Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,277,384	C→T	13.3%	Q260Q (CAG→CAA)	ampC ←	beta‑lactamase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,277,384	0	C	T	13.3%	69.2 / 3.8	30	Q260Q (CAG→CAA)	ampC	beta‑lactamase
Reads supporting (aligned to +/- strand):  ref base C (10/16);  new base T (2/2);  total (12/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01

GCTGTTGCCATCGATCAGTGTGCTCAGCGTGACCGGGTAGGGGTAGCGTTCCCAGCCCAGGCCTTGCGTCATGGCGCCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGTAGGCCTCATCGGCGT‑AAGGGCCGGGCCCTACACGCACCGGCTTGTCGTCGGCGTCATACCCTTGGGCATAAAGCCCCTGGGCGCTGGCC  >  NC_002947/3277240‑3277528                                                                                                                                                 |                                                                                                                                                  gCTGTTGCCATCGATCAGTGTGCTCAGCGTGACCGGGTAGGGGTAGCGTTCCCAGCCCAGGCCTTGCGTCATGGCGCCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCAt                                                                                                                                              <  2:695966/150‑1 (MQ=255)  cTGTTGCCATCGATCAGTGTGCTCAGCGTGACCGGGTAGGGGTAGCGTTCCCAGCCCAGGCCTTGCGTCATGGCGCCAACCTGGAAGTAGCCCTGCTGGGTAATGCCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCAtg                                                                                                                                             >  2:614324/1‑150 (MQ=255)     ttGCCATCGATCAGTGTGCTCAGAGTGACCGGGTAGGGGTAGCGTTCCCAGCCCAGGCCTTGCGTCATGGCGCCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGc                                                                                                                                          <  2:412480/150‑1 (MQ=255)       gCCATCGATCAGTGTGCTCAGCGTGACCGGGTAGGGGTAGCGTTCCCAGCCCAGGCCTTGCGTCATGGCGCCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCaa                                                                                                                                        >  2:317508/1‑150 (MQ=255)          aTCGATCAGTGTGCTCAGCGTGACCGTGGAGGGGTAGCGTTCCCAGCCCAGGCCTTGCGTCATGGCGCCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCg                                                                                                                                     >  2:715843/1‑150 (MQ=255)          aTCGATCAGTGTGCTCAGCGTGACCGGGTAGGGGTAGCGTTCCCAGCCCAGGCCTTGCGTCATGGCGCCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCg                                                                                                                                     >  1:434532/1‑150 (MQ=255)                        tCAGCGTGACCGGGTAGGGGTAGCGTTCCCAGCCCAGGCCTTGCGTCATGGCGCCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCGGTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATCTGCGACCGCGCATAGCgcagca                                                                                                                       >  1:527279/1‑150 (MQ=255)                                   gggtaggggtagCGTTCCCAGCCCAGGCCTTGCGTCATGGCGCCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCgcagca                                                                                                                       <  2:587284/139‑1 (MQ=255)                                   gggtaggggtagCGTTCCCAGCCCAGGCCTTGCGTCATGGCGCCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCgcagca                                                                                                                       >  1:587284/1‑139 (MQ=255)                                               cGTTCCCAGCCCAGGCCTTGCGTCATGGCGCCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCGAACCAGGTCGCTGGCGCTGGTTTTGATg                                                                                                <  1:542942/150‑1 (MQ=255)                                                   cccagcccagGCCTTGCGTCATGGCGCCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGt                                                                                            <  1:529265/150‑1 (MQ=255)                                                        cccagGCCTTGCGTCATGGCGCCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGTAGGcc                                                                                       >  1:171833/1‑150 (MQ=255)                                                           agGCCTTGCGTCATGGCGCCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGTAGGCCTCa                                                                                    >  1:706786/1‑150 (MQ=255)                                                                     tCATGGCGTCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGTAGGCCTCATCGGCGT‑AAg                                                                         <  1:36960/150‑1 (MQ=255)                                                                         ggCGCCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGTAGGCCTCATCGGCGT‑AAgggcc                                                                     <  1:317508/150‑1 (MQ=255)                                                                            gcCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGTTGCACATGCAGCCGcagg                                                                                                                                 <  1:550204/88‑3 (MQ=38)                                                                            gcCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGTTGCACATGCAGCCGcagg                                                                                                                                 >  2:550204/1‑86 (MQ=38)                                                                                  cTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGTTGCACATGCAGCCGca                                                                                                                                   <  1:247516/80‑1 (MQ=38)                                                                                  cTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGTTGCACATGCAGCCGca                                                                                                                                   >  2:247516/1‑80 (MQ=38)                                                                                  cTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGTAGGCCTCATCGGCGTGTAGGGCCCGGCCCtt                                                             >  1:819960/1‑149 (MQ=255)                                                                                             ccTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGTAGGCCTCATCGGCGT‑AAGGGCCGGGCCCTACACGCACCGGCt                                                 <  1:715843/150‑1 (MQ=255)                                                                                              ctgctgGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGTAGGCCTCATCGGCGT‑AAGGGCCGGGCCCTACACGCACCGGCtt                                                <  2:453596/150‑1 (MQ=255)                                                                                                                 gCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGTAGGCCTCATCGGCGT‑AAGGGCCGGGCCCTacac                                                          <  2:359962/121‑1 (MQ=255)                                                                                                                 gCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGTAGGCCTCATCGGCGT‑AAGGGCCGGGCCCTacac                                                          >  1:359962/1‑121 (MQ=255)                                                                                                                     tCGCCAGGGCCGGTGGCAGGCGCGGTGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGTAGGCCTCTGCGGCTG‑AAGGGCCGGGCCCTACACGCACCGGCTTGTCGTCGGCGTCATACCCTTggg                         <  2:634188/150‑1 (MQ=255)                                                                                                                     tCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGTAGGCCTCATCGGCGT‑AAGGGCCGGGCCCTACACGCACCGGCTTGTCGTCGGCGTCATACCCTTggg                         <  2:706786/150‑1 (MQ=255)                                                                                                                            ggCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGTAGGCCTCATCGGCGT‑AAGGGCCGGGCCCTACACGCACCGGCTTGTCGTCGGCGTCATACCCTTGGGCATAAAg                  <  2:192721/150‑1 (MQ=255)                                                                                                                                  tGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGTAGGCCTCATCGGCGT‑AAGGGCCGGGCCCTACACGCACCGGCTTGTCGTCGGCGTCATACCCTTGGGCATAAAGCCCCTg            <  1:614324/150‑1 (MQ=255)                                                                                                                                     cAGGCCCTGCGGCTGCATATGCAACCGCACAGAGCCTAGCAGGTCGCTGGCGCTGGTTTTCATGCCGTAGGCCTCATTGGCAC‑CAGCGCCGGGCCTGACACGCATCGGCTTGTCGCCGGCATCATACCCTTGGGCATAAAGcccgtacgc         <  2:118396/150‑7 (MQ=255)                                                                                                                                            tGCGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGTAGGCCTCATCGGCGT‑AAGGGCCGGGCCCTACACGCACCGGCTTGTCGTCGGCGTCATACCCTTGGGCATAAAGCCCCTGGGCGCTGGcc  <  2:527279/150‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                  GCTGTTGCCATCGATCAGTGTGCTCAGCGTGACCGGGTAGGGGTAGCGTTCCCAGCCCAGGCCTTGCGTCATGGCGCCAACCTGGAAGTAGCCCTGCTGGGTAATGGCGGTGGCTTTCGCCAGGGCCGGTGGCAGGCCCTGCGGCTGCATGTGCAACCGCACATAGCGCAGCAGGTCGCTGGCGCTGGTTTTGATGCCGTAGGCCTCATCGGCGT‑AAGGGCCGGGCCCTACACGCACCGGCTTGTCGTCGGCGTCATACCCTTGGGCATAAAGCCCCTGGGCGCTGGCC  >  NC_002947/3277240‑3277528

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑