Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,048,605	A→C	15.2%	intergenic (+60/‑236)	PP_2661 → / → PP_2662	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,048,605	0	A	C	15.2%	104.2 / 12.9	46	intergenic (+60/‑236)	PP_2661/PP_2662	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (18/21);  new base C (2/5);  total (20/26)
Fisher's exact test for biased strand distribution p-value = 4.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.65e-01

TGCAGGCACGGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGACCCAAGCAGGTACCGGGACCAAATCACCGGGCCGTACCCTCCCGCCCCA  >  NC_002947/3048466‑3048746                                                                                                                                             |                                                                                                                                              tgCAGGCGCGGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCCGCCTTGCGGCCCTTCGCGGGCTCGCCCGCGaa                                                                                                                                      <  3:107258/149‑1 (MQ=39) tgCAGGCACGGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGTCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGCGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGaa                                                                                                                                      <  4:88830/149‑1 (MQ=255)   cAGGCACGGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCCTGCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCTCGCCCGCGAAg                                                                                                                                     <  1:294624/149‑1 (MQ=255)   cAGGCACGGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCCGCCTTGCGGCCCTTCGCGGGCTCGCCCGCGAAg                                                                                                                                     <  2:140548/148‑1 (MQ=39)      gCACGGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGTCACTGGCTTCATGAAGACAGGAGATTCC‑GCTCAGATAATGTAATTGGGTCTGCTTTGCAGCCCTTCGCGGGAGAGCACGCGAAGGGcc                                                                                                                                 >  2:363008/1‑149 (MQ=255)                 ctggcAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCCGCCTTGCGGCCCTTCGCGGGCTCGCCCGCGAAGGGCTGCAAagc                                                                                                                          <  4:253849/145‑1 (MQ=37)                 ctggcAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCCGCCTTGCGGCCCTTCGCGGGCTCGCCCGCGAAGGGCTGCAAagc                                                                                                                          >  3:253849/1‑145 (MQ=37)                      agcaACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCTCGCCCGCGAAGGGCCGCAAGGCGGCCCCGGt                                                                                                                 >  4:288689/1‑149 (MQ=255)                       gcaACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAggcggc                                                                                                                       <  5:81143/142‑1 (MQ=255)                       gcaACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAggcggc                                                                                                                       >  6:81143/1‑142 (MQ=255)                       gcaACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGtt                                                                                                                >  7:211345/1‑149 (MQ=255)                        caACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGttc                                                                                                               <  8:341915/149‑1 (MQ=255)                           ccGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGttcatt                                                                                                            <  2:197283/149‑1 (MQ=255)                             gCACCGTTATGAAATGCCCGCTTGCCAGCGGTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGttcattca                                                                                                          <  5:344254/149‑1 (MQ=255)                                       gAAATGCCTGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGa                                                                                                                                               <  7:273386/102‑1 (MQ=255)                                       gAAATGCCTGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGa                                                                                                                                               >  8:273386/1‑102 (MQ=255)                                              ccGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGc                                                                                         <  8:211345/149‑1 (MQ=255)                                               cGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGcc                                                                                        >  6:44086/1‑149 (MQ=255)                                               cGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGc                                                                                         >  4:30292/1‑148 (MQ=255)                                                    gCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGTAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGcc                                                                                    <  8:361011/148‑1 (MQ=255)                                                    gCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGttca                                                                                                              >  6:177577/1‑122 (MQ=255)                                                    gCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGttca                                                                                                              <  5:177577/122‑1 (MQ=255)                                                    gCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGc                                                                                     <  6:99022/147‑1 (MQ=255)                                                        gCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTcc                                                                               >  8:242514/1‑149 (MQ=255)                                                          gTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTcctg                                                                             <  5:44086/149‑1 (MQ=255)                                                                  gCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGTCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGc                                                                      >  3:330486/1‑148 (MQ=255)                                                                        gCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTcctgc                                                                            >  8:63736/1‑136 (MQ=255)                                                                        gCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATACAATCGTATTGATACCCGCCTGCCACTcctgc                                                                            <  7:63736/136‑1 (MQ=255)                                                                            ccTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGTCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGtct                                                             <  4:330486/147‑1 (MQ=255)                                                                               gAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGc                                                                                         >  1:225470/1‑116 (MQ=255)                                                                               gAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGc                                                                                         <  2:225470/116‑1 (MQ=255)                                                                               gAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTcct                                                                              >  1:145063/1‑127 (MQ=255)                                                                               gAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTcct                                                                              <  2:145063/127‑1 (MQ=255)                                                                                    cAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGa                                                                        <  5:304054/128‑1 (MQ=255)                                                                                    cAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGa                                                                        >  6:304054/1‑128 (MQ=255)                                                                                     aGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGAc                                                  >  6:154068/1‑149 (MQ=255)                                                                                      ggAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGttcat                                                                                                             <  2:311237/89‑1 (MQ=255)                                                                                      ggAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGttcaa                                                                                                             >  1:311237/1‑88 (MQ=255)                                                                                             cc‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGACCCAAGCa                                           <  7:242514/148‑1 (MQ=255)                                                                                                  tCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCaa                                                                                                         <  1:135223/82‑1 (MQ=255)                                                                                                  tCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCaa                                                                                                         >  2:135223/1‑82 (MQ=255)                                                                                                    aGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGACCCAAGCAGGTAc                                      <  5:154068/147‑1 (MQ=255)                                                                                                       tAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCTCGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGACCCAAGCAGGTACCGGGa                                 <  3:288689/149‑1 (MQ=255)                                                                                                        aaTGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGACCCAAGCAGGTACCGGGAc                                >  7:59364/1‑149 (MQ=255)                                                                                                             aaTTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGACCCAAGCAGGTACCGGGACCaaa                            >  1:265150/1‑148 (MQ=255)                                                                                                                             cAGCCATTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCAGCCACTCCTGCCTGAGCCATAAGTCTCG‑ACCAGGACCCAAGCAGGTACCGTGACCAAATCACCGGGCCGTACCCt           <  3:30292/148‑1 (MQ=255)                                                                                                                                cccTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGACCCAAGCAGGTACCGGGACCAAATCACCGGGCCGTACCCTccc        <  2:265150/149‑1 (MQ=255)                                                                                                                                        gggCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGACCCAAGCAGGTACCGGGACCAAATCACCGGGCCGTACCCTCCCGCCCCa  >  1:293326/1‑147 (MQ=255)                                                                                                                                             |                                                                                                                                              TGCAGGCACGGCTGGCCTGGCAGCAACCGCACCGTTATGAAATGCCCGCTTGCCAGCGTTCGCAGGCACTGGCTTCCTGAAGCCAGGAGATTCC‑GCTCAGATAATGTAATTGGGGCTGCTTTGCAGCCCTTCGCGGGCGAGCCCGCGAAGGGCCGCAAGGCGGCCCCGGTTCATTCAATCGTATTGATACCCGCCTGCCACTCCTGCCTGAGCCATAAGTCTCGAACCAGGACCCAAGCAGGTACCGGGACCAAATCACCGGGCCGTACCCTCCCGCCCCA  >  NC_002947/3048466‑3048746

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑