Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	701,647	G→A	P33P (CCG→CCA)	glnS →	glutamine‑‑tRNA ligase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	701,647	0	G	A	97.4%	136.5 / ‑4.0	39	P33P (CCG→CCA)	glnS	glutamine‑‑tRNA ligase
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (22/16);  total (22/17)
Fisher's exact test for biased strand distribution p-value = 4.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.20e-01

GAAGCCCGCCCGACTAACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCGCCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGCC  >  NZ_CP009273/701561‑701729                                                                                       |                                                                                   gAAGCCCGCCCGACGAACTTTATCCGTCAGATCAGCGATTAAGATCTGTCCAGTGGTAAGCACACCACAGTACACACCCGTTTCccaccg                                                                                 >  2:80570/1‑90 (MQ=255)  aaGCCCGCCCGACTAACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCGCCgg                                                                                <  2:656124/90‑1 (MQ=255)      ccgcccgACTAACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGcc                                                                            >  2:867314/1‑90 (MQ=255)              cTAACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACCCCACAGTACACCCCCGTTTCCCACCGGAGCCGAATGGCt                                                                    <  1:80570/90‑1 (MQ=255)                 aCTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATc                                                                 <  1:48155/90‑1 (MQ=255)                 aCTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATc                                                                 <  1:650306/90‑1 (MQ=255)                  cTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCt                                                                <  2:91243/90‑1 (MQ=255)                  cTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCt                                                                <  2:728480/90‑1 (MQ=255)                  cTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCt                                                                <  1:395102/90‑1 (MQ=255)                          gTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTg                                                        >  1:852091/1‑90 (MQ=255)                           tCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTgg                                                       >  2:595315/1‑90 (MQ=255)                           tCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTgg                                                       >  2:210906/1‑90 (MQ=255)                            cAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGc                                                      >  1:186447/1‑90 (MQ=255)                                 catcGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGc                                                 <  1:656038/90‑1 (MQ=255)                                  atcGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGcc                                                     >  1:704373/1‑85 (MQ=255)                                  atcGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGcc                                                     <  2:704373/85‑1 (MQ=255)                                   tcGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGa                                               >  2:873300/1‑90 (MQ=255)                                                ggCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCt                                  >  1:458672/1‑90 (MQ=255)                                                  ccAGTGGTAAGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGa                                <  2:19549/90‑1 (MQ=255)                                                     gTGGTAAGCACACCACAGTACACACCCGTTTCCGACCGGAGCCGAATGGCTATCTGCATATTGGCAATGCGAAATCTATCTGCCTGAACt                             >  2:202693/1‑90 (MQ=255)                                                          aaGCACACCACAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCggg                        >  2:910064/1‑90 (MQ=255)                                                               caccacAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGc                   >  2:265919/1‑90 (MQ=255)                                                               caccacAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGc                   >  1:376369/1‑90 (MQ=255)                                                                 ccacAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGccc                 <  2:714777/90‑1 (MQ=255)                                                                 ccacAGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGccc                 >  2:488727/1‑90 (MQ=255)                                                                  cacaGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGccc                 <  1:474711/89‑1 (MQ=255)                                                                  cacaGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGccc                 >  2:474711/1‑89 (MQ=255)                                                                    caGTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAgg              <  2:526355/90‑1 (MQ=255)                                                                      gTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGAc            <  2:95442/90‑1 (MQ=255)                                                                      gTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGAc            <  2:526861/90‑1 (MQ=255)                                                                      gTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGAc            <  1:910064/90‑1 (MQ=255)                                                                      gTACACACCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGAc            >  1:243924/1‑90 (MQ=255)                                                                         cacacCCGTTTCCCACCGGGGCCGGATGGCTATCTGCATATTGGCCAGGCGAAATCTATCGGCCTGAACTTCGGGATCGCCCAGGACtat         >  2:192521/1‑90 (MQ=255)                                                                           cacCCGTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATaa       >  1:295405/1‑90 (MQ=255)                                                                                gTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGAc            <  2:275178/80‑1 (MQ=255)                                                                                gTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGAc            >  1:275178/1‑80 (MQ=255)                                                                                gTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGcc  >  2:28765/1‑90 (MQ=255)                                                                                gTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGcc  >  1:82853/1‑90 (MQ=255)                                                                                gTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGcc  >  1:508312/1‑90 (MQ=255)                                                                                gTTTCCCACCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGcc  >  1:338563/1‑90 (MQ=255)                                                                                       |                                                                                   GAAGCCCGCCCGACTAACTTTATCCGTCAGATCATCGATGAAGATCTGGCCAGTGGTAAGCACACCACAGTACACACCCGTTTCCCGCCGGAGCCGAATGGCTATCTGCATATTGGCCATGCGAAATCTATCTGCCTGAACTTCGGGATCGCCCAGGACTATAAAGGCC  >  NZ_CP009273/701561‑701729

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑