Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,704,538	T→C	11.8%	intergenic (+63/+49)	PP_5006 → / ← PP_5007	TetR family transcriptional regulator/polyhydroxyalkanoate granule‑associated protein GA2

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,704,538	0	T	C	11.8%	99.8 / 6.0	43	intergenic (+63/+49)	PP_5006/PP_5007	TetR family transcriptional regulator/polyhydroxyalkanoate granule‑associated protein GA2
Reads supporting (aligned to +/- strand):  ref base T (21/16);  new base C (3/2);  total (24/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.37e-01

AGGTGATGATGCTGGTGGCGCCGCATCTGCAGGCCCAGGCCCGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTGCTGCTGGCCGGGGTGGCGGCAGTTGCCGGTGCTGTGGTCGCTGCAGGCGCAGCGCTGGC  >  NC_002947/5704390‑5704685                                                                                                                                                      |                                                                                                                                                     aGGTGATGATGCTGGTGGCGCCGCATCTGCAGGCCCAGGCCCGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGttt                                                                                                                                                      <  1:63392/149‑1 (MQ=255)  ggTGATGATGCTGGTGGCGCCGCATCTGCAGGCCCAGGCCCGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTg                                                                                                                                                     >  3:132069/1‑149 (MQ=255)    tgatgaTGCTGGTGGCGCCGCATCTGCAGGCCCAGGCCCGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGgc                                                                                                                                                   <  5:134474/149‑1 (MQ=255)                    gccgcATCTGCAGGCCCAGGCCCGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑g                                                                                                                                  >  5:88144/1‑149 (MQ=255)                     ccgcATCTGCAGGCCCAGGCCCGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑gg                                                                                                                                 <  1:193867/149‑1 (MQ=255)                      cgcATCTGCAGGCCCAGGCCCGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGATGCGCCAAACCTTGTAGGAGC‑ggg                                                                                                                                <  6:361904/149‑1 (MQ=37)                       gcATCTGCAGGCCCAGGCCCGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGATGCGCCAAACCTTGTAGGAGC‑GGGt                                                                                                                               <  5:65616/149‑1 (MQ=37)                         aTCTGCAGGCCCAGGCCCGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑gg                                                                                                                                 >  1:165111/1‑145 (MQ=255)                         aTCTGCAGGCCCAGGCCCGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑gg                                                                                                                                 <  2:165111/145‑1 (MQ=255)                              caggcccaggccCGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTAccc                                                                                                                         <  4:132069/148‑1 (MQ=255)                              caggcccaggccCGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCcg                                                                                                                        <  7:142000/149‑1 (MQ=255)                                 gcccaggcccGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCcgcg                                                                                                                      >  2:239010/1‑148 (MQ=255)                                 gcccaggcccGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCcgcg                                                                                                                      >  6:79956/1‑148 (MQ=255)                                  cccaggcccGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGGATCTTGTAGGAGC‑GGGTTTACCcgcg                                                                                                                      >  5:292686/1‑147 (MQ=255)                                   ccaggcccGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCcgcg                                                                                                                      >  7:340539/1‑146 (MQ=255)                                     aggcccGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCgaagaa                                                                                                                 <  5:224991/149‑1 (MQ=255)                                               ggcggcggAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCgg                                                                                                       >  6:773/1‑149 (MQ=255)                                                      gacccgcTGGCAGTCACGACCCGGGAGGGGTCGGCCGGCGGGCGATGTCGTGTGGCCGCCGCCGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTGGTCGGAGG‑GGGTTTACCCGCGAAGAAGGCGACGCGGTatcaga                                                                                                <  6:311938/144‑1 (MQ=255)                                                              ggCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCGCCT‑ACAAGGGTTGGCGCATCGTGTAGGCGC‑GGGTTTACCCGCGACGAAGGCGCCGCGGTATCAGATCAAGGTa                                                                                        >  3:228001/1‑149 (MQ=255)                                                                     aaGTACCTGGCGGGGTAGGCCGGCTGGAGATGTTGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGTGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGc                                                                                 <  2:15673/149‑1 (MQ=255)                                                                         aCCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAAACCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGt                                                                             >  3:377006/1‑149 (MQ=255)                                                                              gAGGGGTAGGCCTGCTGGTGATGTTGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCGGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTg                                                                        <  5:130893/149‑1 (MQ=255)                                                                              gAGGGGTAGGCCTGCTGGAGTTGTCGTGTTCCCGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGt                                                                         <  1:178412/148‑1 (MQ=255)                                                                                           gctgGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGtgct                                                           >  1:243660/1‑149 (MQ=255)                                                                                              ggAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTgctgct                                                        >  2:92699/1‑149 (MQ=255)                                                                                               gagaTGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTGctgctg                                                       <  5:773/149‑1 (MQ=255)                                                                                               gagaTGTAGTGTTGCAGCCGACGCATTCGCGGGTAAAACCCCTGCTAAAAAGGTTTGG‑GGGTATTGTAGGGGCGGGGTTTACCC‑CGAAGAAGGGGGCGCGGGTTGAGATAAGGGTTCCGGTGGCAGTCGGGGGCGACGGGGtggggcgg                                                       >  4:192814/1‑143 (MQ=255)                                                                                                     tAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTGCTGCTGGCCgg                                                  <  3:192814/148‑1 (MQ=255)                                                                                                     tAGGGTTCCAGCCGACCCATTCGCGGGCAACCCCCCTCCC‑ACACGGTTGGGCGCCTCTTGTAGGAGC‑GGGATTACCCGCGAAGAAGGCGACGCGGTATCAGATCCGGGTACCGGTGCCAGTCGGTGCCGACGGCGTGCTGCTGGCCggg                                                 <  8:340539/149‑1 (MQ=37)                                                                                                        ggtTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTTCTGCTGGCCGGGGTg                                              <  2:157915/148‑1 (MQ=255)                                                                                                              aGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGtg                                                             <  5:303910/128‑1 (MQ=255)                                                                                                              aGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGtg                                                             >  6:303910/1‑128 (MQ=255)                                                                                                                  gACGCATTCGCGGGTAAACCCGCTGCT‑ACAAGGTTTGGGGCATGTTGTTGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGGATGAGCTGAGGGGACCGGTGGCAGTGGGTGGCGCCGGGGTGGTGCTGGGCGGGGTGGCGGGAGTTg                                    >  4:273011/1‑149 (MQ=255)                                                                                                                           gcgGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTGCTGCTGGCCGGGGTGGCGGCAGTTGCCGGTGCtg                           <  4:377006/149‑1 (MQ=255)                                                                                                                             gggTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTGCTGCTGGCCGGGGTGGCGGCAGTTGCCGGTGCtgtg                         >  1:188305/1‑149 (MQ=255)                                                                                                                              ggTAACCCCGCTCCT‑ACACGGTTTGGCGCATCTTGTCGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTGCTGCTGGCCGGGGTGGCGGCAGTTGCCGGTGCTGTgg                        <  4:226911/149‑1 (MQ=255)                                                                                                                                     ccGCTCCT‑ACAAGATGCGCCAAACCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTGCTGCTGGCCGGGGTGGGGGGTGTTGGGGgtggtgtggtgggtgg                 >  2:156342/1‑143 (MQ=21)                                                                                                                                       gCTCCT‑ACAAGATGCGCCAAACCTTGTAGGAGC‑GGGTTTACCCGCGAATAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTGCTGCTGGCCGGGGTGGCGGCAGTTGCCGGTGCTGTGGTCGCTGCAg               >  4:66790/1‑149 (MQ=37)                                                                                                                                       gCTCCT‑ACAAGATGCGCCAAACCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTGCTGCTGGCCGGGGTGGCGGCAGTTGCCGGTGCTGTGGTCGCTGCAg               >  5:386922/1‑149 (MQ=38)                                                                                                                                        cTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGCAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTGCTGCTGGCCGGGGTGGCGGCAGTTGCCGGTGCGGTGGTCGCTGCAgg              >  5:213250/1‑149 (MQ=255)                                                                                                                                         tCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTGCTGCTGGCCGGGGTGGCGGCAGTTGCCGGTGCTGTGGTCGCTGCAGgc             >  5:154683/1‑149 (MQ=255)                                                                                                                                              aCAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGATGGCGTGCTGCTGGCCGGGGTGGCGGCAGTTGCCGGTGCTGTGGTCGCTGCAGGCGCAg         >  6:235614/1‑149 (MQ=255)                                                                                                                                              aCAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTGCTGCTGGCCGGGGTGGCGGCAGTTGCCGGTGCTGTGGTCGCTGCAGGCGCAg         >  6:105737/1‑149 (MQ=255)                                                                                                                                                   gTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTGCTGCTGGCCGGGGTGGCGGCAGTTGCCGGTGCTGTGGTCGCTGCAGGCGCAGCGCTg    >  8:207650/1‑149 (MQ=255)                                                                                                                                                    tttGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTGCTGCTGGCCGGGGTGGCGGCAGTTGCCGGTGCTGTGGTCGCTGCAGGCGCAGCGCTgg   <  1:92699/149‑1 (MQ=255)                                                                                                                                                     ttGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTCCCGGTGCCAGGCGGTGCCGACGGCGTGCTGCTGGCCGGGGTGGCGGCAGTTGCCGGTGCTGTGGTCGCTGCAGGCGCAGCGCTGGc  <  7:207650/149‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                     AGGTGATGATGCTGGTGGCGCCGCATCTGCAGGCCCAGGCCCGGGCGGCGGCGGAGCAGCTGGCAGTGAAGTACCTGGAGGGGTAGGCCTGCTGGAGATGTAGTGTTGCAGCCGACGCATTCGCGGGTAAACCCGCTCCT‑ACAAGGTTTGGCGCATCTTGTAGGAGC‑GGGTTTACCCGCGAAGAAGGCGACGCGGTATCAGATCAGGGTACCGGTGCCAGTCGGTGCCGACGGCGTGCTGCTGGCCGGGGTGGCGGCAGTTGCCGGTGCTGTGGTCGCTGCAGGCGCAGCGCTGGC  >  NC_002947/5704390‑5704685

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: ‑