Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,402,000	A→G	I18T (ATC→ACC)	dgcM ←	diguanylate cyclase DgcM

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,402,000	0	A	G	95.3%	126.0 / ‑0.6	43	I18T (ATC→ACC)	dgcM	diguanylate cyclase DgcM
Reads supporting (aligned to +/- strand):  ref base A (0/2);  new base G (15/26);  total (15/28)
Fisher's exact test for biased strand distribution p-value = 5.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.33e-01

GTTCGTAGCTGACTAAACGTGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGATCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGTAATCATTGAGATCCCGTTATTTTTATCAATTTTT  >  NZ_CP009273/1401913‑1402080                                                                                        |                                                                                 gTTCGTAGCTGACTAAACGTGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTc                                                                                <  1:296628/90‑1 (MQ=255) gTTCGTAGCTGACTAAACGTGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTc                                                                                <  1:204668/90‑1 (MQ=255)   tCGTAGCTGACTAAACGTGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCa                                                                              >  1:132910/1‑90 (MQ=255)      tAGCTGACTAAACGTGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGAc                                                                           <  1:1183270/90‑1 (MQ=255)      tAGCTGACTAAACGTGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGAc                                                                           <  2:1443137/90‑1 (MQ=255)      tAGCTGACTAAACGTGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGAc                                                                           <  1:1564698/90‑1 (MQ=255)           gACTAAACGTGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGAc                                                                      >  1:888941/1‑90 (MQ=255)           gACTAAACGTGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGAc                                                                      >  2:1248116/1‑90 (MQ=255)           gACTAAACGTGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGAc                                                                      >  1:107108/1‑90 (MQ=255)           gACTAAACGTGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGAc                                                                      >  2:883328/1‑90 (MQ=255)            aCTAAACGTGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTATCTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACt                                                                     <  1:1085359/90‑1 (MQ=255)              tAAACGTGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTgg                                                                   <  1:1146574/90‑1 (MQ=255)                   gTGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGt                                                              <  2:1319411/90‑1 (MQ=255)                    tGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTa                                                             <  2:1376360/90‑1 (MQ=255)                    tGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTa                                                             <  2:1524787/90‑1 (MQ=255)                    tGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTa                                                             <  2:1089515/90‑1 (MQ=255)                    tGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTa                                                             <  1:914620/90‑1 (MQ=255)                     gAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTaa                                                            >  2:943124/1‑90 (MQ=255)                           ttGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAg                                                      <  2:77623/90‑1 (MQ=255)                           ttGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAg                                                      <  2:1006214/90‑1 (MQ=255)                           ttGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAg                                                      <  2:810457/90‑1 (MQ=255)                           ttGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAg                                                      <  2:321398/90‑1 (MQ=255)                           ttGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAg                                                      <  2:1551156/90‑1 (MQ=255)                           ttGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAg                                                      <  1:1330900/90‑1 (MQ=255)                              cATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGATCCAGACAGGACTGGTGAGTAAGTCCAGGGt                                                   <  1:496796/90‑1 (MQ=255)                                 cAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGAc                                                                           <  2:484961/63‑1 (MQ=255)                                 cAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGAc                                                                           >  1:484961/1‑63 (MQ=255)                                        ttCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTtg                                         >  1:1456170/1‑90 (MQ=255)                                             cgcgCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGt                                    <  2:884785/90‑1 (MQ=255)                                             cgcgCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGt                                    <  2:1010264/90‑1 (MQ=255)                                              gcgcTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGTa                                   >  1:657341/1‑90 (MQ=255)                                               cgcTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGATCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGTaa                                  <  2:1108865/90‑1 (MQ=255)                                                gcTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGTAAt                                 <  1:125465/90‑1 (MQ=255)                                                gcTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGTAAt                                 >  2:125465/1‑90 (MQ=255)                                                      ggCATAAATTAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGTAATCATTga                           <  1:1248116/90‑1 (MQ=255)                                                              ttAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGTAATCATTGAGATCCCGt                   <  1:1578690/90‑1 (MQ=255)                                                              ttAACTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGTAATCATTGAGATCCCGt                   <  2:657341/90‑1 (MQ=255)                                                                aaCTGTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGTAATCATTGAGATCCCGTTa                 >  2:1439534/1‑90 (MQ=255)                                                                    gTTCCTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGTAATCATTGAGATCCCGTTAtttt             >  1:1241467/1‑90 (MQ=255)                                                                       ccTCAAAGGGCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGTAATCATTGAGATCCCGTTATTTTTAt          >  2:711088/1‑90 (MQ=255)                                                                              gggCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGTAATCATTgaga                         <  2:607955/68‑1 (MQ=255)                                                                              gggCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGTAATCATTgaga                         >  1:607955/1‑68 (MQ=255)                                                                               ggCGAAACGGTCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGTAATCATTGAGATCCCGTTATTTTTATCAAttttt  >  2:1033052/1‑90 (MQ=255)                                                                                        |                                                                                 GTTCGTAGCTGACTAAACGTGAGGTCTTGCATCAACAGTTTCGCCGCGCTATTGGCATAAATTAACTGTTCCTCAAAGGGCGAAACGATCCAGACAGGACTGGTGAGTAAGTCCAGGGTATTGAAGTTGTGCGTAATCATTGAGATCCCGTTATTTTTATCAATTTTT  >  NZ_CP009273/1401913‑1402080

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑