Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	1,414,184	T→C	12.7%	R105R (AGA→AGG)	racR ←	Rac prophage; putative DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	1,414,184	0	T	C	12.7%	80.4 / 3.7	37	R105R (AGA→AGG)	racR	Rac prophage; putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (18/14);  new base C (3/2);  total (21/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

GCTTTTCCGTTCAGATTCAAGAGCTTTCAGATACTTACCCACTTTCATTTCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTGGGGGTTGGTATGGGGTATTCGTTAAGCCCCCAATGCTCTGGACCAACAACATCAGAAAAGAAACGCCATA  >  CP009273/1414049‑1414326                                                                                                                                        |                                                                                                                                               gctatgccGTTCAGATTCGAGAGCTTTCAGATACTTACCCACTTTCATTTCCATCGCTGCTATGTGGGGGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGTTACAATCGCTCTTAttt                                                                                                                                         >  1:166371/7‑143 (MQ=255)    tttCCGTTCAGATTCAAGAGCTTTCAGATACTTACCCACTTTCATTTCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTtcat                                                                                                                                      <  1:327385/143‑1 (MQ=255)    tttCCGTTCAGATTCAAGAGCTTTCAGATACTTACCCACTTTCATTTCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCCCTTATTtcat                                                                                                                                      >  1:527061/1‑143 (MQ=255)    tttCCGTTCAGATTCAAGAGCTTTCAGATACTTACCAACCTTCATTTCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCCCTTATTtcat                                                                                                                                      >  1:235702/1‑143 (MQ=255)     ttCCGTTCAGATTCAAGAGCTTTCAGATACTTACCCACTTTCATTTCCATCGCTGCTATGTAGGCGCGAACATCGGGGTGAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGgc                                                                                                                               <  2:246692/149‑1 (MQ=255)         gTTCAGATTCAAGAGCTTTCAGATACTTACCCACTTTCATTTCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCagag                                                                                                                                 >  1:439463/1‑143 (MQ=255)         gTTCAGATTCAAGAGCTTTCAGATACTTACCCACTTTCATTTCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGgctgct                                                                                                                           >  2:610243/1‑149 (MQ=255)         gTTCAGATTCAAGAGCTTTCAGATACTTACCCACTTTCATTTCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGATCCTGTAGCATTTCCAGGTAACAGGAAAGGTCCAATCGCTCTTAGTTCATCCGAGgctggt                                                                                                                           >  2:210699/1‑147 (MQ=255)                 tCAAGAGCTTTCAGATACTTACCCACTTTCATTTCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTCCGAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAg                                                                                                                   <  2:281916/149‑1 (MQ=255)                         tttCAGATACTTACCCACTTTCATTTCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGTTAAGGGTTTTTta                                                                                                           >  2:60223/1‑149 (MQ=255)                          ttCAGATACTTACCCACTTTCATTTCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCCCTTATTTCATCAGAGGCTGCTTGATAAAggttggttgt                                                                                                          >  2:11877/1‑147 (MQ=255)                            cAGATACTTACCCACTTTCATTTCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTatat                                                                                                        <  2:45483/149‑1 (MQ=255)                            cAGATACTTACCCACTTTCATTTCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGATGCTTGATAAAGGTTGTTTatat                                                                                                        <  2:342966/149‑1 (MQ=255)                                 aCTTACCCACTTTCATTTCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAACGGTTGTTTATATCTaaa                                                                                                   >  2:111481/1‑149 (MQ=255)                                             tCATTTCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACttttt                                                                                       <  2:541309/149‑1 (MQ=255)                                             tCATTTCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATAAGAGGCTGCTTGATAAAGGTTGTTTATATCTAACAGTTCACttttt                                                                                       >  2:211123/1‑149 (MQ=255)                                                  tCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACtttt                                                                                        >  1:205088/1‑143 (MQ=255)                                                            ctATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATtggtg                                                                        <  2:619315/149‑1 (MQ=255)                                                              aTGTAGGCGCGAACATCGTGGTCAAGCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCCCTTTTTGTATCTGAATTGGTggg                                                                      >  2:319236/1‑149 (MQ=255)                                                              aTGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAAtt                                                                            <  1:502797/143‑1 (MQ=255)                                                               ggTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTgggg                                                                     <  2:212179/148‑1 (MQ=255)                                                                  aGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTGGGGGtt                                                                  >  2:397040/1‑149 (MQ=255)                                                                    gcgcGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTGGGGGTTgg                                                                >  2:126348/1‑149 (MQ=255)                                                                       cgAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTTTCTGAATTGGTGGGGGt                                                                   >  1:481176/1‑143 (MQ=255)                                                                          aCATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCCCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTGGGGGTTGGTATggg                                                          <  2:266881/149‑1 (MQ=255)                                                                          aCATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCCCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTGGGGGTTGGTATggg                                                          <  2:583868/149‑1 (MQ=255)                                                                             tCGTGGACAACCCAATTTGGTTCTGTAGCGTTTCCAGATAACAGGAAAGCTACAATTGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGGTCACTTTTTGTATCTGAATTGGTGGGGGTTGGTATGGGGTa                                                       <  2:551846/149‑1 (MQ=255)                                                                                    cAACCCAATTTGGTTCTGTAGCATTTCCAGATACAAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTGGGGGTTGGTATGGGGTATTCGTTa                                                <  2:217968/149‑1 (MQ=255)                                                                                                 ttCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTGGGGGTTGGTATGGGGTATGCGTTAGGccccc                                         >  1:339367/1‑143 (MQ=255)                                                                                                             tCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTGGGGGTTGGTATGGGGTATTCGTTAAGCCCCCAATGCTCTGGACcaacaa                       <  2:113759/149‑1 (MQ=255)                                                                                                                aGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTGGGGGTTGGTATGGGGTATTCGTTAAGCCCCCAATGCTCTGGACcaa                          <  1:551919/143‑1 (MQ=255)                                                                                                                  aTAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCGGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTGGGGGTTGGTATGGGGTATTCGTTAAGCCCCCAATGCTCTGGACCAACAACATCa                  <  2:283641/149‑1 (MQ=255)                                                                                                                    aaCAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTGGGGGTTGGTATGGGGTATTCGTTAAGCCCCCAATGCTCTGGACCAACAACATCaga                >  2:610608/1‑149 (MQ=255)                                                                                                                       aGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTGGGGGTTGGTATGGGGTATTCGTTAAGCCCCCAATGCTCTGGACCAACAACATCagaaaa             >  2:41813/1‑149 (MQ=255)                                                                                                                          aaaGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTACAAGTTCACTTTTTGTATCTGAATTGGTGGGGGTTGGTCTGGGGTAGGCGTTAAGCCCCCGATGCTCTGGACCAACAGCATCagaaaagaa          >  2:530520/1‑149 (MQ=255)                                                                                                                          aaaGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTGGGGGTTGGTATGGGGTATTCGTTAAGCCCCCAATGCTCTGGACCAACAACATCagaaaagaa          >  2:556979/1‑149 (MQ=255)                                                                                                                               tACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAACGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTGGGGGTTCGTATGGGGTATTCGTTAAGCCCCCAATGCTCTGGACCAACAACATCAGAAAAGAAACGcc     >  2:411914/1‑149 (MQ=255)                                                                                                                                        tctTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTGGGGGTTGGTATGGAGTATTCGTTAAGCCCCCAATGAACTGGACCCACAACATCAGAAAAGAAACGCCATa  >  1:186186/1‑143 (MQ=255)                                                                                                                                        |                                                                                                                                               GCTTTTCCGTTCAGATTCAAGAGCTTTCAGATACTTACCCACTTTCATTTCCATCGCTGCTATGTAGGCGCGAACATCGTGGTCAACCCAATCTGGTTCTGTAGCATTTCCAGATAACAGGAAAGCTACAATCGCTCTTATTTCATCAGAGGCTGCTTGATAAAGGTTGTTTATATCTAAAAGTTCACTTTTTGTATCTGAATTGGTGGGGGTTGGTATGGGGTATTCGTTAAGCCCCCAATGCTCTGGACCAACAACATCAGAAAAGAAACGCCATA  >  CP009273/1414049‑1414326

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑