Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,215,724	T→G	W657G (TGG→GGG)	metH →	methionine synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,215,724	0	T	G	96.2%	167.2 / ‑1.3	53	W657G (TGG→GGG)	metH	methionine synthase
Reads supporting (aligned to +/- strand):  ref base T (0/2);  new base G (14/37);  total (14/39)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.13e-01

CGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGC  >  NZ_CP009273/4215639‑4215808                                                                                      |                                                                                     ctaGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGa                                                                                  <  1:1003724/88‑1 (MQ=255)  gAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGaa                                                                                 >  1:1016464/1‑90 (MQ=255)   aGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAg                                                                                <  2:937823/90‑1 (MQ=255)   aGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAg                                                                                <  2:287087/90‑1 (MQ=255)   aGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAg                                                                                <  1:908397/90‑1 (MQ=255)          aCTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATaa                                                                         <  1:1429786/90‑1 (MQ=255)          aCTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATaa                                                                         <  2:1527095/90‑1 (MQ=255)           cTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATaaa                                                                        <  1:1555434/90‑1 (MQ=255)            tGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAAc                                                                       >  1:762445/1‑90 (MQ=255)             ggAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACg                                                                      >  2:959862/1‑90 (MQ=255)              gAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGt                                                                     >  1:24946/1‑90 (MQ=255)               aGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTc                                                                    <  2:192884/90‑1 (MQ=255)                gCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCt                                                                   <  1:1122119/90‑1 (MQ=255)                 cTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTg                                                                  <  2:970193/90‑1 (MQ=255)                 cTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTg                                                                  >  2:926914/1‑90 (MQ=255)                   tGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAg                                                                                >  2:895032/1‑74 (MQ=255)                   tGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAg                                                                                <  1:895032/74‑1 (MQ=255)                   tGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGa                                                                >  2:570228/1‑90 (MQ=255)                           aaTATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGc                                                        <  1:380038/90‑1 (MQ=255)                           aaTATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGc                                                        <  1:836089/90‑1 (MQ=255)                           aaTATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGc                                                        <  1:693984/90‑1 (MQ=255)                           aaTATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGc                                                        <  1:823139/90‑1 (MQ=255)                            atatCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCt                                                       <  1:281131/90‑1 (MQ=255)                              atCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTgg                                                     <  2:1330064/90‑1 (MQ=255)                                 gcgGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCa                                                  <  2:1437071/90‑1 (MQ=255)                                 gcgGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCa                                                  <  2:918536/90‑1 (MQ=255)                                   ggCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCaaa                                                <  2:445732/90‑1 (MQ=255)                                      agcaAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGc                                             <  1:942779/90‑1 (MQ=255)                                                 cgacACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGtt                                  <  1:694772/90‑1 (MQ=255)                                                      ccGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGTGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCg                             <  2:1195758/90‑1 (MQ=255)                                                      ccGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCg                             <  2:767480/90‑1 (MQ=255)                                                      ccGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCg                             >  1:1090413/1‑90 (MQ=255)                                                        gCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAg                           >  1:833185/1‑90 (MQ=255)                                                         ccAAGGCACAGCCGGCGGAGTGGGGCTCGGGGGAAGTGAAAAAACGTCTGGAAAACTCGCTGGTCAAAGGGATTACCGAGTTTATCGAGc                          <  1:1409554/90‑1 (MQ=255)                                                         ccAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGc                          <  2:24946/90‑1 (MQ=255)                                                         ccAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGc                          <  2:1090413/90‑1 (MQ=255)                                                         ccAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGc                          <  2:448713/90‑1 (MQ=255)                                                         ccAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGc                          <  2:471033/90‑1 (MQ=255)                                                         ccAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGc                          <  2:471034/90‑1 (MQ=255)                                                         ccAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGc                          <  1:855343/90‑1 (MQ=255)                                                         ccAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGc                          <  1:536486/90‑1 (MQ=255)                                                         ccAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGc                          <  1:1545166/90‑1 (MQ=255)                                                           aaCGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAg                        <  2:1181730/90‑1 (MQ=255)                                                           aaCGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAg                        <  1:1520405/90‑1 (MQ=255)                                                           aaCGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAg                        <  2:928166/90‑1 (MQ=255)                                                                ccAGCAGGCGGAGTGGCGCTCCGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATAc                   >  1:695431/1‑90 (MQ=255)                                                                   gcagGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCga                >  2:754807/1‑90 (MQ=255)                                                                       gCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCgaagaa            >  1:184221/1‑90 (MQ=255)                                                                         ggAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGc          >  1:1551530/1‑90 (MQ=255)                                                                           aGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGccc        <  2:481049/90‑1 (MQ=255)                                                                             tGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGc      >  2:705113/1‑90 (MQ=255)                                                                                 gcTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCcagc  <  1:705113/90‑1 (MQ=255)                                                                                 gcTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCcagc  <  2:878032/90‑1 (MQ=255)                                                                                      |                                                                                     CGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGC  >  NZ_CP009273/4215639‑4215808

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑