Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,758,726	G→C	A1062P (GCC→CCC)	rhsA →	RHS element protein RhsA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,758,726	0	G	C	97.5%	113.9 / ‑3.8	40	A1062P (GCC→CCC)	rhsA	RHS element protein RhsA
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base C (25/14);  total (26/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.93e-01

CGGCTGACCACAATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGT  >  NZ_CP009273/3758639‑3758806                                                                                        |                                                                                 cGGCTGACCACAATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACcccc                                                                                <  1:308424/90‑1 (MQ=255)        ccACAATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTg                                                                         <  2:1026360/90‑1 (MQ=255)                cAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCg                                                                 >  2:776029/1‑90 (MQ=18)                  gAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGaa                                                               >  1:1009097/1‑90 (MQ=18)                  gAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGaa                                                               >  1:859031/1‑90 (MQ=18)                  gAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGaa                                                               >  1:60039/1‑90 (MQ=18)                  gAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACAGGTGAGCTGGCGaa                                                               <  2:529135/90‑1 (MQ=255)                     cGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAAc                                                            <  2:961929/90‑1 (MQ=18)                     cGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAAc                                                            >  1:786075/1‑90 (MQ=18)                     cGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAAc                                                            >  1:512848/1‑90 (MQ=18)                       aCAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGc                                                          >  1:47424/1‑90 (MQ=18)                       aCAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGc                                                          >  2:794712/1‑90 (MQ=18)                       aCAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGc                                                          >  1:971309/1‑90 (MQ=18)                       aCAGAACCCGCATCCAGACGATTTATCAGCCGAGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGc                                                          <  1:31796/90‑1 (MQ=11)                            aCCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTTGCGAAAACGCAgcgc                                                     >  1:604227/1‑90 (MQ=255)                              ccGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGcgccg                                                   <  2:197110/90‑1 (MQ=18)                               cGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGcgccgc                                                  <  1:271427/90‑1 (MQ=18)                                gCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCa                                                 >  1:24585/1‑90 (MQ=18)                                 cATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGAGCCGCAg                                                >  2:579002/1‑90 (MQ=255)                                    ccAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCt                                             >  1:548153/1‑90 (MQ=18)                                           aTTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGAt                                      >  1:731512/1‑90 (MQ=25)                                             ttATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGTCGAAAACGCAGCGCCGCAGCCTGGCGGATgc                                    >  1:706622/1‑90 (MQ=255)                                             ttATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATgc                                    <  1:601744/90‑1 (MQ=37)                                                   gCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTca                              >  1:866062/1‑90 (MQ=255)                                                     cGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGAt                                      <  2:1072276/80‑1 (MQ=21)                                                     cGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGAt                                      >  1:1072276/1‑80 (MQ=19)                                                        ggAGCTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGt                         >  1:902948/1‑90 (MQ=255)                                                            cTTCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCcgg                     <  2:937132/90‑1 (MQ=255)                                                             ttCACGCCACTCATCAGAGTTGAAACCGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCcggc                    >  1:787888/1‑90 (MQ=255)                                                              tCACGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGAGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCcggcg                   <  1:579002/90‑1 (MQ=255)                                                                 cGCCACTCATCAGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGgcggcg                >  1:359207/1‑90 (MQ=255)                                                                        catcaGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACgg         >  1:627754/1‑90 (MQ=255)                                                                         atcaGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGt        <  2:24585/90‑1 (MQ=255)                                                                         atcaGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGt        <  2:786075/90‑1 (MQ=255)                                                                         atcaGAGTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGt        <  2:512848/90‑1 (MQ=255)                                                                             gagTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCa    >  1:422544/1‑90 (MQ=255)                                                                               gTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAgt  >  2:785709/1‑90 (MQ=255)                                                                               gTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAgt  >  1:940975/1‑90 (MQ=255)                                                                               gTTGAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAgc  >  2:808618/1‑89 (MQ=255)                                                                                  gAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGa               >  2:1008705/1‑74 (MQ=255)                                                                                  gAAACCCCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGa               <  1:1008705/74‑1 (MQ=255)                                                                                        |                                                                                 CGGCTGACCACAATACAGAACGACAGAACCCGCATCCAGACGATTTATCAGCCGGGGAGCTTCACGCCACTCATCAGAGTTGAAACCGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATGCGCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGT  >  NZ_CP009273/3758639‑3758806

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑