Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	697,231	C→G	15.6%	intergenic (+155/‑596)	mmsA‑I → / → PP_16SD	methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	697,231	0	C	G	15.6%	124.9 / 15.4	45	intergenic (+155/‑596)	mmsA‑I/PP_16SD	methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base C (15/23);  new base G (3/4);  total (18/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01

GCGGGGAGGCCGTCAGGCCTCCCCGCTTTGTTTTTGGGGGTTGGTTGTTGCTGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACACCCTCTTGAATCCCCTTATAATGCGC  >  NC_002947/697091‑697363                                                                                                                                             |                                                                                                                                     gCGGGGAGGCCGTCAGGCCTCCCCGCTTTGTTTTTGGGGGTTGGTTGTTGCTGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTc                                                                                                                             <  1:24789/150‑1 (MQ=255)     ggAGGCCGTCAGGCCTCCCCGCTTTGTTTTTGGGGGTTGGTTGTTGCTGTTGGGGAGGAACTGTTTTGAGAGGCTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGtc                                                                                                                         <  1:493157/150‑1 (MQ=255)      gAGGCCGTCAGGCCTCCCCGCTTTGTTTTTGGGGGTTGGTTGTTGCTGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGtct                                                                                                                        >  2:246498/1‑150 (MQ=255)      aaGGCCGCCAGCCTTCCCCGCTTTGTTTTTGGGGGTTGGTTGTTGCTGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGACCGAGCGCCGCGCGGGCGGCGCTCgacct                                                                                                                        <  1:751218/149‑5 (MQ=21)        ggCCGTCAGGCCTCCCCGCTTTGTTTTTGGGGGTTGGTTGTTGCTGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTca                                                                                                                      <  1:246498/150‑1 (MQ=255)            gTCAGGCCTCCCCGCTTTGTTTTTGGGGGTTGGTTGTTGCTGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGCGCCTGTGAGACCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAgg                                                                                                                  <  1:597912/150‑1 (MQ=21)             tCAGGCCTCCCCGCTTTGTTTTTGGGGGTTGGTTGTTGCTGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGAGCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGgc                                                                                                                 <  1:631419/150‑1 (MQ=255)                   cTCCCCGCTTTGTTTTTGGGGGTTGGTTGTTGCTGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGaa                                                                                                           >  1:314092/1‑150 (MQ=255)                      cccGCTTTGTTTTTGGGGGTTGGTTGTTGCTGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGCCA‑A‑GTGTTCGCCACGACAGTTTCAGCGCCTGTGAGACCGAGCGCCGCGCGGGCGGCGCTCgat                                                                                                                          <  2:488014/130‑3 (MQ=2)                      cccGCTTTGTTTTTGGGGGTTGGTTGTTGCTGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGCCA‑A‑GTGTTCGCCACGACAGTTTCAGCGCCTGTGAGACCGAGCGCCGCGCGGGCGGCGCTCgat                                                                                                                          >  1:488014/1‑128 (MQ=2)                           tttGTTTTTGGGGGTTGGTTGTTGCTGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGt                                                                                                   <  1:429974/150‑1 (MQ=255)                               tttttGGGGGTTGGTTGTTGCTGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCg                                                                                               <  2:314092/150‑1 (MQ=255)                                   tGGGGGTTGGTTGTTGCTGTTGGGGAGGAACTGTTTTGAGAGGGTGCAGGCTGTGAGATGTGTCCACCTCAACCCTTGCAGTGTCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAaca                                                                                           <  2:273232/150‑1 (MQ=37)                                       ggttggttGTTGCTGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTg                                                                                       >  2:596456/1‑150 (MQ=255)                                              tgttgCTGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGccc                                                                                <  1:193824/150‑1 (MQ=255)                                                  gCTGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGAt                                                                            <  2:575672/150‑1 (MQ=255)                                                    tGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATAc                                                                          <  1:292709/150‑1 (MQ=255)                                                           gaggaACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGACCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAgg                                                                                                                  <  2:483848/103‑1 (MQ=18)                                                           gaggaACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGACCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAgg                                                                                                                  >  1:483848/1‑103 (MQ=18)                                                                aCTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTcccc                                                              >  2:176137/1‑150 (MQ=255)                                                                  tGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTCCCCtt                                                            >  1:642511/1‑150 (MQ=255)                                                                      ttGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTCCCCTTatat                                                        <  1:286436/150‑1 (MQ=255)                                                                                gtTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTCCCCTTATATTTCACTTTCt                                              <  2:642511/150‑1 (MQ=255)                                                                                 ttGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGc                                                                                                <  2:538218/99‑1 (MQ=255)                                                                                 ttGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGc                                                                                                >  1:538218/1‑99 (MQ=255)                                                                                   ggCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGaaa                                                                                                          <  1:117737/87‑1 (MQ=255)                                                                                   ggCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGaaa                                                                                                          >  2:117737/1‑87 (MQ=255)                                                                                     cTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGaaa                                         <  1:596456/150‑1 (MQ=255)                                                                                      tgtgAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTcc                                                                <  1:359570/126‑1 (MQ=255)                                                                                      tgtgAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTcc                                                                >  2:359570/1‑126 (MQ=255)                                                                                            aTGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAgg                                  <  2:429594/150‑1 (MQ=255)                                                                                            aTGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAgg                                  >  2:294331/1‑150 (MQ=255)                                                                                               tgtCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTg                               <  1:176137/150‑1 (MQ=255)                                                                                                           cccTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACACCCTCTTGa                   >  2:142931/1‑150 (MQ=255)                                                                                                             cTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTca                                                                                                                      >  2:750771/1‑49 (MQ=255)                                                                                                             cTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCCca                                                                                                                      <  1:750771/49‑1 (MQ=255)                                                                                                                         gtgAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAg                                   <  1:723411/120‑1 (MQ=255)                                                                                                                         gtgAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAg                                   >  2:723411/1‑120 (MQ=255)                                                                                                                            agaCCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCACTGCAAGGGTTGTGGCGGACACTTGGCAGCCCCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACACCCTCTTGAATCCCCTTATAATgcgc  >  1:422758/1‑150 (MQ=11)                                                                                                                             gaccGAGCGCCGCCCGCGCGGCGCTCGGTTTCATAGGCGGTGAAACTGTCGTGGCGAACACTTg                                                                                       >  2:400534/4‑64 (MQ=11)                                                                                                                             gaccGAGCGCCGCCCGCGCGGCGCTCGGTTTCATAGGCGGTGAAACTGTCGTGGCGAACACTTg                                                                                       <  1:400534/61‑1 (MQ=11)                                                                                                                              aTCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTcccc                                                              >  1:652030/1‑88 (MQ=255)                                                                                                                              aTCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTcccc                                                              <  2:652030/88‑1 (MQ=255)                                                                                                                              aTCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTCCCCTTATATTTCACTTTCt                                              >  2:202344/1‑104 (MQ=255)                                                                                                                              aTCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTCCCCTTATATTTCACTTTCt                                              <  1:202344/104‑1 (MQ=255)                                                                                                                                             |                                                                                                                                     GCGGGGAGGCCGTCAGGCCTCCCCGCTTTGTTTTTGGGGGTTGGTTGTTGCTGTTGGGGAGGAACTGTTTTGAGAGGGTGTTGGCTGTGAGATGTGTCCGCCACAACCCTTGCAGTGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGGTCTCACAGGCGCTGAAACTGTCGTGGCGAACACTTGGCAGCCCCGATACGGTCTTTTCCCCTTATATTTCACTTTCTTGAAATTAAAGGTTGACACCCTCTTGAATCCCCTTATAATGCGC  >  NC_002947/697091‑697363

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑