Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	171,746	T→C	12.1%	V51V (GTT→GTC)	clcA →	H(+)/Cl(‑) exchange transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	171,746	0	T	C	12.1%	86.1 / 4.7	33	V51V (GTT→GTC)	clcA	H(+)/Cl(‑) exchange transporter
Reads supporting (aligned to +/- strand):  ref base T (14/15);  new base C (2/2);  total (16/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.64e-01

TTACGCTTTGCAAAGGATTTTCATGGAACGTGCGAGTAAAATGCCGTCATCTTATTTGTATGACCAATAAGTGATCATTGGATGAAAACTGATACTCCCTCTTTAGAAACACCGCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑GGCGCTGGTACATACTGCTGATAATTATCCGCTTCTGTTAACCGTCGCTTTTCTCTGTTCGGCGGTGCTGGCGATGTTTGGCTACTTTTTGGTGCGCAAATACGCGCCGGAAGCAGGTGGTTCGGGGATCCCGGAAATTGAAGGGGCGCTGGAAGATCAACGTCCCGTTCGCTGGTGGCGTGTATTGCCGGTGAAGTTCTTTGGCGGGCTGGGGACACTCG  >  CP009273/171513‑172011                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                                           aagacagttGAAAAGGATTTTAATGGAACGTGCGAGTAAAATGCCGTCATCTTATTTGTTTGCCCAATAAGTGATCATTGGATGAAAACTGATACTCCCTCTTTAGAAACACCGCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTAt                                                                                                                                                                                                                                   <  2:6371/268‑1 (MQ=255)                   tttCATGGAACGTGCGAGTAAAATGCCGTCATCTTATTTGTATGACCAATAAGTGATCATTGGATGAAAACTGATACTCCCTCTTTAGAAACACCGCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAAc                                                                                                                                                                                                                                       >  1:6371/1‑253 (MQ=255)                                    gTAAAATGCCGTTATTTTATTTGTATGACCAATAAGTGATCATTGGATGAAAACTGATACTCCCTCTTTAGAAACACCGCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑GGCGCTGGTACATACTGCTGATAATTATCCGc                                                                                                                                                                                               <  1:532248/275‑1 (MQ=255)                                                           tATGACCAATAAGTGATCATTGGATGAAAACTGATACTCCCTCTTTAGAAACACCGCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTg                                                                                                                                                                                                                                                 >  1:157835/1‑203 (MQ=255)                                                           tATGACCAATAAGTGATCATTGGATGAAAACTGATAATCCCTCTTTAGAAACACCGCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTATCCATTTTGTTTATGGCGGCATTCGTCGGCACGCTTGTTGGGCTGGCAGCGTGTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGT‑GGCGCTGTTAAATACTGCTGATAATTATCCACTTCTGTTAACAGTCGCtttt                                                                                                                                                                           >  1:308958/1‑272 (MQ=255)                                                               aCCAATAAGTGATCATTGGATGAAAACTGATACTCCCTCTTTAGAAACACCGCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGa                                                                                                                                                                                                                                             <  2:157834/203‑1 (MQ=255)                                                                          aTCATTGGATGAAAACTGATACTCCCTCTTTAGAAACACCGCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGc                                                                                                                                                                                                                                                >  1:677546/1‑189 (MQ=255)                                                                              ttGGATGAAAACTGATACTCCCTCTTTAGAAACACCGCANGCCGCGCGNCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTAAGGG‑GGCGCTGGTACATACTGCTGATAATTATCCg                                                                                                                                                                                                <  1:541982/232‑1 (MQ=255)                                                                              ttGGATGAAAACTGATACTCCCTCTTTAGAAACACCGCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGaa                                                                                                                                                                                                                                            <  2:677540/189‑1 (MQ=255)                                                                                  aTGAAAACTGATCCTCCCTCTTTAGAANCACCGCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAATCCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGT‑GGCGCTGGTACATa                                                                                                                                                                                                                 <  1:601335/211‑1 (MQ=255)                                                                                            aTACTCCCTCTTTAGAAACACCGCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑Ggc                                                                                                                                                                                                                            >  2:53509/1‑190 (MQ=255)                                                                                                tCCCTCTTTAGAAACACCGCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑GGCGCTg                                                                                                                                                                                                                        <  1:53509/190‑1 (MQ=255)                                                                                                     ctTTAGAAACACCGCAGGTCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑Ggcg                                                                                                                                                                                                                           <  1:630399/182‑1 (MQ=255)                                                                                                      tttAGAAACACCGCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑GCCGCTGGTACATACTGCTGATAATTATCCGCTTCTGTTAACCGTCGCTTTTCTCTGTTCGGCGGTGCTGGCGATGTTTGGCTACTTTTTGTTTCGCa                                                                                                                             >  1:111970/1‑275 (MQ=255)                                                                                                              cacCGCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑GGCGCTGGTACATACTGCTGATAATTATCCGCTTCTGTTAACCGTCGCTTTTCTCTGTTCGGCGGTGCTGGCGATGTTTGGCTACTTTTTGGTGGGCAAATAcgcg                                                                                                                     >  1:340150/1‑275 (MQ=255)                                                                                                                ccGCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCa                                                                                                                                                                                                                                               >  2:664154/1‑152 (MQ=255)                                                                                                                  gCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGGGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGa                                                                                                                                                                                                                                             >  1:778012/1‑152 (MQ=255)                                                                                                                    aGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAAc                                                                                                                                                                                                                                           <  1:664160/152‑1 (MQ=255)                                                                                                                      gacgcgcgCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGTGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCa                                                                                                                                                                                                                                         <  2:778006/150‑1 (MQ=255)                                                                                                                         gccagccggggACGCCGACAACTGCTTCGCCAAATTCTTGGGCGCGATAAAACCCCGTTAGCCATGTTGTTTATGTCGGCAGTCTGCGGCACGGTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑GGCGCTGGTACATACTGCTGATAATTATCCGCTTCTGTTAACCGTCGCTTTTCTCTGTTCGGCGGTGCTGGCGATGTTTGGCTACTTTTTGGTGCGCAAATACGCGCCGGAAGCAg                                                                                                           <  2:279996/264‑1 (MQ=255)                                                                                                                                         gACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑GGCGCTGGTACATACTGCTGATAATTATCCGCTTCTGTTAACCGTCGCTTTTCTCTGTTCGGCGGTGCTGGCGATGTTTGGCTACTTTTTGGTGCGCAAATACGCGCCGGAAGCAGGTGGTTCggggctgtc                                                                                           >  1:279999/1‑269 (MQ=255)                                                                                                                                                                         taaaCCCCGTTAGCCATTTTGTTTATGGTGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑GGCGCTGGTACATActgct                                                                                                                                                                                                            <  1:294094/128‑1 (MQ=255)                                                                                                                                                                                cGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑GGCGCTGGTa                                                                                                                                                                                                                     >  1:447357/1‑113 (MQ=255)                                                                                                                                                                                    aGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGTGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑GGCGCTGGTACATa                                                                                                                                                                                                                 <  2:447354/113‑1 (MQ=255)                                                                                                                                                                                                tATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAAc                                                                                                                                                                                                                                       >  2:456365/1‑80 (MQ=255)                                                                                                                                                                                                    gcggcAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTAt                                                                                                                                                                                                                                   <  1:456368/80‑1 (MQ=255)                                                                                                                                                                                                                      atagttagacTGGCTGCGTTTGTGTGTGACCGAGGTGTCCTCTGTTTGCAGAACCAACGTTTGGGTGTTGGTTG‑AAACACTTCTGGTAAGTTTCGGATTTTGATAACCGTGTGTTTTGTTTGGTGGGCGGTGGTGGCGTTGTTTGGCTAATGTTTGGCGGGGAAATTCGCGACGGAAGAAGGTGGTTCGGGGATCGCGGAAATTGACGGGGCGATGGAAGATCAACGTCCCGTTCGCTGGTGGCGTGTATTGCGGGTGAAGTTCTTTGGCgggt              <  2:111970/265‑2 (MQ=255)                                                                                                                                                                                                                            gggCTGGCAGCGGTCGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑GGCGCTGGTACATa                                                                                                                                                                                                                 >  2:160201/1‑73 (MQ=255)                                                                                                                                                                                                                               cTGGCAGCGGTCGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATggg                                                                                                                                                                                                                                >  1:100529/1‑56 (MQ=255)                                                                                                                                                                                                                                tGGCAGCGGTCGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑GGCGCTGGTACATActgc                                                                                                                                                                                                             <  1:160202/73‑1 (MQ=255)                                                                                                                                                                                                                                 ggCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑GGCGCTGGTACATACTGCTGATAATTATCCGCTTCTGTTAACCGTCGCTTTTCTCTGTTCGGCGGTGCTGGCGATGTTTGGCTACTTTTTGGTGCGCCAATACGCGCAGGAAGCAGGTGGTTCGGGAATCCCGGAAATTGAAGGGGCGCTGGAAGATCAACGTCACGTTCGCTGGTGGCGTGTATTGCGGGGGAATGTCGTTGGAGTGCGGGGGacgttcg  >  2:55711/1‑270 (MQ=255)                                                                                                                                                                                                                                 ggCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑GGCGCTGGTACATACTGCTGATAATTATCCGCTTCTGTTAACCGTCGCTTTTCTCTGTTCGGCGGTGCTGGCGATGTTTGGCTACTTTTTGGTGCGCAAATACGCGCGGGAAGCAGGTGGTTCGGGGATCCCGGAAGTTGAATGGGCGCTGGAAGATCAACGTCCCGTTCGCTGGTGGCGGGTATTGCCGGTGGAGGTCTTTGGCGGGCTggggtcgcgcg  >  2:795604/1‑268 (MQ=255)                                                                                                                                                                                                                                   cAGCGGTCGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑Ggcg                                                                                                                                                                                                                           <  2:100529/56‑1 (MQ=255)                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                                           TTACGCTTTGCAAAGGATTTTCATGGAACGTGCGAGTAAAATGCCGTCATCTTATTTGTATGACCAATAAGTGATCATTGGATGAAAACTGATACTCCCTCTTTAGAAACACCGCAGGCCGCGCGCCTGCGACGCAGACAACTGATTCGCCAACTTCTTGAGCGCGATAAAACCCCGTTAGCCATTTTGTTTATGGCGGCAGTCGTCGGCACGCTTGTTGGGCTGGCAGCGGTTGCTTTTGACAAAGGTGTCGCCTGGTTGCAGAACCAACGTATGGG‑GGCGCTGGTACATACTGCTGATAATTATCCGCTTCTGTTAACCGTCGCTTTTCTCTGTTCGGCGGTGCTGGCGATGTTTGGCTACTTTTTGGTGCGCAAATACGCGCCGGAAGCAGGTGGTTCGGGGATCCCGGAAATTGAAGGGGCGCTGGAAGATCAACGTCCCGTTCGCTGGTGGCGTGTATTGCCGGTGAAGTTCTTTGGCGGGCTGGGGACACTCG  >  CP009273/171513‑172011

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑