Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,713,202	A→G	intergenic (+74/‑207)	yiaG → / → cspA	HTH‑type transcriptional regulator/RNA chaperone/antiterminator CspA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,713,202	0	A	G	76.9%	42.5 / 0.5	26	intergenic (+74/‑207)	yiaG/cspA	HTH‑type transcriptional regulator/RNA chaperone/antiterminator CspA
Reads supporting (aligned to +/- strand):  ref base A (0/6);  new base G (13/7);  total (13/13)
Fisher's exact test for biased strand distribution p-value = 1.49e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAATAGACTTTTATCCACTTTATTGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGAAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTAAAGCAGTGTAGTA  >  NZ_CP009273/3713123‑3713285                                                                                |                                                                                    gAATAGACTTTTATCCACTTTATTGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAAttg                                                                           >  2:73743/1‑90 (MQ=255)  aaTAGACTTTTATCCACTTTATTGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAAttgt                                                                          >  1:119439/1‑90 (MQ=255)                      aTTGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGt                                                      <  1:3215/90‑1 (MQ=255)                           tGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCtt                                                 >  1:444903/1‑90 (MQ=255)                            gTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTgg                                                    <  1:325560/86‑1 (MQ=255)                            gTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTgg                                                    >  2:325560/1‑86 (MQ=255)                                      cTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCa                                      >  1:322466/1‑90 (MQ=255)                                      cTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCa                                      >  2:399441/1‑90 (MQ=255)                                        gatgaCAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAAc                                    >  1:372964/1‑90 (MQ=255)                                            aCAGGACCGTTTTCCACCCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGtt                                <  1:297767/90‑1 (MQ=255)                                             cAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGttt                               >  1:398964/1‑90 (MQ=255)                                             cAGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGttt                               >  2:107831/1‑90 (MQ=255)                                              aGGACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCCCCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTg                              <  1:74508/90‑1 (MQ=255)                                               ggACCTTTTTCCAACCGATTAATCAAAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGa                             <  2:76322/90‑1 (MQ=255)                                               ggACCGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGa                             >  2:294756/1‑90 (MQ=255)                                                  ccGTTTTCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGt                          >  1:167266/1‑90 (MQ=255)                                                    tttttCCAACCGATTAATCATAAATATGAAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTAc                        <  1:451465/89‑1 (MQ=255)                                                    tttttCCAACCGATTAATCAAAAATATGAAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTAc                        <  2:192361/89‑1 (MQ=255)                                                       ttCCAACCGATTAATCATAAATATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGa                     >  2:168911/1‑90 (MQ=255)                                                       ttCCAACCGATTAATCATAAATATGAAAAATAATTGTTGCACCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGa                     <  2:448432/90‑1 (MQ=255)                                                               gATAAATCATAAATATGAAAAATAATTTTTGCACCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTaaa             <  2:372964/90‑1 (MQ=255)                                                                 ttAATCATAAATATGAAAAATATTTGTTGCATCCCCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTAAAGc           <  2:337521/90‑1 (MQ=255)                                                                   aaTCATAAATATGGAAAATAATTGTTGCATCACACGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTAAAGCAg         <  1:450468/90‑1 (MQ=255)                                                                          aaTATGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTAAAGCAGTgtagta  >  2:133056/1‑90 (MQ=255)                                                                          aaTATGAAAAATAATTGTTGCATCCCCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTAAAGCAGTgtagta  <  2:453377/90‑1 (MQ=255)                                                                             atGGAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTg                              <  1:122457/59‑1 (MQ=255)                                                                                |                                                                                    GAATAGACTTTTATCCACTTTATTGCTGTTTACGGTCCTGATGACAGGACCGTTTTCCAACCGATTAATCATAAATATGAAAAATAATTGTTGCATCACCCGCCAATGCGTGGCTTAATGCACATCAACGGTTTGACGTACAGACCATTAAAGCAGTGTAGTA  >  NZ_CP009273/3713123‑3713285

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑