Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	337,816:1	+A	15.9%	intergenic (‑66/+63)	PP_0279 ← / ← PP_0280	hypothetical protein/amino acid ABC transporter permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	337,816	1	.	A	15.9%	141.1 / 25.1	44	intergenic (‑66/+63)	PP_0279/PP_0280	hypothetical protein/amino acid ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base . (20/17);  new base A (5/2);  total (25/19)
Fisher's exact test for biased strand distribution p-value = 6.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.12e-01

GCTGGTGCTCGATCAGGAACTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACGAGATCACC  >  NC_002947/337675‑337957                                                                                                                                               |                                                                                                                                               gctgGTGCTCGATCAGGAACTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCa                                                                                                                                         <  5:304852/149‑1 (MQ=255)           gATCAGGAACTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGgcgc                                                                                                                               >  3:101387/1‑149 (MQ=255)               aGGAACTGGTCGAGGGCCTGGAAGCGGGTGCTAAGGTGGGGGCTGTGGAGGTGGTTGGTAATGGCAAGGATGTGTTGTGGTTTTGAGGGCCTCTTCGCGGGCCCGCCCGCTCCCACAGGTATAGCGCA‑ACATTCAAGGTTGGCGCTaca                                                                                                                           >  5:312016/1‑149 (MQ=255)                    cTGGTCTAGGGCCTGGTAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGTCCTCTTCGCTGTCACTCACGCTCCCACAGGTATAGCGCC‑AAATTCAAGTTTGGAGCTACACCtgt                                                                                                                      <  6:312016/149‑1 (MQ=255)                                      gCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTAAAGCGCC‑ACATTCAAGGTTGGCGCTAACCCTTTGGGAGCGGGCGTGCCcgc                                                                                                    >  8:284772/1‑149 (MQ=255)                                                  gTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑Gcagtcagt                                                                                       >  1:43227/1‑149 (MQ=255)                                                   tGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTac                                                                                                                            <  2:251174/112‑1 (MQ=255)                                                   tGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACAATCAAGGTTGGCGCTac                                                                                                                            >  1:251174/1‑112 (MQ=255)                                                                ggtggtTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑Gcagtca                                                                                         >  2:56281/1‑133 (MQ=255)                                                                ggtggtTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑Gcagtca                                                                                         <  1:56281/133‑1 (MQ=255)                                                                        ggCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTggca                                                                  <  7:284772/148‑1 (MQ=255)                                                                         gCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTTGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTAAGTGAGGTCTCAGCGGCCTTggcagg                                                                >  1:202563/1‑149 (MQ=255)                                                                              gCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGGC‑ACATTGAAGGGTGGCGCGACACCGGGGGGGGCGGGCGTGCCCGCGCA‑GCAGTCAGTGAGGtcaga                                                                              >  4:72119/1‑127 (MQ=37)                                                                              gCAAGGATGTGTGGGGGTTTTGAGGCCCTCTTCGCGGCCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCa                                                                              <  3:72119/130‑1 (MQ=255)                                                                                aaGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCAc                                                         >  5:118718/1‑149 (MQ=255)                                                                                 aGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCACCCACAGGTTTAGCGCC‑ACCTTGAAGGTTGGGGCGACCCCAGGGGGAGCGGGCGTGCCCGCGAG‑GGAGGGAGTGAGGGGGCAGCGGGCGTGGCAGGCAGCCAcc                                                        >  6:301649/1‑148 (MQ=19)                                                                                   gATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCAcgcg                                                      <  2:43227/149‑1 (MQ=255)                                                                                       tgggggggtTTTGCGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAATGCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCaa                                                   <  1:62386/143‑1 (MQ=37)                                                                                            tggtTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATTGCGCC‑ACATTCAAGGTTGGCGGTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAgcg                                             >  7:8283/1‑149 (MQ=255)                                                                                                  tgtgggCCTTTTCGCGGGCACGCCGGATCCCACTGTTTTAGGCCA‑AAATTCATGGTTGGCGCTAAACCTGTGGTTGGGGGGGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCca                                        <  8:40350/145‑1 (MQ=255)                                                                                                      ggCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTAAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTTGCAGGCATCCCCGCGCACCCAGCGCTCCagcagc                                   >  2:243286/1‑149 (MQ=255)                                                                                                         ctctTCGCGGGCACGCCCCCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCAGTGGGAGCCGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCATGGCAGGCATCCACGCGCAACCAGCGCTCCaccagcat                                 >  6:118059/1‑146 (MQ=255)                                                                                                            ttCGCGGGCACGCCCGCTCCCACAGGTATAGTGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAg                             <  5:135412/149‑1 (MQ=255)                                                                                                               gcgGCCACGCCCGCACCCACAGGAATACCGCC‑ACAATCAAGCTTGGCTCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGCTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCt                          <  8:234815/149‑1 (MQ=38)                                                                                                                 gggCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTg                        <  8:8283/149‑1 (MQ=255)                                                                                                                  ggCACGCCCGCTCCCACAGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTg                        >  8:206347/1‑148 (MQ=18)                                                                                                                        cccGCTCCCACAGGTATTGCGCC‑ACATTCAAGGTTGGCGCTACACGTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGc                 <  4:101387/149‑1 (MQ=255)                                                                                                                          cGCTCCCACAGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCAt               <  7:206347/149‑1 (MQ=21)                                                                                                                               ccACAGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCagcagc                                   <  1:6320/124‑1 (MQ=18)                                                                                                                               ccACAGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCagcagc                                   >  2:6320/1‑124 (MQ=18)                                                                                                                               ccACAGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAAc           >  5:100059/1‑148 (MQ=25)                                                                                                                               ccACAGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAAc           >  7:289565/1‑148 (MQ=25)                                                                                                                               ccACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGc                 <  6:57966/142‑1 (MQ=255)                                                                                                                               ccACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGc                 >  5:57966/1‑142 (MQ=255)                                                                                                                                cacaGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAAc           >  3:205972/1‑147 (MQ=255)                                                                                                                                 acaGGTGTAGCGCCAACCTTGAATG‑TGGCGCTATACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAAc           >  4:116635/1‑146 (MQ=25)                                                                                                                                 acaGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAAc           >  6:133529/1‑146 (MQ=255)                                                                                                                                     gTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACGAGATCa    >  5:104413/1‑149 (MQ=255)                                                                                                                                     gTATAGCGCC‑ACATTAATGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGGCTCAGCGGCCATGGCAGGCATAAACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACGAGATCa    >  3:103516/1‑149 (MQ=255)                                                                                                                                      tataGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCtt                         >  7:215454/1‑127 (MQ=255)                                                                                                                                      tataGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCtt                         <  8:215454/127‑1 (MQ=255)                                                                                                                                        taGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACGAGATCAcc  <  4:205972/148‑1 (MQ=255)                                                                                                                                            gcC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCt                                  <  3:48832/112‑1 (MQ=255)                                                                                                                                            gcC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCt                                  >  4:48832/1‑112 (MQ=255)                                                                                                                                               |                                                                                                                                               GCTGGTGCTCGATCAGGAACTGGTCGAGGGCCTGGAAGCGGGTGCTTAGGTGGGGGCTGTGGAGGTGGTTGGGCATGGCAAGGATGTGTGGTGGTTTTGAGGGCCTCTTCGCGGGCACGCCCGCTCCCACAGGTATAGCGCC‑ACATTCAAGGTTGGCGCTACACCTGTGGGAGCGGGCGTGCCCGCGAA‑GCAGTCAGTGAGGTCTCAGCGGCCTTGGCAGGCATCCACGCGCAACCAGCGCTCCAGCAGCTTGAAGCCTTGCACCAGCATGAACGAGATCACC  >  NC_002947/337675‑337957

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: ‑