Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,158,702:1	+G	9.3%	coding (721/2097 nt)	opuA →	glycine betaine ABC transporter ATP‑binding protein/permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,158,702	1	.	G	9.3%	157.6 / 12.1	43	coding (721/2097 nt)	opuA	glycine betaine ABC transporter ATP‑binding protein/permease
Reads supporting (aligned to +/- strand):  ref base . (21/18);  new base G (2/2);  total (23/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.88e-01

CTGACATTCTGCTGATGGACGAACCCTTCAGTGCACTGGATCCCACCATCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGCGGCCGCATATCGGCCCGAGCATTGCGTCGTCTA  >  NC_002947/3158562‑3158849                                                                                                                                               |                                                                                                                                                    cTGACATTCTGCTGATGGACGAACCCTTCAGTGCACTGGATCCCACCATCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGc                                                                                                                                              <  3:304140/148‑1 (MQ=255)          tgctgATGGACGAACCCTTCAGTGCACTGGATCCCACCATCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATc                                                                                                                                    >  2:99268/1‑149 (MQ=255)           gctgATGGACGAACCCTTCAGTGCACTGGATCCCACCATCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCg                                                                                                                                   >  5:73980/1‑149 (MQ=255)                tGGACGAACCCTTCAGTGCACTGGATCCCACCATCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTc                                                                                                                              <  6:238624/149‑1 (MQ=255)                 ggACGAACCCTTCAGTGCACTGGATCCCACCATCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCt                                                                                                                             >  6:695/1‑149 (MQ=255)                  taCGAACCCTTCAGTGCACTGGATCCCAGCATCCGCCTCGATTTGAAGGGGCGATTCCTGCAACTGGGGCGCGAACGTGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGATACGGTCTGCCAGA‑CGTAACGcctcac                                                                                                                             <  6:18816/147‑5 (MQ=255)                  gACGAACCCTTCAGTGCACTGGATCCCACCATCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCtt                                                                                                                            <  4:293444/149‑1 (MQ=255)                  gACGAACCCTTCAGTGCACTGGATCCCACCATCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCtt                                                                                                                            >  7:197341/1‑149 (MQ=255)                    cGAACCCTTCAGTGCACTGGATCCCACCATCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTgc                                                                                                                          >  5:311595/1‑149 (MQ=255)                     gAACCCTTCAGTGCACTGGATCCCACCATCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTgcg                                                                                                                         <  6:83107/149‑1 (MQ=255)                                tGCACTGGATCCCACCATCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGc                                                                                                              <  1:99268/149‑1 (MQ=255)                                   aCTGGATCCCACCATCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGa                                                                                                           <  8:197341/149‑1 (MQ=255)                                            caccaTCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCg                                                                                                  >  8:282962/1‑149 (MQ=255)                                                     ccgcGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTc                                                                                                        <  6:71290/134‑1 (MQ=255)                                                     ccgcGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTc                                                                                                        >  5:71290/1‑134 (MQ=255)                                                               cAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGc                                                                                <  7:282962/148‑1 (MQ=255)                                                                  gggCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTg                                                                             >  2:139946/1‑148 (MQ=255)                                                                    gCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGaa                                                                           >  1:42184/1‑148 (MQ=255)                                                                           cTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCcggc                                                                   >  1:64131/1‑149 (MQ=255)                                                                           cTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCcgg                                                                    <  6:311595/148‑1 (MQ=255)                                                                                      gcgcGAACGGGGAATCACGACGCTGCGTAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCggtg                                                                                                                    >  1:166129/1‑90 (MQ=255)                                                                                      gcgcGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCggtg                                                                                                                    <  2:166129/89‑1 (MQ=255)                                                                                                 gAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTttc                                             >  8:97536/1‑149 (MQ=255)                                                                                                 gAATCACGACGCTGC‑TAGTGACCCACGACACGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTttc                                             >  7:143901/1‑149 (MQ=255)                                                                                                    tCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTttcttc                                          <  1:126729/149‑1 (MQ=255)                                                                                                     cACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAg                                                           <  1:251081/131‑1 (MQ=255)                                                                                                     cACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAg                                                           >  2:251081/1‑131 (MQ=255)                                                                                                     cACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTttcttc                                          >  3:9012/1‑148 (MQ=255)                                                                                                       cgacgCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTcgac                                       <  7:97536/149‑1 (MQ=255)                                                                                                       cgacgCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTcgac                                       <  6:73980/149‑1 (MQ=255)                                                                                                             tgc‑tAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGCgg                                 >  3:240864/1‑149 (MQ=255)                                                                                                                      aCCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTcg                                         <  3:250998/133‑1 (MQ=255)                                                                                                                      aCCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTcg                                         >  4:250998/1‑133 (MQ=255)                                                                                                                        ccACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGCGGCCGCATATCg                       <  5:147970/149‑1 (MQ=255)                                                                                                                        ccACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGCGGCCGCATATCg                       >  5:266952/1‑149 (MQ=255)                                                                                                                         cACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGc                                   <  3:227945/136‑1 (MQ=255)                                                                                                                         cACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGc                                   >  4:227945/1‑136 (MQ=255)                                                                                                                                 gggTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACTCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGCGGCCGCATATCGGCCCGAGCa              >  4:140218/1‑149 (MQ=255)                                                                                                                                  aagacggCGATACGGTCTGCCAGA‑CGTAACGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGCGGCCGCATATCGGCCCGAGCAt             >  2:317574/6‑149 (MQ=255)                                                                                                                                   gTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGCGGCCGCATATCGGCCCGAGCAtt            <  2:42184/149‑1 (MQ=255)                                                                                                                                    gacggCGATACGGTCTGCCAGA‑CGTAACGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTttc                                             <  6:141104/112‑1 (MQ=38)                                                                                                                                    gacggCGATACGGTCTGCCAGA‑CGTAACGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTttc                                             >  5:141104/4‑115 (MQ=38)                                                                                                                                      aGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGCGGCCGCATATCGGCCCGAGCATTGcg         >  3:283939/1‑149 (MQ=255)                                                                                                                                              c‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGCGGCCGCATATCGGCCCGAGCATTGCGTCGTCTa  <  5:695/148‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                    CTGACATTCTGCTGATGGACGAACCCTTCAGTGCACTGGATCCCACCATCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGCGGCCGCATATCGGCCCGAGCATTGCGTCGTCTA  >  NC_002947/3158562‑3158849

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑