCTGCATTTCGGCACGTTGACCATCGATCCCATCAACCGCGTAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCAAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGt                                                                                                                                                                                >  1:15641/1‑249 (MQ=255)                                                                                 cctgtccAAAGGTCTTCAGGAAACGTCTCTGACTCCCTACTAAGCCCTGCATTTCTGCACGTTTGCCTTCTAGCCCATCAACCTCGTAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGAAGTATTGTGTGAATTAGCTACCCATGCCGGTCTAATCATGGACCGCGATGCATGGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGACGTGGCTAttt                                                                                                                                                             <  1:46768/246‑1 (MQ=255)                                                                                            gTCTTCAGGAAACGTCTCTGACTCCCTACAAAGCCCTGCATTTCGGCACGTTGACCATCGATCCCATCAACCGCGTAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCTAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGACGTGGCTATTTCGCGATTa                                                                                                                                                     >  1:224154/1‑248 (MQ=255)                                                                                                     aaaCGTCTCTGACTCCCTACAAAGCCCTGCATTTCGGCACGTTGACCATCGATCCCATCAACCGCGTAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCTAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGACGTGGCTATTTCGCGGTTAAGAAAAAAACTg                                                                                                                                         <  1:269801/251‑1 (MQ=255)                                                                                                         gTCTCTGACTCCCTACAAAGCCCTGCATTTCGGCACGTTGACCATCGATCCCATCAACCGCGTAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCTAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGACGTGGCTATTTCGCGGTTAAGAAAAAAACTGCTCg                                                                                                                                     >  1:106877/1‑251 (MQ=255)                                                                                                               gACTCCCTACAAAGCCCTTCTTTTCTGTACGTTGACCCTCGATCCCATCAACCGACTAGTCACCCTGGCTAACACTTAAAACGCGCTCTCGACAGCTGATTTTGAATTATTGTTGGAATTAGCTACCCATGCCGGGCTAATCATGTACCGCTATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGTATCGTAGCGTGGACGTGGTTATCTCGCGGTTAATAAAAAAACTGCTCGATAAc                                                                                                                                <  1:31510/250‑1 (MQ=255)                                                                                                               gACTCCCTACAAAGCCCTGCCTTTCGGCACGTTGACCATCGATCCCATCAACCGCGTAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCTAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGCCTGGCTCGTAGCGTGGACGTGGCTATTTCGCGGTTAAGAAAAAAACAGCTCGATAAcg                                                                                                                               >  2:294559/1‑251 (MQ=255)                                                                                                               gACTCCCTACAAAGCCCTGCATTTCGGCACGTTGACCATCGATCCCATCAACCGCGTAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCTAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGACGTGGCTATTTCGCGGTTAAGAAAAAAACTGCTCGATAAcg                                                                                                                               <  1:336097/251‑1 (MQ=255)                                                                                                               gACTCCCTACAAAGCCCTGCATTTCGGCACGTTGACCATCGATCCCATCAACCGCGTAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCTAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGACGTGGCTATTTCGCGGTTAAGAAAAAAACTGCTCGATAAcg                                                                                                                               <  1:329635/251‑1 (MQ=255)                                                                                                               gACTCCCTACAAAGCCCTGCATTTCGGCACGGTGACCATCGATCCCATCACCCGCGTAGTCACCCTGGCTAACACTAAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCTAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGAATGGATCGTAGCGTGGACGTGGCTATTTCGCGGTTAAGAAAAAAACTGCTCGATa                                                                                                                                  <  2:216559/248‑1 (MQ=255)                                                                                                                   cccTACAAAGCCCTGCATTTCGGCACGTTGACCATCGATCCCATCAACCGCGTAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCTAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGACGTGGCTATTTCGCGGTTAAGAAAAAAACTGCTCGATAAcgccg                                                                                                                            <  1:64308/250‑1 (MQ=255)                                                                                                                                  cATTTCGGCACGTTGACCATCGATCCCATCAACCGCGTAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCTAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGACGTGGCTATTTCGCGGTTAAGAAAAAAACTGCTCGATAACGCCGCAGAACCTTATCGCAt                                                                                                            <  1:313776/251‑1 (MQ=255)                                                                                                                                                      cgttcccagaaaCCGCGTAGTCACCCAGGCTAATACTGAAATCTCGCTATCGACAGCTGATTGCGAATTATTGTGGTAATTTGCTACCCATGCCGGGCTAATCATGTACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGAAGGACTGGATCGTAGCTTGGACGTGGCTATTTTGCGGTTAAGAAAAAATCTGCTCGATAACGCCGCAGAACCTTATCGCATTAAAACTGTGTGTAACAAAg                                                                                        <  2:252376/241‑1 (MQ=255)                                                                                                                                                       aaTCCAATCAACCGCGTAGTAAACCTGGCAAACACTGTAATCCCGATCCAGACAGCACATTTCGAATTATCGGGGGAATTAGCTACCCCTGCCGGGCTAATCATGACCCGAGATGCATTGCTGAAACCATTACGCGGAGTCCGTAATGACGGACTGGTCCCTAGCGTGGACGTGGCTATTTCGCGGTTAAGAACAACAATGCACGATAACGCAGCAGAACCTTATCGCATTAGAACtacgcgcaaaaaa                                                                                         >  2:332484/2‑237 (MQ=255)                                                                                                                                                           ccATCAACAGCGTATTCACCCTGGCTAACTCTGAATTCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCTAATCATTGACCGCGATGCATTGCTGAAAAATTTACGTGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGACGTGGCTATTTCGCGGTTAAGAAAAAAACTGCTCGAGAACGCCGCAGAACCTTATCGCATTAAAACTGTGCGTAACAAAGGCTag                                                                                   <  2:232969/251‑2 (MQ=255)                                                                                                                                                                             tctggtcTAACACTGAAATCTCTCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCTAATCATTGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGCCGTGGCTATTTCGCGGTTAAGAAAAAAACTGCTCGATAACGCCGCAGAACCTTATCGCATTAAAACTGTGCGTAACAAAGGCTATCTTTTTGCGCCTcatg                                                                   <  2:143069/243‑1 (MQ=255)                                                                                                                                                                                     aaCACTGAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCTAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGACGTGGCTATTTCGCGGTTAAGAAAAAAACTGCTCGATAACGCCGCAGAACCTTATCGCATTAAAACTGTGCGTAACAAAGGCTATCTTTTTGCGCCTCATGCATGGGAATa                                                         <  1:134721/251‑1 (MQ=255)                                                                                                                                                                                                              cgtaTTTCGAATTATGGTGGGAATTAGCTACTCATGCCGGGCAAATCATGTACCGTGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGACGTGGCTATTT‑GCGGTTAAGAAAAAAACTGCTCGATAACGCCGCAGAACCTTATCGCATTAAAACTGTGCGTAACAAAGGCTATCTTTTTGCGCCTCATGCATGGGACTAAGCGATGAAAAAACTGTTTATCCAGt                               <  2:15641/248‑1 (MQ=255)                                                                                                                                                                                                                                      tAGCTACCCATGCCGGGCTAATCATGGACCGCGATGTATTGCTGAAAAATTTACGCGGCGTCAGTTATGGCGGACTGGATCGTAGCGTGGACGGGTCTATTTCGCGGTTAAGAAAAAAACTGCTCGATAACGCCGCAGAACCTTATCGCATTAAAACTGTGCGTAACAAAGGCTATCTTTTTGCGTCTCATGCATGGTAATAAGCGATGAAAAGACTGTTTATCCAGTTTTACCTGGGATTGTTTGTCTg         <  2:326207/250‑1 (MQ=255)                                                                                                                                                                                                                                           aCCCATGCCGGGCTAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGACGTGGCTATTTCGCGGTTAAGAAAAAAACTGCTCGATAACGCCGCAGAACCTTATCGCATTAAAACTGTGCGTAACAAAGGCTATCTTTTTGCGCCTCATGCATGGGAATAAGCGATGAAAAAACTGTTTATCCAGTTTTACCTGTTATTGTTTGTCTGCTTcc    <  1:319425/250‑1 (MQ=255)                                                                                                                                                                                                                                            cccATGCCGGGCTAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGACGTGGCTATTTCGCGGTTAAGAAAAAAACTGCTCGATAACGCCGCAGAACCTTATCGCATTAAAACTGTGCGTAACAAAGGCTATCTTTTTTCGCCTCATGCATGGGAATAATCGATGAAAAAACTGTTTATCCAGTTTTACCTGTTATTGTTTGTCGGCTTCCtt  <  2:106877/251‑1 (MQ=255)                                                                                                                                                                                                                                            cccATGCCGGGCTAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGACGTGGCTATTTCGCGGTTAAGAAAAAAACTGCTCGATAACGCCGCAGAACCTTATCGCATTAAAACTGTGCGTAACAAAGGCTATCTTTTTGCGCCTCATGCATGGGAATAAGCGATGAAAAAACTGTTTATCCAGTTTTACCTGTTATTGTTTTTCTGCTTCCtt  >  2:287807/1‑251 (MQ=255)                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                               GACTATATTCTCAAAACGACGCCCCCTGCTGTTTTGCTAGCGCGTTTACGTTTGCATTTGCGTCAGAATGAGCAAGCCACACTGACCAAAGGTCTTCAGGAAACGTCTCTGACTCCCTACAAAGCCCTGCATTTCGGCACGTTGACCATCGATCCCATCAACCGCGTAGTCACCCTGGCTAACACTGAAATCTCGCTCTCGACAGCTGATTTCGAATTATTGTGGGAATTAGCTACCCATGCCGGGCAAATCATGGACCGCGATGCATTGCTGAAAAATTTACGCGGCGTCAGTTATGACGGACTGGATCGTAGCGTGGACGTGGCTATTTCGCGGTTAAGAAAAAAACTGCTCGATAACGCCGCAGAACCTTATCGCATTAAAACTGTGCGTAACAAAGGCTATCTTTTTGCGCCTCATGCATGGGAATAAGCGATGAAAAAACTGTTTATCCAGTTTTACCTGTTATTGTTTGTCTGCTTCCTT  >  NC_000913/1682447‑1682932

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑