Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,246,443	A→T	13.9%	Q233L (CAG→CTG)	PP_2841 →	site‑specific recombinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,246,443	0	A	T	13.9%	107.3 / 8.5	43	Q233L (CAG→CTG)	PP_2841	site‑specific recombinase
Reads supporting (aligned to +/- strand):  ref base A (14/23);  new base T (3/3);  total (17/26)
Fisher's exact test for biased strand distribution p-value = 6.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01

TGGCTTGAACTGCGCCGCCAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTATGACCGGCGTGATGACAA  >  NC_002947/3246298‑3246587                                                                                                                                                  |                                                                                                                                                  tGGCTTGAACTGCGCCGCCAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTTCTACATTGCCCGCCAGCGCGGCGCGCAGGt                                                                                                                                                >  4:1277/1‑149 (MQ=255)   gCTTGAACTGCGCCGCCAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTgg                                                                                                                                              >  3:71356/1‑149 (MQ=255)   gCTTGAACTGCGCCGCCAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCACCTGCGCGCCGCGCTGGCgg                                                                                                                                              <  7:37013/149‑1 (MQ=255)    cTTGAACTGCGCCGCCAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGTTggg                                                                                                                                             <  7:175495/149‑1 (MQ=255)    cTTGAACTGCGCCGCCAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTggg                                                                                                                                             <  6:229537/149‑1 (MQ=255)       gAACTGCGCCGCCAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATAGCCCGCCAGCGCGGCGCGCAGGTgggg                                                                                                                                            <  7:83300/147‑1 (MQ=255)        aaCTGCGCCGCCAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTg                                                                                                                                         <  5:31418/149‑1 (MQ=255)          cTGCGCCGCCAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGaa                                                                                                                                       <  4:71356/149‑1 (MQ=255)                          tgcctgccGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGAt                                                                                                                       >  5:71162/1‑149 (MQ=255)                                ccGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTc                                                                                                                   <  8:133732/147‑1 (MQ=255)                                   gggCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCgg                                                                                                              <  7:189142/149‑1 (MQ=255)                                         aaGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTTCTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGcattc                                                                                                        <  3:1277/149‑1 (MQ=255)                                              gACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGAGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAc                                                                                                   >  7:39688/1‑149 (MQ=255)                                               aCCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAc‑c                                                                                                 >  7:9669/1‑149 (MQ=255)                                                  cGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGTGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCgg                                                                                              <  1:148234/149‑1 (MQ=255)                                                    ttCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGt                                                                                            <  8:9669/149‑1 (MQ=255)                                                              aCCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGcattc                                                                                                        >  5:38508/1‑128 (MQ=255)                                                              aCCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGcattc                                                                                                        <  6:38508/128‑1 (MQ=255)                                                                         cgcgGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTc                                                                       <  7:182967/149‑1 (MQ=255)                                                                                 ccACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTgcg                                                                >  3:221003/1‑148 (MQ=255)                                                                                          ccGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTgg                                                      <  8:60033/149‑1 (MQ=255)                                                                                            gggCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑ACGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGgcg                                                    >  2:209140/1‑149 (MQ=255)                                                                                               cACGCATTACCAAGCATGGGTTCTACTACATTGCCCGCCTGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCAGGAGTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGATGGCGCAc                                                 <  5:193408/149‑1 (MQ=255)                                                                                                aCGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGAc                                                                            >  2:263962/1‑121 (MQ=255)                                                                                                aCGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGAc                                                                            <  1:263962/121‑1 (MQ=255)                                                                                                 cGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCa                                               <  4:221003/149‑1 (MQ=255)                                                                                                       aCCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTACTCCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGcc                                           <  1:209140/148‑1 (MQ=255)                                                                                                       aCCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATTGAAGAGCATGATCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCa                                          <  8:39688/148‑1 (MQ=255)                                                                                                               tGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGa                                 >  6:225532/1‑149 (MQ=255)                                                                                                                       actacATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGcattc                                                                                                        <  6:44370/71‑1 (MQ=255)                                                                                                                       actacATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGcattc                                                                                                        >  5:44370/1‑71 (MQ=255)                                                                                                                        ctacATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGcc                         <  7:214309/148‑1 (MQ=255)                                                                                                                         tacATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCa                                   <  4:24932/137‑1 (MQ=255)                                                                                                                         tacATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCa                                   >  3:24932/1‑137 (MQ=255)                                                                                                                            cacccccACCTGCGCGCCGCGCTGGCGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTa                    >  7:95128/5‑149 (MQ=255)                                                                                                                               ccccACCTGCGCGCCGCGCTGGCGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTATGa                 >  5:70957/2‑149 (MQ=255)                                                                                                                                 ccacctgcgcgccgcgCTGGCGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAat                                        <  7:233019/118‑1 (MQ=255)                                                                                                                                 ccacctgcgcgccgcgCTGGCGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAat                                        >  8:233019/7‑124 (MQ=255)                                                                                                                                   accAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTATGACCgg             >  4:11960/2‑149 (MQ=255)                                                                                                                                       gcgcggcgcgCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTATGACCGGCGt          >  7:26009/1‑148 (MQ=255)                                                                                                                                         gcggcgcgCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTATGACCGGCGtgat       <  3:11960/149‑1 (MQ=255)                                                                                                                                         gcgccgcgCTGGCGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTATGACCGGCGtgat       <  8:95128/149‑1 (MQ=255)                                                                                                                                              gcgcAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTATGACCGGCGTGATGACaa  <  8:26009/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                  TGGCTTGAACTGCGCCGCCAGGACCTGCCTGCCGGGGCGGAAGATGACCCGTTCCTGTTCAACCGCATCCGTCGCGGCAACCACATTACCCGGGCACGCATTACCAAGCATGCGATCTACTACATTGCCCGCCAGCGCGGCGCGCAGGTGGGGGTGAAGATCATGCCGCACGATTTTCGCCGGGCATTCATTAC‑CCGGGTGATCGAAGAGCACGACCTGTCGATTGCGCAGAAGCTGGCGCACCATGCCAATATCCAGACCACGGCCATCTATGACCGGCGTGATGACAA  >  NC_002947/3246298‑3246587

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: ‑