Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,570,422	G→A	13.2%	intergenic (+30/‑158)	pcaF‑I → / → pcaT	beta‑ketoadipyl‑CoA thiolase/alpha‑ketoglutarate permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,570,422	0	G	A	13.2%	67.4 / 3.3	31	intergenic (+30/‑158)	pcaF‑I/pcaT	beta‑ketoadipyl‑CoA thiolase/alpha‑ketoglutarate permease
Reads supporting (aligned to +/- strand):  ref base G (15/11);  new base A (2/2);  total (18/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.24e-02

CACGCCTGGTACTGACTGCGTTGCACCAGCTGGAGAAGAGTGGCGGTCGCAAGGGCCTGGCGACCATGTGTGTGGGTGTCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCCACGCAATCACCTGTGGGAGCGGGCTTCCCCGCGAAGAGGCCTCTCCTGTGAGACATAAGGCCCATTGCCAGCCCGATAGCGGAACGAGTGTGTTACTAGGTATGTCTAGAACTACCTAGGACCCTCCAGGAG  >  NC_002947/1570277‑1570569                                                                                                                                                  |                                                                                                                                                    cACGCCTGGTACTGACTGCGTTGCACCAGCTGGAGAAGAGTGGCGGTCGCAAGGGCCTGGCGACCATGTGTGTGGGTGTCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTc                                                                                                                                                  <  5:97908/149‑1 (MQ=255)  aCGCCTGGTACTGACTGCGTTGCACCAGCTGGAGAAGAGTGGCGGTCGCAAGGGCCTGGCGACCATGTGTGTGGGTGTCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGGAGCCCCCTc                                                                                                                                                  >  4:117202/1‑148 (MQ=255)      cTGGTACTGACTGCGTTGCACCAGCTGGAGAAGAGTGGCGGTCGCAAGGGCCTGGCGACCATGTGTGTGGGTGTCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACa                                                                                                                                             <  3:238542/149‑1 (MQ=255)                         aCCAGCTGGAGAAGAGTGGCGGTCGCAAGGGCCTGGCGACCATGTGTGTGGGTGTCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCCACGCAATCACCt                                                                                                                          >  3:189535/1‑149 (MQ=255)                          ccAGCTGGAGAAGAGTGGCGGTCGCAAGGGCCTGGCGACCATGTGTGTGGGTGTCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCCACGCAATCACCtg                                                                                                                         <  5:144051/149‑1 (MQ=255)                            aGCTGGAGAAGAGTGGCGGTCGCAAGGGCCTGGCGACCATGTGTGTGGGTGTCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCCACGCAATCACCtgtg                                                                                                                       >  2:196154/1‑149 (MQ=255)                                    aagaGTGGCGGTCGCAAGGGCCTGGCGACCATGTGTGTGGGTGTCGGCCAAGGTATGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCCACGCAATCACCGGGGGGAGCggg                                                                                                               >  3:164564/1‑149 (MQ=255)                                      gagTGGCGGTCGCAAGGGCCTGGCGACCATGTGTGTGGGTGTCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCTACGCAATCACCTGTGGGAGCGGGCt                                                                                                             >  2:189179/1‑149 (MQ=255)                                      gagTGGCGGTCGCAAGGGCCTGGCGACCATGTGTGTGGGTGTCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCCACGCAATCACCTGTGGGAGCGGGCt                                                                                                             >  5:211653/1‑149 (MQ=255)                                                   aaGGGCCTGGCGACCATGTGTGTGGGTGTCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGAGCCACGCAATCACCTGTGGGAGCGGGCTTCCCCGCGCagag                                                                                                >  5:230601/1‑149 (MQ=255)                                                           ggCGACCATGTGTGTGGGTGTCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCCACGCAATCACCTGTGGGAGCGGGc                                                                                                              <  6:93323/127‑1 (MQ=255)                                                           ggCGACCATGTGTGTGGGTGTCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCCACGCAATCACCTGTGGGAGCGGGc                                                                                                              >  5:93323/1‑127 (MQ=255)                                                              gACCATGTGTGTGGGTGTCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCCACGCAATCACCTGTGGGAGCGGGCTTGCCCGCGCAGAGGCCTCTCCtgt                                                                                     >  4:247530/1‑149 (MQ=255)                                                                 cATGTGTGTGGGTGTCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCCACGCAATCACCTGTGGGAGCGGGCTTCCCCGCGAAGAGGCCTCTCCtgtg                                                                                    >  7:202702/1‑147 (MQ=255)                                                                 cATGTGTGTGGGTGTCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCCACGCAATCACCTGTGGGAGCGGGCTTCCCCGCGAAGAGGCCTCTCCtgtg                                                                                    <  8:202702/147‑1 (MQ=255)                                                                             tgtCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCCACAGGGATCCCCGCAATCACCGGTGGGAGCGGGCTTGCCCGCGAAGAGGCCTCTCCTGTGAGACATAAGGCCCa                                                                      >  1:186423/1‑149 (MQ=255)                                                                                  gCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCCACGCaa                                                                                                                                <  6:14/86‑1 (MQ=255)                                                                                  gCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCCACGCaa                                                                                                                                >  5:14/1‑86 (MQ=255)                                                                                       ggTCTGGCGTTGGCCATCGCGCCGGCTTGACCGGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACCGGCAGCCCCGCACTCACCTCTGGGAGCGGGCTTCCCCGCGAAGAGGCCTCTCCTGTGAGACATAAGGCCCATTGCCAGccc                                                            <  6:211653/149‑1 (MQ=255)                                                                                                   gCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCCACAGGGCTCCCCGCAATCACCTGTGGGCGCGGGCTTCCCCGCGAAGAGGCCGCTCCTGTGAGACa                                                                               >  1:10749/1‑118 (MQ=37)                                                                                                   gCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCCACAGGGCTCCACGCAATCACCTGTGGGAGCGGGCTTCCCCGCGAAGAGGCCTCTCCAGTGAGACATAACGCCCATTGCCAGCCCGATAGCGGAAc                                                 >  7:20029/1‑148 (MQ=255)                                                                                                      aTCGTGGGGGTTTTACTTGAACGGGCCTTTTGGCGGGTAAGCCGGCTCAAACTGGTATCCCCCAAATCACCTGGGGTTGGGGGTTTCCCCGCGAATAGGCCTCTCCTGTGAGACATAAGGCCCATTGCCAGCCCGATAGCGGAACGAgt                                             <  8:20029/149‑1 (MQ=255)                                                                                                      aTCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCCACGCAATCACCTGGGGGAGCGGGCTTCCCCGCGAAGAGGCCTCTCCTGTGAGACATAAGGCCCATTGCCAGCCCGATAGCGGAACGAgt                                             <  4:164564/149‑1 (MQ=255)                                                                                                       tCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCTACGCAATCACCTGTGGGAGCGGGCTTCCCCGCGAAGAGGCCTCTCCTGTGAGACATAAGGCCCATTGCCAGCCCGATAGCGGAACGAgtg                                            <  1:189179/149‑1 (MQ=255)                                                                                                                                        ggggAAGCCCACTCCAACAGGGATCCACGCAATCACCTGTGGGAGCGGGCTTCCCCGCGAAGAGGCCTCTCCTGTGAGACATAAGGCCCATTGCCAGCCCGATAGCGGAACGAGTGTGTTACTAGGTa                                >  4:34161/1‑128 (MQ=255)                                                                                                                                        ggggAAGCCCACTCCAACAGGGATCCACGCAATCACCTGTGGGAGCGGGCTTCCCCGCGAAGAGGCCTCTCCTGTGAGACATAAGGCCCATTGCCAGCCCGATAGCGGAACGAGTGTGTTACTAGGTa                                >  4:37629/1‑128 (MQ=255)                                                                                                                                        ggggAAGCCCACTCCAACAGGGATCCACGCAATCACCTGTGGGAGCGGGCTTCCCCGCGAAGAGGCCTCTCCTGTGAGACATAAGGCCCATTGCCAGCCCGATAGCGGAACGAGTGTGTTACTAGGTa                                <  3:37629/128‑1 (MQ=255)                                                                                                                                        ggggAAGCCCACTCCAACAGGGATCCACGCAATCACCTGTGGGAGCGGGCTTCCCCGCGAAGAGGCCTCTCCTGTGAGACATAAGGCCCATTGCCAGCCCGATAGCGGAACGAGTGTGTTACTAGGTa                                <  3:34161/128‑1 (MQ=255)                                                                                                                                         gggAAGCCCGCTCCAACAGGGATCCACGCAATCACCTGTGGGAGCGGGCTTCCCCGCGAAGAGGCCTCTCCTGTGAGACATAAGGCCCATTGCCAGCCCGATAGCGGAACGAGTGTGTTACTAGGTATGTCTAGAACTATCTAGGAccc          >  3:16779/1‑149 (MQ=255)                                                                                                                                               cccGCTCCAACAGGGATCCACGCAATCACCTGTGGGAGCGGGCTTCCCCGCGAAGAGGCCTCTCCTGTGAGACATAAGGCCCATTGCCAGCCCGATAGCGGAACGAGTGTGTTACTAGGTATGTCTAGAACTACCTAGGACACTCCAg     >  1:163264/1‑148 (MQ=255)                                                                                                                                                ccGCTCCAACAGGGACCCACGCAACCACCTGTGGGAGCGGGCTTCCCCGCGAAGAGGCCTCTCCTGTGAGACATAAGGCCCATTGCCAGCCCGATAGCGGAACGAGTGTGTTACTAGGTATGTCTAGAACTACCTAGGACCCTCCAGGa   <  3:247530/149‑1 (MQ=255)                                                                                                                                                  gCTCCAACAGGGATCCACGCAATCACCTGTGGGAGCGGGCTTCCCCGCGAAGAGGCCTCTCCTGTGAGACATAAGGCCCATTGCCAGCCCGATAGCGGAACGAGTGTGTTACTAGGTATGTCTAGAACTACCTAGGACCCTCCAGGAg  >  4:34813/1‑148 (MQ=255)                                                                                                                                                  |                                                                                                                                                    CACGCCTGGTACTGACTGCGTTGCACCAGCTGGAGAAGAGTGGCGGTCGCAAGGGCCTGGCGACCATGTGTGTGGGTGTCGGCCAAGGTCTGGCGTTGGCCATCGAGCGGGTTTGACCTGTACCGGCCTCTTCGCGGGGAAGCCCGCTCCAACAGGGATCCACGCAATCACCTGTGGGAGCGGGCTTCCCCGCGAAGAGGCCTCTCCTGTGAGACATAAGGCCCATTGCCAGCCCGATAGCGGAACGAGTGTGTTACTAGGTATGTCTAGAACTACCTAGGACCCTCCAGGAG  >  NC_002947/1570277‑1570569

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: ‑