Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,652,965	T→C	10.4%	intergenic (‑66/+95)	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	5,652,965	0	T	C	10.4%	119.3 / 5.5	48	intergenic (‑66/+95)	PP_4961/PP_4962	lipoprotein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (18/25);  new base C (2/3);  total (20/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.08e-01

CGGGGCCGGTTGCGCCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCTTCGTCGTACTTTTCCAG  >  NC_002947/5652822‑5653110                                                                                                                                                |                                                                                                                                                  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)                                                                                                                                                tGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCt                                                              <  6:156780/86‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                  CGGGGCCGGTTGCGCCGGCTGCAGCAGTGAGCATCCTGCCAGTGTCGCCAGGGCCGTCACGGCCAAAAGCGCTTTCATTCAGTTTCCTCGATTTGGGGCTGCTGTGCAGCCCTTCTCGGGCTCGCCCGCTCCCACAGGTACAGTGCAGTCTCTGTGGGAGCGGGCGAGCCCGCGAAGGGCCGCACAGCGGCCCCTTCTTCAAGACCACAAATCAACGTTCAGGTTGCCTATTACCCGATCAAGGGCAACCCGGCGCCTTGCGCTGGTGGTCTTCGTCGTACTTTTCCAG  >  NC_002947/5652822‑5653110

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: ‑