Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	459,907	A→C	8.5%	intergenic (‑50/+29)	pqqB ← / ← pqqA	coenzyme PQQ synthesis protein B/coenzyme PQQ synthesis protein A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	459,907	0	A	C	8.5%	117.1 / 3.0	46	intergenic (‑50/+29)	pqqB/pqqA	coenzyme PQQ synthesis protein B/coenzyme PQQ synthesis protein A
Reads supporting (aligned to +/- strand):  ref base A (20/22);  new base C (2/2);  total (22/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

TTTCAGGGTGCCATCACGGTAGCCCTTGCAGTTGACGCAGTTGCAGTTCCACTGCGGGAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGCAGGTCAGTGTATGCAGGTTTGGTCCACATGGAATTACTCCTTCCGAATGAGGGTTGGGTTGTTCAG  >  NC_002947/459759‑460044                                                                                                                                                     |                                                                                                                                          tttCAGGGTGCCATCACGGTAGCCCTTGCAGTTGACGCAGTTGCAGTTCCACTGCGGGAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAg                                                                                                                                          <  1:507170/150‑1 (MQ=255) tttCAGGGTGCCATCACGGTAGCCCTTGCAGTTGACGCAGTTGCAGTTCCACTGCGGGAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAg                                                                                                                                          >  1:423844/1‑150 (MQ=255)             aTCACGGTAGCCCTTGCAGTTGACGCAGTTGCAGTTCCACTGCGGGAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGa                                                                                                                              >  1:59124/1‑150 (MQ=255)              tCACGGTAGCCCTTGCAGTTGACGCAGTTGCAGTTCCACTGCGGGAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGCGTAATATGGCCACTCTCTATGCAGAAACCGGATCGAACAACAGAAAACGCCCCGGCAGGCCGAGGCGTGaa                                                                                                                             >  1:13471/1‑150 (MQ=255)                   gTAGCCCTTGCAGTTGACGCAGTTGCAGTTCCACTGCGGGAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCt                                                                                                                        >  1:698771/1‑150 (MQ=255)                         cTTGCAGTTGACGCAGTTGCAGTTCCACTGCGGGAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCt                                                                                                                  >  2:284509/1‑150 (MQ=255)                          ttGCAGTTGACGCAGTTGCAGTTCCACTGCGGGAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTg                                                                                                                 >  1:24569/1‑150 (MQ=255)                                     gcagttgcagttCCACTGCGGGAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCTCGGCCTGCCGGGGCGttttcgt                                                                                                                          <  2:377536/130‑7 (MQ=255)                                     gcagttgcagttCCACTGCGGGAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCTCGGCCTGCCGGGGCGttttcgt                                                                                                                          >  1:377536/1‑124 (MQ=255)                                      cagttgcagttCCACTGCGGGAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGTCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTa                                                                                                     <  1:28069/150‑1 (MQ=255)                                              gttCCACTGCGGGAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTa                                                                                             >  1:127540/1‑150 (MQ=255)                                              gttCCACTGCGGGAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAAACGAAACGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTa                                                                                             <  2:13471/150‑1 (MQ=255)                                               ttCCACTGCGGGAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCTCGGCCTGCCGGGGCGtt                                                                                                                               <  2:450429/115‑2 (MQ=255)                                               ttCCACTGCGGGAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCTCGGCCTGCCGGGGCGtt                                                                                                                               >  1:450429/1‑114 (MQ=255)                                                        gggAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCAGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACt                                                                                   >  1:638404/1‑150 (MQ=255)                                                             cccGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGaa                                                                              <  2:683125/150‑1 (MQ=255)                                                              ccGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCTGAGGCGTGAAACCCTAAGCCTGGCTTa                                                                                                            >  2:732301/1‑119 (MQ=255)                                                              ccGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTa                                                                                                            <  1:732301/119‑1 (MQ=255)                                                              ccGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCCGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAg                                                                             >  2:56522/1‑150 (MQ=255)                                                               cGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGc                                                                            <  2:24569/150‑1 (MQ=255)                                                                   aCCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCGGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTa                                                                                                     >  1:243901/1‑121 (MQ=255)                                                                   aCCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTa                                                                                                     <  2:243901/121‑1 (MQ=255)                                                                               gCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGCAGGTCAgt                                                            <  1:284509/150‑1 (MQ=255)                                                                               gCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGCAGGTCAgt                                                            <  2:59124/150‑1 (MQ=255)                                                                                   agaACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGCAGGTCAGTGTAt                                                        <  2:127540/150‑1 (MQ=255)                                                                                       ccTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGCAGGTCAGTGTATGCAg                                                    <  1:751673/150‑1 (MQ=255)                                                                                       ccTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCAGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGCAGGTCAGTGTATGCAg                                                    <  2:638404/150‑1 (MQ=255)                                                                                        cTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGc                                                                                                          >  1:169657/1‑95 (MQ=255)                                                                                        cTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGc                                                                                                          <  2:169657/95‑1 (MQ=255)                                                                                             tGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGCAGGTCAGTGTATGCAGGTTTgg                                              <  2:423844/150‑1 (MQ=255)                                                                                              gTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGt                                                                                       <  2:616364/108‑1 (MQ=255)                                                                                              gTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGt                                                                                       >  1:616364/1‑108 (MQ=255)                                                                                               tACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGt                                                                                       >  1:411304/1‑107 (MQ=255)                                                                                               tACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGt                                                                                       <  2:411304/107‑1 (MQ=255)                                                                                                        aCTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGCAGGTCAGTGTATGCAGGTGTGTGACACATGGaa                                   >  1:153939/1‑150 (MQ=255)                                                                                                              tATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCATAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGCAGGTCAGTGTATGCAGGTTTGGTCCACATGGAATTACTc                             >  1:335671/1‑150 (MQ=255)                                                                                                                 gCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGc                                                                    >  2:745075/1‑108 (MQ=255)                                                                                                                 gCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGc                                                                    <  1:745075/108‑1 (MQ=255)                                                                                                                   aGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGccag                                                                                                                 <  1:671849/61‑3 (MQ=255)                                                                                                                   aGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGccag                                                                                                                 >  2:671849/1‑59 (MQ=255)                                                                                                                         cGGAGCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGCAGGTCAGTGTATGCAGGTTTGGTCCACATGGAATTACTCCTTCCGAATGa                  <  1:75134/150‑1 (MQ=255)                                                                                                                          ggATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGCAGGTCAGTGTATGCAGGTTTGGTCCACATGGAATTACTCCTTCCGAATGAg                 <  2:698771/150‑1 (MQ=255)                                                                                                                          ggATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAACCGATACGCAGGTCAGTGTATGCAGGTTTGGTCCACATGGAATTACTCCTTCCGAATGAg                 >  2:248549/1‑150 (MQ=255)                                                                                                                          ggATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGAGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGCAGGTCAGTGTATGCAGGTTTGGTCCACATGGAATTACTCCTTCCGAATgcg                 >  1:201714/1‑148 (MQ=255)                                                                                                                                         aaacgCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGCAGGTCAGTGTATGCAGGTTTGGTCCACATGGAATTACTCCTTCCGAATGAGGGTTGGGTTGTTCAg  <  1:248549/150‑1 (MQ=255)                                                                                                                                         aaacgCCCCCGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGCAGGTCAGTGTATGCAGGTTTGGTCCACATGGAATTACTCCTTCCGAATGAGGGTTGGGTTGTTCAg  <  1:56522/150‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                          TTTCAGGGTGCCATCACGGTAGCCCTTGCAGTTGACGCAGTTGCAGTTCCACTGCGGGAACCCGCCACCGGCGGCGGAGCCGAGAACCTGGATGTACATGGCCACTCTCTATGCAGAAACCGGATCGAAAAAACGAAAACGCCCCGGCAGGCCGAGGCGTGAAACCCTAAGCCTGGCTTAGCGGTTAGCGAAGTACATGGTGACTTCGAAGCCGATACGCAGGTCAGTGTATGCAGGTTTGGTCCACATGGAATTACTCCTTCCGAATGAGGGTTGGGTTGTTCAG  >  NC_002947/459759‑460044

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑