Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,169,767	A→C	13.8%	D446A (GAC→GCC)	PP_4547 →	glutamine synthetase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,169,767	0	A	C	13.8%	62.5 / 6.0	29	D446A (GAC→GCC)	PP_4547	glutamine synthetase
Reads supporting (aligned to +/- strand):  ref base A (14/11);  new base C (2/2);  total (16/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.82e-01

CCCACTGACTGGCTGACCGCACTCGACGCCCTGCAACATTCCGATTGGGCCCGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTGCACCAGGCCTGAGCCCCTAAATAACAAGGAACACCCATGAACGCAGCATTGAACAACGGCCCGGCGCAGCGCGCGCCGTCCTACTACAGCGCCACCCTCAACGACCACACTGCGTACCCGCAACTCAA  >  NC_002947/5169625‑5169911                                                                                                                                               |                                                                                                                                                 cccACTGACTGGCTGACCGCACTCGACGCCCTGCAACATTCCGATTGGGCCCGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGgcgc                                                                                                                                           <  1:134750/150‑1 (MQ=255)      tgactgGCTGACCGCACTCGACGCCCTGCAACATTCCGATTGGGCCCGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTa                                                                                                                                      >  1:553901/1‑150 (MQ=255)          tgGCTGACCGCACTCGACGCCCTGCAACATTCCGATTGGGCCCGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTg                                                                                                                                  <  2:553901/150‑1 (MQ=255)                  cGCACTCGACGCCCTGCAACATTCCGATTGGGCCCGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGTGCAGGTACCAGCGCCAgt                                                                                                                           <  1:609436/149‑2 (MQ=255)                  agCACTCGACGCCCTGCAACATTCCGATTGGGCCCGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGTGCAGGTACCAGCGCCAgt                                                                                                                           >  2:609436/2‑148 (MQ=255)                    cACTCGACGCCCTGCAACATTCCGATTGGGCCCGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTa                                                                                                                                      <  2:363777/136‑1 (MQ=255)                    cACTCGACGCCCTGCAACATTCCGATTGGGCCCGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTa                                                                                                                                      >  1:363777/1‑136 (MQ=255)                    cACTCGACGCCCTGCAACATTCCGATTGGGCCCGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTGCACCAGGCCt                                                                                                                        <  1:250710/150‑1 (MQ=255)                          aCGCCCTGCAACATTCCGATTGGGCCCGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGCCTGGTGCAGGTACCAGCGCCAGTCCTgttcgc                                                                                                                  <  1:203146/150‑6 (MQ=38)                                tGCAACATTCCGATTGGGCCCGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTGCACCAGGCCTGAGCCCCTAAAt                                                                                                            >  1:186867/1‑150 (MQ=255)                                      aTTCCGATTGGGCCCGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTGCACCAGGCCTGAGCCCCTAAATAACAAg                                                                                                      >  1:446439/1‑150 (MQ=255)                                                   ccGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTGCACCAGGCCTGAGCCCCTAAATAACAAGGAACACCCATGaa                                                                                         >  2:590202/1‑150 (MQ=255)                                                    cGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTGCACCAGGCCTg                                                                                                                       <  2:405431/119‑1 (MQ=255)                                                    cGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTGCACCAGGCCTg                                                                                                                       >  1:405431/1‑119 (MQ=255)                                                    cGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTGCACCAGACCTGAGCCCCTAAATAAAAAGGAACACCCATGAAc                                                                                        >  1:284260/1‑150 (MQ=255)                                                            aTTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTGCACCAGGCCTGAGCCCCTAAATAACAAGGAACACCCATGAACGCAGCAtt                                                                                <  2:186867/150‑1 (MQ=255)                                                                         ttCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGTCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTGCACCAGGCCTGAGCCCCTAAATAACAAGGAACACCCATGAACGCAGCATTGAACAACGGCCCg                                                                   <  2:301038/150‑1 (MQ=255)                                                                         ttCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTGCACCAGGCCt                                                                                                                        <  2:338320/97‑1 (MQ=255)                                                                         ttCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTGCACCAGGCCt                                                                                                                        >  1:338320/1‑97 (MQ=255)                                                                         ttCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTGCACCAGGCCTGAGCCCCTAAATAACAAGGAACACCCATGAACGCAGCATTGAACAACGGCCCg                                                                   >  2:14489/1‑150 (MQ=255)                                                                           ccTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGCCTGGTGCAGGTACCAGCGCCAGTCCTgt                                                                                                                      <  1:174828/97‑2 (MQ=25)                                                                           ccTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGCCTGGTGCAGGTACCAGCGCCAGTCCTgt                                                                                                                      >  2:174828/1‑96 (MQ=25)                                                                                                   gcgcgcCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTGCACCAGGCCTGAGCCCCTAAATAACAAGGAACACCCATGAACGCAGCATTGAACAACGGCCCGGCGCAGCGCGCGCCGTcc                                                 <  1:516913/142‑1 (MQ=255)                                                                                                   gcgcgcCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTGCACCAGGCCTGAGCCCCTAAATAACAAGGAACACCCATGAACGCAGCATTGAACAACGGCCCGGCGCAGCGCGCGCCGTcc                                                 >  2:516913/1‑142 (MQ=255)                                                                                                                                        gAACAGGACTGGCGCTGGTACCTGCACCAGGCCTGAGCCCCTAAGTAACAAGGAACACCCATGAACGCAGCATTGAACAACGGCCCGGCGCAGCGCGCGCCGTCCTACTACAGCGCCACCCTCAACGACAACACTGCGTACCCGCAACTc    >  2:17218/1‑150 (MQ=255)                                                                                                                                          tcAGGCCTGGTGCAGGTACCAGCGCCAGTCCTGAGCCCCTAAATAACAAGGAACACCCATGAACGCAGCATTGAACAACGGCCCGGCGCAGCGCGCGCCGTCCTACTACAGCGCCACCCTCAACGACCACACTGCGTACCCGCAACTCaa  >  2:297337/2‑150 (MQ=255)                                                                                                                                          aCAGGACTGGCGCTGGTACCTGCACCAGGCCTGAGCCCCTAAATAACAAGGAACACCCATGAACGCAGCATTGAACAACGGCCCGGCGCAGCGCGCGCCGTCCTACTACAGCGCCACCCTCAACGACCACACTGCGTACCCGCAACTCaa  >  1:393027/1‑150 (MQ=255)                                                                                                                                              gACTGGCGCTGGTACCTGCACCAGGCCTGAGCCCCTAAATAACAAGGAACACCCATGAACGCAGCATTGAACAACGGCCCGgcg                                                                <  2:170490/84‑1 (MQ=255)                                                                                                                                              gACTGGCGCTGGTACCTGCACCAGGCCTGAGCCCCTAAATAACAAGGAACACCCATGAACGCAGCATTGAACAACGGCCCGgcg                                                                >  1:170490/1‑84 (MQ=255)                                                                                                                                               |                                                                                                                                                 CCCACTGACTGGCTGACCGCACTCGACGCCCTGCAACATTCCGATTGGGCCCGTGAAGCATTGGGCGAAGACTTCCTTGGCGTGTACCTGAAGGTCAAGCGCGCCGAGTACCGCCAGTTCATGGCCGAAGTCAGCGAACAGGACTGGCGCTGGTACCTGCACCAGGCCTGAGCCCCTAAATAACAAGGAACACCCATGAACGCAGCATTGAACAACGGCCCGGCGCAGCGCGCGCCGTCCTACTACAGCGCCACCCTCAACGACCACACTGCGTACCCGCAACTCAA  >  NC_002947/5169625‑5169911

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑