Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	1,649,631	G→T	14.4%	I100I (ATC→ATA)	ynfA ←	UPF0060 family inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	1,649,631	0	G	T	14.4%	65.4 / 2.2	28	I100I (ATC→ATA)	ynfA	UPF0060 family inner membrane protein
Reads supporting (aligned to +/- strand):  ref base G (10/14);  new base T (2/2);  total (12/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.37e-01

CTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAA‑AAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACGCCACCATAAGCCGCGTAAACACGCCCACTCGCCGCTGGATGCAACGTTAACAACCAGACAAACAGCGCCAGTGAAATCCCCGCCGGAAGCAACAGCCAGATACTGGCGTTTCGTTTTAACCACAACCAGGGCAGAAAGCATCCAATAATTTCACAC  >  CP009273/1649417‑1649892                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                                      cTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAA‑AAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGATGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGAACAACATGCCGCAAAGCGAACTCAACGCAACCGTCCAGTCATAAAGAGTCAGTTTCAc                                                                                                                                                                                                            >  1:10328/1‑274 (MQ=255)                                    caaagcATAAAAGTAAATAGA‑CGAAAAGAAGACGGAGTGAGCACGAAGATAGGCTGTCATATTGGCTGTTAATTGTTGACAAAAGAATAAATAGGATACTTTTGGTCAGCTGACACTTCCTCTTATCTTATGGATAAAATGGATTTATGTGCACACGCACGCCCCCAGCCCCCAACAATGTCCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGCGTCAGTTTCACGCCATCAACAACGCGCAGCCACATCAACGCCGTGCa                                                                                                                                                                        <  2:10328/270‑1 (MQ=255)                                                        agcGAAAA‑AGGCCGCAAGGATAAAAAAAAAAGGCTTGTATTTGCGCAGTTATTGGTTGACAAAAGATGAAATAGAATACCCTTTGTCAGCTGACACTTCCTATTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCCCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAAAGCACCCGGCCAGTCATAAAGAGTCAGTTTCACGCCAGCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACGCCACCATAAg                                                                                                                                                    <  2:454289/273‑1 (MQ=255)                                                              aa‑aaGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCa                                                                                                                                                                                           <  1:156011/230‑1 (MQ=255)                                                                                           gTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAAcgcg                                                                                                                                                                                             >  2:355401/1‑200 (MQ=255)                                                                                           gTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAAcgcg                                                                                                                                                                                             >  1:417547/1‑200 (MQ=255)                                                                                               atTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGc                                                                                                                                                                                         <  2:417534/200‑1 (MQ=255)                                                                                               atTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGc                                                                                                                                                                                         <  1:355413/200‑1 (MQ=255)                                                                                                       tgtgAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACTCTTCCTCTTATCTTATTGATAAAATGTATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACg                                                                                                                                                              <  1:312033/219‑1 (MQ=255)                                                                                                                 tGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCaa                                                                                                                                                                                                                                                 >  1:382568/1‑126 (MQ=255)                                                                                                                   aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTTCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACGCCACCATAAGCCGCGTAAACACGCCCACTCGCCGCTGGATGCAACGTTAACAACCAGACAAACAgcgc                                                                                          <  1:212699/275‑1 (MQ=255)                                                                                                                     aaaaGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCaa                                                                                                                                                                                                                                             <  2:382555/126‑1 (MQ=255)                                                                                                                                            tGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGTATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACGCCACCATAAGCCGCGTAAACACGCCCACTCGCCGCTGGATGCAACGTTAACAACCAGACAAACAGCGCCAGTGAAATCCCCACCGGAAGCaa                                                                  <  1:488961/274‑1 (MQ=255)                                                                                                                                                                      atTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATc                                                                                                                                                                                   >  1:142101/1‑135 (MQ=255)                                                                                                                                                                      atTGATAAAATGGATGTATGTTCCCACGCTCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACGCCACCATAAGCCGCGTAAACACGCCCANTCGCCGCTGGa                                                                                                                       >  1:351138/1‑195 (MQ=255)                                                                                                                                                                         gATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAg                                                                                                                                                                                                                                                      >  1:235380/1‑65 (MQ=255)                                                                                                                                                                          aTAAAATGGATTTATGTTCCTCCGGGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACGCCACCATAAGCCGCGTAAACACGCCCACTCGCCGCTGGATGCa                                                                                                                   <  2:351126/195‑1 (MQ=255)                                                                                                                                                                          aTAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACg                                                                                                                                                                               <  2:142095/135‑1 (MQ=255)                                                                                                                                                                             aaaTGGATTTATGTTCATACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCa                                                                                                                                                                                                                                                  <  2:235373/65‑1 (MQ=255)                                                                                                                                                                                        tGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTAACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAAAGCCACCATAAGCCGCGTAAACACGCCCACTCGCCGCTGGATGCAACGTTAACAACCAGAAAAACAGCGCCAGTGAAATCCCCGCCGGAAGCAACAGCCAGATACTGGCGATTCGTTTTAACCAACACAAGGGCAGaaa                     >  1:49876/1‑275 (MQ=255)                                                                                                                                                                                           agaccgggccccccccAGCCCCCAACCATGATCAACCTGCCGCAAACCGCAATCAACGCACCCGCCCCGTCATAAAGAGTCCGGTTCACGCCATCCACACCGCGCAGCCACATCAACGCCGTGCAGACATAAACGCAACCATAAGCCGCGTAAACACGCCCACTCGCCGCTGGATGCAACGTTAACAACCAGACAAACAGCGCCAGTGAAATCCCCGCCGGAAGCAACAGCCAGATACTGGCGTTTCGTTTTAACCACAACCAGGGCAGAAAGCa                  <  2:488590/264‑1 (MQ=255)                                                                                                                                                                                             cTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAttt                                                                                                                                                                                                                >  2:476944/1‑83 (MQ=255)                                                                                                                                                                                                 gTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCAc                                                                                                                                                                                                            <  1:476957/83‑1 (MQ=255)                                                                                                                                                                                                      cccccAGCCCGCAACAATTATCAACATGCCGCAAAGCGCAATCAACGCAcc                                                                                                                                                                                                                                       >  2:205761/1‑51 (MQ=255)                                                                                                                                                                                                      cccccAGCCCGCAACAATTATCAACATGCCGCAAAGCGCAATCAACGCAcc                                                                                                                                                                                                                                       >  2:252968/1‑51 (MQ=255)                                                                                                                                                                                                          cAGCCCGCAACAATTATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                                                                                                                                                                                                   <  1:252975/51‑1 (MQ=255)                                                                                                                                                                                                          cAGCCCGCAACAATTATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                                                                                                                                                                                                   <  1:205767/51‑1 (MQ=255)                                                                                                                                                                                                            gCCCGCAACATTGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACGCCACCATAAGCCGCGTAACCACGCCCACTCGCCGCTGGATGCAACGTTAACAACCAGACAAACAGCGCCAGTGAAATGCCCGCCGGAAGCAACAGCCAGATACTGGCGTTTCGTTTTAACCACAACCAGGGCAGAAAGCATCCAATAATTTctgac  >  1:488603/1‑270 (MQ=255)                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                                      CTTGTCGTGATGCATGAAATCTACGCAACTGAGCTACTACCATACAAGTATAAAGATCGAAAA‑AAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACGCCACCATAAGCCGCGTAAACACGCCCACTCGCCGCTGGATGCAACGTTAACAACCAGACAAACAGCGCCAGTGAAATCCCCGCCGGAAGCAACAGCCAGATACTGGCGTTTCGTTTTAACCACAACCAGGGCAGAAAGCATCCAATAATTTCACAC  >  CP009273/1649417‑1649892

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑