Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,652,972	T→C	10.8%	intergenic (‑73/+88)	PP_4961 ← / ← PP_4962	lipoprotein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,652,972	0	T	C	10.8%	113.4 / 4.9	47	intergenic (‑73/+88)	PP_4961/PP_4962	lipoprotein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (18/23);  new base C (2/3);  total (20/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.66e-01

CGGTTGCGCCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCTTCGTCGTACTTTTCCAGGCCTTCCG  >  NC_002947/5652828‑5653118                                                                                                                                                 |                                                                                                                                                   cGGTTGTGCCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCtgt                                                                                                                                                <  3:269944/149‑1 (MQ=255)   gTTGCGCCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTgg                                                                                                                                              >  4:104987/1‑149 (MQ=255)       cgcCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGc                                                                                                                                          <  6:39639/149‑1 (MQ=255)        gcCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCGCGGGCTCGCCCGCTCCCACAGAGACTGCACTGTACCTGTGGGAGCg                                                                                                                                         >  4:267508/1‑149 (MQ=25)         ccGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCgg                                                                                                                                        <  8:27666/149‑1 (MQ=255)           ggCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGAGACTGCACTGTACCTGTGGGAGCGGGc                                                                                                                                      <  3:323120/149‑1 (MQ=25)             cTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGa                                                                                                                                    <  3:140437/149‑1 (MQ=255)               gcagcaGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCATTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGc                                                                                                                                  >  8:73026/1‑149 (MQ=255)                cagcagTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCGCGGGCTCGCCCGCTCCCACAGAGACTGCACTGTACCTGTGGGAGCGGGCGAg                                                                                                                                   <  3:267508/147‑1 (MQ=21)                   cagTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCtgt                                                                                                                                                <  1:106294/131‑1 (MQ=255)                   cagTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCtgt                                                                                                                                                >  2:106294/1‑131 (MQ=255)                     gTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGAGACTGCACTGTACCTGTGGGAGCGGGCGa                                                                                                                                    >  3:216815/1‑141 (MQ=21)                     gTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGAGACTGCACTGTACCTGTGGGAGCGGGCGa                                                                                                                                    <  4:216815/141‑1 (MQ=21)                               tGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGcac                                                                                                                  >  1:307329/1‑149 (MQ=255)                                     tgtCGCCCGGGCCGTCACGCCAAAAAGCGCTTTCATTCAGTTTCCTCTATTTGGGGCTGCTGTCCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGGGGGCGAGCCCGCGAAGGGCCGCACAGCgg                                                                                                             <  2:90036/148‑1 (MQ=38)                                      gtCGCCAGGGCCGTCACGGCAAAAAGCGCTTTCTTTCCGTTTCCTGGTTTTGGGGCTGCTGTGCCGCCTTTCTCGGGCTCCCCCGCTCCCACAGGTACTGTGCAGTCTGTGTGGGAGGGGGCGAGCCCGCGAAGGGCCGCACAGCGGc                                                                                                            <  2:93832/148‑1 (MQ=255)                                          ccAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTGCTCGGGCGCGCCCGCTCCCCCCGGTCCAGTGCAGTCTCTGGGGGAGCGGGCGAGCCCGCGAAGGGCCGCTGTGCGGcccttc                                                                                                       <  3:28901/149‑4 (MQ=255)                                              ggCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGTTTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTGGCCCGATCCCACAGTTACAGTGAATTCTCTGTGGGAGCGGGCTAGCCCGCGAAGGGCCGCACAGCGGCCCcttct                                                                                                     <  8:258759/147‑1 (MQ=38)                                               gCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACCGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCa                                                                                                  <  6:166914/149‑1 (MQ=255)                                                  gTCCCGGCCAAACGCGCTTTCATTCTGTTTCCTCTTTTTGGGGCTGCGGGGCAGCCCTTCTCGGGCGCCCCCGCTCCCCCAGTTACTGTGCAGTCTCTGGGGTTGGGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGa                                                                                               <  2:307329/149‑1 (MQ=255)                                                      cGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGc                                                                                                                       >  7:141815/1‑121 (MQ=255)                                                             aaGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACCGCGGCCCCTTCTTCAAGCCCCCAAAACaa                                                                                    >  4:29152/1‑149 (MQ=255)                                                                   tttCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGtt                                                                                >  4:150240/1‑147 (MQ=255)                                                                           aGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCt                                                                      <  3:104987/149‑1 (MQ=255)                                                                                         ggggCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAg                                                                                                                          >  4:214454/1‑83 (MQ=255)                                                                                         ggggCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAg                                                                                                                          <  3:214454/83‑1 (MQ=255)                                                                                          gggCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAg                                                        <  3:150240/148‑1 (MQ=255)                                                                                          gggCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAg                                                        <  7:73026/148‑1 (MQ=255)                                                                                                ctgTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTAtt                                                                   <  8:156871/131‑1 (MQ=255)                                                                                                ctgTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTAtt                                                                   >  7:156871/1‑131 (MQ=255)                                                                                                    gctgCCCTTCTCGGGCGCGCCCGCTCCCACTGGTCCTGTCCAGTCGCTGTGGGAGGGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTAt                                                                    <  6:291175/123‑1 (MQ=255)                                                                                                       gCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGcc                                          >  8:272781/1‑149 (MQ=255)                                                                                                              tcGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAgg                                                       <  3:313124/129‑1 (MQ=255)                                                                                                              tcGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAgg                                                       >  4:313124/1‑129 (MQ=255)                                                                                                               cGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCtg                                  >  8:144890/1‑149 (MQ=255)                                                                                                                       cccGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCtggt                                <  3:39739/143‑1 (MQ=255)                                                                                                                       cccGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCtggt                                >  4:39739/1‑143 (MQ=255)                                                                                                                        ccGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCTtc                         >  6:316956/1‑149 (MQ=255)                                                                                                                           cTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCTtcgtc                      <  7:272781/149‑1 (MQ=255)                                                                                                                               cacaGGTACAGTGCAGTCTCTGTGGGAGCGGGAGAGCCCGCGAAGGGCCGCACAGCGGCCCCGTCTTCAAGACCACAAATAAACGTTCAGGTTGCCTATTAACCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCGTCGGCGTAc                  >  8:164638/1‑149 (MQ=255)                                                                                                                                  aGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAAc                                                                                   <  5:239077/81‑1 (MQ=255)                                                                                                                                  aGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAAc                                                                                   >  6:239077/1‑81 (MQ=255)                                                                                                                                  aGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCTTCGTCGTACttt               >  2:65674/1‑149 (MQ=255)                                                                                                                                       cAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCTTCGTCGTACTTTTCCAg          <  7:144890/149‑1 (MQ=255)                                                                                                                                          tGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCt                                                                      <  6:156780/86‑1 (MQ=255)                                                                                                                                             aGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAg                                                        <  1:215143/97‑1 (MQ=255)                                                                                                                                             aGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAg                                                        >  2:215143/1‑97 (MQ=255)                                                                                                                                               actctGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCTTCGTCGTACTTTTCCAGGCCTTCCg  <  4:321998/148‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                   CGGTTGCGCCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCTTCGTCGTACTTTTCCAGGCCTTCCG  >  NC_002947/5652828‑5653118

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑