Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,607,944	C→T	11.3%	R209Q (CGG→CAG)	rsuA ←	16S rRNA pseudouridine(516) synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,607,944	0	C	T	11.3%	112.0 / 5.9	44	R209Q (CGG→CAG)	rsuA	16S rRNA pseudouridine(516) synthase
Reads supporting (aligned to +/- strand):  ref base C (19/20);  new base T (3/2);  total (22/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.93e-01

GATCGCGCAAGTGCCGTTCGGTAAGTAATGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATCGCCAGCCGGGCTCGGTGGGGGCCGAGGATGTCCAGCTGGGCAGGTTGGGT  >  NC_002947/1607796‑1608089                                                                                                                                                     |                                                                                                                                                  gATCGCGCAAGTGCCGTTCGGTAAGTAATGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGcc                                                                                                                                                   >  3:196346/1‑149 (MQ=255)     gcgcAAGTGCCGTTCGGTAAGTAATGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGAt                                                                                                                                               >  8:40546/1‑149 (MQ=255)     gcgcAAGTGCCGTTCGGTAAGTAATGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTACCCCGGCGCCAACCCCGGATCCAGCCGGAt                                                                                                                                               >  1:96008/1‑149 (MQ=255)      cgcAAGTGCCGTTCGGTAAGTAATGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATc                                                                                                                                              <  1:264584/149‑1 (MQ=255)         aaGTGCCGTTCGGTAAGTAATGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGcc                                                                                                                                           <  7:40546/149‑1 (MQ=255)            tGCCGTTCGGTAAGTAATGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCGGCTGGATccggg                                                                                                                                          >  4:265059/1‑143 (MQ=255)            tGCCGTTCGGTAAGTAATGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCGGCTGGATccggg                                                                                                                                          <  3:265059/147‑5 (MQ=255)            tGCCGTTCGGTAAGTAATGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGcc                                                                                                                                                   >  1:24600/1‑138 (MQ=255)            tGCCGTTCGGTAAGTAATGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGcc                                                                                                                                                   <  2:24600/138‑1 (MQ=255)              ccGTTCGGTAAGTAATGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCa                                                                                                                                       <  6:227038/148‑1 (MQ=255)                   cGGTAAGTAATGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGctct                                                                                                                                 >  5:231891/1‑149 (MQ=255)                     gtaagtaaTGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCGGCTGGATccggg                                                                                                                                          <  4:216151/138‑5 (MQ=255)                     gtaagtaaTGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCGGCTGGATccggg                                                                                                                                          >  3:216151/1‑134 (MQ=255)                        agtaaTGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGa                                                                                                                            <  5:109246/149‑1 (MQ=255)                          taaTGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATg                                                                                                                          <  6:231891/149‑1 (MQ=255)                            aTGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGc                                                                                                                         <  1:15283/148‑1 (MQ=255)                                gACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCACCCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCCGccc                                                                                                                    >  2:221674/1‑149 (MQ=255)                                              aGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCttgttg                                                                                                       <  2:97222/148‑1 (MQ=255)                                                       aTGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGcc                                                                                             >  3:42315/1‑149 (MQ=255)                                                        tGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACACCGGAACCAACCGGATCGCCCCCAAGCTCTCCAGAAGAAGCCCGATCAACATGTTGTTGAAATGc                                                                                              >  2:275070/1‑147 (MQ=255)                                                        tGACGACACGGGCTGGCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGcc                                                                                             <  8:106669/148‑1 (MQ=255)                                                            gacACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGcc                                                                                             <  3:294070/144‑1 (MQ=255)                                                            gacACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGcc                                                                                             >  4:294070/1‑144 (MQ=255)                                                                             aCGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCtggt                                                                        >  6:208866/1‑148 (MQ=255)                                                                             aCGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCtggt                                                                        <  5:208866/148‑1 (MQ=255)                                                                             aCGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGAACtggtg                                                                       >  3:164476/1‑149 (MQ=255)                                                                               ggCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTggtggt                                                                     <  4:196346/149‑1 (MQ=255)                                                                                 ccTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGaa                                                                                         <  7:18829/127‑1 (MQ=255)                                                                                 ccTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGaa                                                                                         >  8:18829/1‑127 (MQ=255)                                                                                          tGGCTATCTCATTGGCCGTCATTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCTATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTcg                                                          <  2:96008/149‑1 (MQ=255)                                                                                                tctcATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATc                                                    >  1:44171/1‑149 (MQ=255)                                                                                                tctcATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATc                                                    >  7:6514/1‑149 (MQ=255)                                                                                                                   aCGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATCGCCAGCCGGGCTCGGTggg                                 <  4:42315/149‑1 (MQ=255)                                                                                                                            ccccGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATCGCCAGCCGGGCTCGGTGGGGGCCGAGGa                        >  1:169083/1‑149 (MQ=255)                                                                                                                              ccGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATCGCCAGCCGGGCTCGGTGGGGGCCGAGGATg                      <  4:164476/149‑1 (MQ=255)                                                                                                                                ggCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATCGCCAGCCGGGCTCGGTGGGGGCCGAGGATGTc                    <  2:44171/149‑1 (MQ=255)                                                                                                                                 gcgcCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATCGCCAGCCGGGCTCGGTGGGGGCCGAGGATGTcc                   <  8:6514/149‑1 (MQ=255)                                                                                                                                   gcCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCATCGACGATCGCCAGCCGGGGCGGGTGGGGGACGAGGATGTCCAg                 >  6:187576/1‑149 (MQ=255)                                                                                                                                    ccAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATCGCCAGCCGGGCTCGGTGGGGGCCGAGGATGTCCAGc                >  4:136893/1‑149 (MQ=255)                                                                                                                                          ggcgATCCGGCTGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATCGCCAGCCGGGCTCGGTGGGGGCCGAGGATGTCCAGCTggg            >  8:40362/4‑147 (MQ=255)                                                                                                                                           cGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAAc                                                                                        >  5:264643/1‑70 (MQ=255)                                                                                                                                           cGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAAc                                                                                        <  6:264643/70‑1 (MQ=255)                                                                                                                                              aTCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATCGCCAGCCGGGCTCGGTGGGGGCCGAGGATGTCCAGCTGGGCAGGtt      <  2:152434/149‑1 (MQ=255)                                                                                                                                                 cAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATCGCCAGCCGGGCTCGGTGGGGGCCGAgg                         <  4:146729/127‑1 (MQ=255)                                                                                                                                                 cAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATCGCCAGCCGGGCTCGGTGGGGGCCGAgg                         >  3:146729/1‑127 (MQ=255)                                                                                                                                                  aGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATCGCCAGCCGGGCTCGGTGGGGGCGGAGGATGTCCAGCTGGGCAGGTTGggt  >  5:164299/1‑149 (MQ=255)                                                                                                                                                  aGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATCGCCAGCCGGGCTCGGTGGGGGCCGAGGATGTCCAGCTGGGCAGGTTGggt  >  7:100020/1‑149 (MQ=255)                                                                                                                                                    ccGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATCGCCAGCCGGGCTCGGTGGGGGCCGAGGATGTCCAGCTGGGCAGGTTGggt  >  4:71243/1‑147 (MQ=255)                                                                                                                                                    ccGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATCGCCAGCCGGGCTCGGTGGGGGCCGAGGATGTCCAGCTGGGCAGGTTGggt  <  3:71243/147‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                  GATCGCGCAAGTGCCGTTCGGTAAGTAATGTGACTTTTGTCGCTGAGCGGTCGTATGACGACACGGGCTGTCTGTCACGGCCTAGACAGTGGCTATCTCATTGGCCGTCAGTTCACGATACTCCCCCGGCGCCAACCCCGGATCCAGCCGGATCGCCCCCATGCTCTCCCGATGCAGCCCGATCACCTTGTTGTTGAAATGCCCGAACATGCGCTTGACCTGGTGGTAACGCCCCTCGACGATCGCCAGCCGGGCTCGGTGGGGGCCGAGGATGTCCAGCTGGGCAGGTTGGGT  >  NC_002947/1607796‑1608089

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: ‑