Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,972,691	A→G	intergenic (‑237/‑543)	flhD ← / → uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,972,691	0	A	G	95.0%	52.6 / ‑3.4	20	intergenic (‑237/‑543)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base G (7/12);  total (8/12)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.54e-01

TACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATAC  >  NZ_CP009273/1972605‑1972771                                                                                       |                                                                                 tACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACgggggg                                                                               >  1:253075/1‑90 (MQ=255) tACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACgggggg                                                                               >  1:79821/1‑90 (MQ=255)             tGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGAttt                                                                   <  1:297493/90‑1 (MQ=255)                    ttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCaataa                                                            <  2:79821/90‑1 (MQ=255)                         cTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGt                                                       <  1:499066/90‑1 (MQ=255)                          ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTg                                                      >  2:352563/1‑90 (MQ=255)                          ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCCGGGATTTTCAAAAATTCggg                                                      >  2:168976/1‑88 (MQ=255)                          ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTg                                                      >  2:9873/1‑90 (MQ=255)                                    tttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATca                                            <  1:242010/90‑1 (MQ=255)                                      tttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATcaca                                          >  1:508909/1‑90 (MQ=255)                                                  aCGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCaa                              <  1:293836/90‑1 (MQ=255)                                                   cGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAt                             <  2:180510/90‑1 (MQ=255)                                                   cGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAt                             <  2:282616/90‑1 (MQ=255)                                                   cGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAt                             <  2:463863/90‑1 (MQ=255)                                                    gCAACTGTCCTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAtt                            <  2:508909/90‑1 (MQ=255)                                                      aaCTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTAc                          <  2:253075/90‑1 (MQ=255)                                                             cTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACCCTCAATTACTTAAgga                   <  1:432552‑M1/90‑4 (MQ=255)                                                               cGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaag                 >  1:362497‑M1/1‑85 (MQ=255)                                                                    cTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAGCACTCAATTACTTAAggaaggtgcg            >  1:308676‑M1/1‑80 (MQ=255)                                                                     tACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcga           <  1:352563‑M1/90‑12 (MQ=255)                                                                           cacaTACAACGGGGGAGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt     >  1:431955‑M1/1‑73 (MQ=255)                                                                              aTACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc  >  1:336510‑M1/1‑70 (MQ=255)                                                                                       |                                                                                 TACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATAC  >  NZ_CP009273/1972605‑1972771

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑