Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,652,963	A→T	15.7%	intergenic (‑64/+97)	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	5,652,963	0	A	T	15.7%	103.4 / 8.8	48	intergenic (‑64/+97)	PP_4961/PP_4962	lipoprotein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (18/21);  new base T (2/6);  total (20/28)
Fisher's exact test for biased strand distribution p-value = 4.37e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTCTGCCGGGGCCGGTTGCGCCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCTTCGTCGTACTTTTCCAG  >  NC_002947/5652816‑5653110                                                                                                                                                    |                                                                                                                                                    gTCTGCCGGGGCCGGTTGCGCCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGTTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACa                                                                                                                                                     <  1:333831/148‑1 (MQ=255)       cGGGGCCGGTTGCGCCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGt                                                                                                                                              <  5:263553/149‑1 (MQ=255)        ggggCCGGTTGCGCCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGtc                                                                                                                                             <  3:337641/149‑1 (MQ=255)             cGGTTGTGCCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCtgt                                                                                                                                        <  3:269944/149‑1 (MQ=255)               gTTGCGCCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTgg                                                                                                                                      >  4:104987/1‑149 (MQ=255)                   cgcCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGc                                                                                                                                  <  6:39639/149‑1 (MQ=255)                    gcCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCTGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCa                                                                                                                                                <  2:123852/134‑1 (MQ=255)                    gcCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCGGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCa                                                                                                                                                >  1:123852/1‑134 (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                                                                                                                  <  3:214454/83‑1 (MQ=255)                                                                                                     ggggCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAg                                                                                                                  >  4:214454/1‑83 (MQ=255)                                                                                                      gggCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAg                                                <  7:73026/148‑1 (MQ=255)                                                                                                      gggCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAg                                                <  3:150240/148‑1 (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                        >  4:39739/1‑143 (MQ=255)                                                                                                                                   cccGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCtggt                        <  3:39739/143‑1 (MQ=255)                                                                                                                                    ccGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCTtc                 >  6:316956/1‑149 (MQ=255)                                                                                                                                       cTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCTtcgtc              <  7:272781/149‑1 (MQ=255)                                                                                                                                           cacaGGTACAGTGCAGTCTCTGTGGGAGCGGGAGAGCCCGCGAAGGGCCGCACAGCGGCCCCGTCTTCAAGACCACAAATAAACGTTCAGGTTGCCTATTAACCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCGTCGGCGTAc          >  8:164638/1‑149 (MQ=255)                                                                                                                                              aGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAAc                                                                           >  6:239077/1‑81 (MQ=255)                                                                                                                                              aGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAAc                                                                           <  5:239077/81‑1 (MQ=255)                                                                                                                                              aGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCTTCGTCGTACttt       >  2:65674/1‑149 (MQ=255)                                                                                                                                                   cAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCTTCGTCGTACTTTTCCAg  <  7:144890/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                    GTCTGCCGGGGCCGGTTGCGCCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCTTCGTCGTACTTTTCCAG  >  NC_002947/5652816‑5653110

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: ‑