Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,344,461:1	+C	9.3%	intergenic (+36/‑142)	pgi‑II → / → acsA‑II	glucose 6‑phosphate isomerase/acetyl‑CoA synthetase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,344,461	1	.	C	9.3%	162.2 / 12.2	43	intergenic (+36/‑142)	pgi‑II/acsA‑II	glucose 6‑phosphate isomerase/acetyl‑CoA synthetase
Reads supporting (aligned to +/- strand):  ref base . (20/19);  new base C (2/2);  total (22/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.02e-02

AGGAGCTGGGCAAGGGCGTTTACCAGCGCTTGGTCGGTAGCCTGGAAGACAGCGCCGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGTTGAACACCGCTCCCAGCTACACTGTCTTATCGAATAGCCGTTGCAGTCCATCGCCCCTTACAAGAGCAGGACCACCCGCCATGTT  >  NC_002947/5344313‑5344607                                                                                                                                                       |                                                                                                                                                    aggagctgggcaaggGCGTTTACCAGCGCTTGGTCGGTAGCCTGGAAGACAGCGCCGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCg                                                                                                                                                      <  1:52158/149‑1 (MQ=255)            aaggGCGTTTACCAGCGCTTGGTCGGTAGCCTGGAAGACAGCGCCGAAGACGGTTCCACCCCAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGAGCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAG‑CCCG‑‑CCTACCAGGcc                                                                                                                                         >  4:159451/1‑148 (MQ=255)              gggCGTTTACCAGCGCTTGGTCGGTAGCCTGGAAGACAGCGCCGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CATACCAGGCAAc                                                                                                                                       >  6:122954/1‑149 (MQ=255)                     tACCAGCGCTTGGTCGGTAGCCTGGAAGACAGCGCCGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTa                                                                                                                                 <  2:229629/148‑1 (MQ=255)                        cAGCGCTTGGTCGGTAGCCTGGAAGACAGCGCCGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACGAGGTAACGCGTTGcc                                                                                                                               <  3:233651/149‑1 (MQ=25)                            gcTTGGTCGGTAGCCTGGAAGACAGCGCCGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAg                                                                                                                         <  4:120843/149‑1 (MQ=255)                              ttGGTCGGTAGCCTGGAAGACAGCGCCGAAGACGGTTCCACCCGAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAg                                                                                                                         >  1:187593/1‑147 (MQ=255)                                  tCGGTAGCCTGGAAGACAGCGCCGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCgg                                                                                                                   <  8:20122/149‑1 (MQ=255)                                  tCGGTAGCCTGGAAGACAGCGCCGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTATTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCCTTAACTCGTAGGCGCgg                                                                                                                   >  3:46100/1‑149 (MQ=255)                                   cGGTAGCCTGGAAGACAGCGCCGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCggg                                                                                                                  <  8:242453/149‑1 (MQ=255)                                     gTAGCCTGGAAGACAGCGCCGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCgg                                                                                                                   >  3:17436/1‑146 (MQ=255)                                     gTAGCCTGGAAGACAGCGCCGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCgg                                                                                                                   <  4:17436/146‑1 (MQ=255)                                         ccTGGAAGACAGCGCCGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTAcc                                                                                                            <  4:146737/149‑1 (MQ=255)                                          cTGGAAGACAGCGCCGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACGAGGTAACGCGTTGCCTGGTAG‑‑GCGGGTTTAccc                                                                                                           <  3:239735/149‑1 (MQ=21)                                          cTGGAAGACAGCGCCGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCGCTCCTACGAGGTAACGCGTTGCCTGGTAG‑‑GCGGGTTTAccc                                                                                                           >  4:239735/1‑149 (MQ=21)                                             gAAGACCGCGCCGAAGACGGTTCCACCCAAGGCCGGAGCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGGGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGGTACCTCGTAGGCGCGGGTTTACCcgcg                                                                                                        <  3:159451/149‑1 (MQ=38)                                                        cGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTAc                                                                                                             <  5:162123/133‑1 (MQ=255)                                                        cGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTAc                                                                                                             >  6:158475/1‑133 (MQ=255)                                                        cGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTAc                                                                                                             <  5:158475/133‑1 (MQ=255)                                                        cGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTAc                                                                                                             >  6:162123/1‑133 (MQ=255)                                                          aaGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCACATAGCGGGTAAA‑CCCG‑‑CCGAACCCGCAACGCGTTACCGCCTAGGAGCGGGTTTACCCGCGAAGCGGCCGGccc                                                                                           >  8:227326/1‑149 (MQ=255)                                                             aCGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTAGCGGGTAAA‑CCCC‑‑CCGAACAAGCACAGCCGTTCCAAGTAGGAGCGGGGTTAACCGCGCAGAGGCCGGCCCAgg                                                                                        >  8:28273/1‑149 (MQ=255)                                                               ggTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGtt                                                                                      >  3:29830/1‑149 (MQ=255)                                                                     aCCCAAGGCCTTATCAACTATTTCCGCGGCCGTCACGGGGGTTGATCCGAGCTTGTGCCGGCCTCTTCGGGGGTAAA‑CCCG‑‑CCTACCTGGCAACGCTTTACCTCGTTGGAGCGGTTTTACCCGCTATTTGGCCGGCCCAGGTTGAacac                                                                                <  2:187593/149‑1 (MQ=255)                                                                         aaGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGa                                                                                                                       <  1:17818/106‑1 (MQ=255)                                                                         aaGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGa                                                                                                                       >  2:17818/1‑106 (MQ=255)                                                                             ccTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCGACCCGGCCACGCGGTTCCTCGTAGGAGCGGGGTTTCCCGCGCAGCGGCCGGCCCAGGTTGGACACCGCGcc                                                                          >  7:112458/1‑147 (MQ=37)                                                                              cTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGTTGAACACCGCTCCCAg                                                                       >  6:121508/1‑149 (MQ=255)                                                                                   cAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTACCCGCGAAGAggccg                                                                                               >  1:13388/1‑120 (MQ=255)                                                                                   cAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTACCCGCGAAGAggccg                                                                                               <  2:13388/120‑1 (MQ=255)                                                                                             cgcgGCCGCCACCGCGTTTTATCCGAGGTTGTGCCGGCCTCTTCG‑GGTTAAACCCCG‑‑CCTACCCGGAAAGCTGTTACCTCTTTGTTGGGGTTTAACCGGCTAAGTGGCCGGCCCAGGTTGAACACCGCTCCCAGCTACACTGTCTTATc                                                        <  2:89770/149‑1 (MQ=255)                                                                                             cgcgCCCGTCACCGGGGTTGATCCGTGTTTGTGCGGGCCTCTTCGGGGTTAAA‑CCCG‑‑CATACCCGGAAAGGGTTTACCTCTTTGGAGGGGTTTTACCCGCTAATTGGCCGGCCCAGGTTGAACACCGCTCCCAGCTACACTGTCTTATc                                                        <  4:29830/149‑1 (MQ=255)                                                                                                         cgcgGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCAACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGTTGAACACCGCTCCCAGCTACACTGTCTTATCGAATAGCCGTTg                                            >  4:215773/1‑149 (MQ=255)                                                                                                                       gCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCACGTAGGAGCGGGGTTACCCGCGAAGAGGCCGGCCCAGGTTGAACACCGCTCCCCCCTACACAGTCTTATCGAATAGCCGGTGCAGTACAAAGccc                               >  6:193820/1‑148 (MQ=37)                                                                                                                        cTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCTGGCAACGCGTTACCTCGTAGTAGCGGTTTTACCCGCTAATAGGCCGGCCCAGGTTGAACACCGCTCCCAGCTACACTGCCTTATCGAATAGCCGTTGCAGTCCATCGCCCCt                             <  5:121508/149‑1 (MQ=38)                                                                                                                               cGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTACCCGCTAAGAGGCCGGCCCAGGTTGAACACCGCTCCCAGCTACACTGTCTTATCGAATAGCCGTTGCAGTCCATCGCCCCTTACAaga                      <  5:193820/149‑1 (MQ=255)                                                                                                                                 gCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGTTGAACACCGCTCCCAGCTACACTGTCTTATCGAATAGCCGTTGCAGTCCATCGCCCCTTACAagag                     >  8:180183/1‑148 (MQ=255)                                                                                                                                  ccTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGTTGAACACCGCTCCCAGCTACACTGTCTTATCGAATAGCCGTTGCAGTCCATCGCCCCTTACAAGAGCa                   <  5:122954/149‑1 (MQ=255)                                                                                                                                   ctctTCGCGGTTAAA‑CCCG‑‑CATACCAGGCAACGCTTTACCTCGTAGTAGCGGGTTTACCCGCTAAGAGGCCGGCCCAGGTTGAACTCCGCTCCCAGCTACACTGTCTTATCGAATAGCCGTTGCAGTCCATCGCCCCTTACAAGAGCAg                  <  1:215129/149‑1 (MQ=255)                                                                                                                                         gcgGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGTTGAACACCGCTCCCAGCTACACTGTCTTATCGAATAGCCGTTGCAGTCCATCGcc                                >  4:144115/1‑129 (MQ=255)                                                                                                                                           gggTAAA‑CCCGCTCCTACGAGGTAACGCGTTGCCTGGTAG‑‑GCGGGTTTACCCGCGAAGAGGCCGGCCCAGGTTGAACACCGCTCCCAGCTACACTGTCTTATCGAATAGCCGTTGCAGTCCATCGCCCCTTACAAGAGAAGGACCAccc          >  7:165420/1‑149 (MQ=21)                                                                                                                                              tAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGTTGAACACCGCTCCCAGCTACACTGTCTTATCGAATAGCCGTTGCAGTCCATCGCCCCTTACAAGAGCAGGACCACCCGcc       <  7:180183/149‑1 (MQ=255)                                                                                                                                               aaa‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGTTGAACACCGCTCCCAGCTACACTGTCTTATCGAATAGCCGTTGCAGTCCATCGCCCCTTACAAGAGCAGGACCACCCGCCa      >  6:5941/1‑149 (MQ=255)                                                                                                                                                    ccG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGTTGAACACCGCTCCCAGCTACACTGTCTTATCGAATAGCCGTTGCAGTCCATCGCCCCTTACAAGAGCAGGACCACCCGCCATGtt  >  7:152429/1‑149 (MQ=255)                                                                                                                                                       |                                                                                                                                                    AGGAGCTGGGCAAGGGCGTTTACCAGCGCTTGGTCGGTAGCCTGGAAGACAGCGCCGAAGACGGTTCCACCCAAGGCCTGATCAACTACTTCCGCGGCCGTCACCGCGGTTGATCCGAGCTTGTGCCGGCCTCTTCGCGGGTAAA‑CCCG‑‑CCTACCAGGCAACGCGTTACCTCGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGTTGAACACCGCTCCCAGCTACACTGTCTTATCGAATAGCCGTTGCAGTCCATCGCCCCTTACAAGAGCAGGACCACCCGCCATGTT  >  NC_002947/5344313‑5344607

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: ‑