Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,158,699	T→A	9.3%	L240I (TTA→ATA)	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	3,158,699	0	T	A	9.3%	118.1 / 3.6	43	L240I (TTA→ATA)	opuA	glycine betaine ABC transporter ATP‑binding protein/permease
Reads supporting (aligned to +/- strand):  ref base T (21/18);  new base A (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 = 9.27e-01

GTCACCAATCCTGACATTCTGCTGATGGACGAACCCTTCAGTGCACTGGATCCCACCATCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGCGGCCGCATATCGGCCCGAGCATTGCG  >  NC_002947/3158552‑3158842                                                                                                                                                     |                                                                                                                                                 gTCACCAATCCTGACATTCTGCTGATGGACGAACCCTTCAGTGCACTGGATCCCACCATCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGtt                                                                                                                                                 <  7:266954/149‑1 (MQ=255)           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                                <  6:73980/149‑1 (MQ=255)                                                                                                                 cgacgCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTcgac                                <  7:97536/149‑1 (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                >  5:266952/1‑149 (MQ=255)                                                                                                                                  ccACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGCGGCCGCATATCg                <  5:147970/149‑1 (MQ=255)                                                                                                                                   cACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGc                            >  4:227945/1‑136 (MQ=255)                                                                                                                                   cACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGc                            <  3:227945/136‑1 (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)                                                                                                                                                     |                                                                                                                                                 GTCACCAATCCTGACATTCTGCTGATGGACGAACCCTTCAGTGCACTGGATCCCACCATCCGCCGCGATTTGCAGGGGCGATTCCTGCAACTGGTGCGCGAACGGGGAATCACGACGCTGC‑TAGTGACCCACGACCCGGGTGAGGCGTTAC‑GTCTGGCAGACCGTATCGCCGTCTTGCGCGGTGGTCGGCTGATTCAGGTCGGCACCCCGGGTGAATTGCTTGAACACCCGGCGGACGAAGGCGTGGCGGTTTTCTTCGACGAGCGGCCGCATATCGGCCCGAGCATTGCG  >  NC_002947/3158552‑3158842

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: ‑