Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,552,024	C→A	14.8%	intergenic (+118/+63)	pydA → / ← rutR	NADP‑dependent dihydropyrimidine dehydrogenase subunit PreA/transcriptional regulator, TetR family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,552,024	0	C	A	14.8%	72.5 / 3.8	27	intergenic (+118/+63)	pydA/rutR	NADP‑dependent dihydropyrimidine dehydrogenase subunit PreA/transcriptional regulator, TetR family
Reads supporting (aligned to +/- strand):  ref base C (10/13);  new base A (2/2);  total (12/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGTAACCCCTACCGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAG‑CAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCATGTCAGACAGCACCT  >  NC_002947/4551879‑4552169                                                                                                                                                   |                                                                                                                                                  gcgTAACCCCTACCGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAG‑CAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTcgcg                                                                                                                                                <  2:94416/149‑1 (MQ=255)     aaCCCCTACCGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAG‑CAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGcc                                                                                                                                             <  6:27926/148‑1 (MQ=255)     aaCCCCTACCGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAG‑CAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGcc                                                                                                                                             >  5:27926/1‑148 (MQ=255)      aCCCCTACCGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAGCCAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCGAAGCGGccc                                                                                                                                            <  1:74059/149‑1 (MQ=39)      aCCCCTACCGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAG‑CAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGccc                                                                                                                                            <  5:298145/148‑1 (MQ=255)       ccccTACCGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAG‑CAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGa                                                                                                                                          <  3:16140/149‑1 (MQ=255)         ccTACCGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAG‑CAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATc                                                                                                                                        <  8:198958/149‑1 (MQ=255)         ccTACCGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAG‑CAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATc                                                                                                                                        <  2:107202/149‑1 (MQ=255)             ccGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAG‑CAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGa                                                                                                                                    <  5:166722/149‑1 (MQ=255)                                           tGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAG‑CAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTcgcg                                                                                                                                                <  8:201488/107‑1 (MQ=255)                                           tGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAG‑CAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTcgcg                                                                                                                                                >  7:201488/1‑107 (MQ=255)                                                                                                 caGCGGCCCCAG‑CAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATc                                                      <  3:93097/143‑1 (MQ=255)                                                                                                 caGCGGCCCCAG‑CAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATc                                                      >  4:93097/1‑143 (MQ=255)                                                                                                                   tttGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCg                                >  2:84729/1‑148 (MQ=255)                                                                                                                       ccGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATtc                           >  5:256226/1‑149 (MQ=255)                                                                                                                        cgcgATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATtct                          >  5:101280/1‑149 (MQ=255)                                                                                                                            aTACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGaa                      <  6:101280/149‑1 (MQ=255)                                                                                                                              aCAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATtct                          <  6:144695/143‑1 (MQ=255)                                                                                                                              aCAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATtct                          >  5:144695/1‑143 (MQ=255)                                                                                                                              aCAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATtct                          <  4:268092/143‑1 (MQ=255)                                                                                                                              aCAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATtct                          >  3:268092/1‑143 (MQ=255)                                                                                                                                      gatcgggCCGCGAAGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATc                                                                  >  1:300677/5‑95 (MQ=37)                                                                                                                                       gAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCAAGCTGGTCACCGTCTGCACCGCATTCTCGAAGGcc                  >  7:193314/1‑142 (MQ=255)                                                                                                                                       gAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCAAGCTGGTCACCGTCTGCACCGCATTCTCGAAGGcc                  <  8:193314/142‑1 (MQ=255)                                                                                                                                        tcgggCCGCGAAGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCATGt              <  7:136467/143‑1 (MQ=255)                                                                                                                                        tcgggCCGCGAAGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCATGt              >  8:136467/3‑145 (MQ=255)                                                                                                                                        aGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCATGTCAGa          <  6:256226/149‑1 (MQ=255)                                                                                                                                               gCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATtctc                         >  5:300544/1‑127 (MQ=255)                                                                                                                                               gCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATtctc                         <  6:300544/127‑1 (MQ=255)                                                                                                                                                cTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCATGTCAGACAGCACCt  >  7:36378/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                  GCGTAACCCCTACCGTGAGGCCAGTTGAAGCGGGTCACCGCCTGAACAGCTGACGCGGCCCCTGTGGGAGCGGCCTTGTGTCGCGATCGGGCCGCACAGCGGCCCCAG‑CAGTCTTTGCCGCGATACAGACATCGAGGGGCCGCTTCGCGGCCCGATCGCGACACAAGGCCGCTCCCACAAAAAGACCACGTCCACCTGGAATGCCGGATCACGGCTCCAGCCCGATCCCCCGCAAGATCACGCTGGTCACCGTCTGCACCGCATTCTCGAAGGCCATGTCAGACAGCACCT  >  NC_002947/4551879‑4552169

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑