Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,656,407:1	+C	10.3%	coding (891/909 nt)	PP_3221 ←	ABC transporter permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,656,407	1	.	C	10.3%	133.9 / 11.9	39	coding (891/909 nt)	PP_3221	ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base . (17/18);  new base C (2/2);  total (19/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.71e-01

CCCACCACCGCCAGGGTCTCGCCCTGGACCAGGCTGAACGACAGCTGGCGCAGGGCCTGGCTGCGTTGCCCGGCGAAGCTGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGACGGCCGTTGGCGATCAGCGTGCCCCATTCCGCGGCGGGTGGCGCCGCGCCAAAG  >  NC_002947/3656265‑3656554                                                                                                                                                |                                                                                                                                                    cccACCACCGCCAGGGTCTCGCCCTGGACCAGGCTGAACGACAGCTGGCGCAGGGCCTGGCTGCGTTGCCCGGCGAAGCTGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTg                                                                                                                                               >  8:29960/1‑149 (MQ=255)        cagCCAGGGTCTCGCCCTGGACCAGGCTGAACGACAGCTGGCGCAGGGCCTGGCTGCGTTGCCCGGCGAAGCTGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTGGCGCGCAgcgcc                                                                                                                                           >  5:142741/3‑146 (MQ=255)           ccAGGGTCTCGCCCTGGACCAGGCTGAACGACAGCTGGCGCAGGGCCTGGCTGCGTTGCCCGGCGAAGCTGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTGGCGCGCAgcgccgagga                                                                                                                                      <  6:142741/149‑7 (MQ=255)               ggTCTCGCCCTGGACCAGGCTGAACGACAGCTGGCGCAGGGCCTGGCTGCGTTGCCCGGCGAAGCTGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGtt                                                                                                                                 <  3:163035/149‑1 (MQ=255)                      cccTGGACCAGGCTGAACGACAGCTGGCGCAGGGCCTGGCTGCGTTGCCCGGCGAAGCTGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTGGCGCGCAgcgccgagga                                                                                                                                      >  6:293706/1‑132 (MQ=255)                      cccTGGACCAGGCTGAACGACAGCTGGCGCAGGGCCTGGCTGCGTTGCCCGGCGAAGCTGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTGGCGCGCAgcgccgagga                                                                                                                                      <  5:293706/138‑7 (MQ=255)                           gACCAGGCTGAACGACAGCTGGCGCAGGGCCTGGCTGCGTTGCCCGGCGAAGCTGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAacac                                                                                                                     <  8:272146/149‑1 (MQ=255)                               aGGCTGAACGACAGCTGGCGCAGGGCCTGGCTGCGTTGCCCGGCGAAGCTGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACg                                                                                                                 <  4:256387/149‑1 (MQ=255)                                   tGAACGACAGCTGGCGCAGGGCCTGGCTGCGTTGCCCGGCGAAGCTGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGa                                                                                                                               >  2:209908/1‑131 (MQ=255)                                    gAACGACAGCTGGCGCAGGGCCTGGCTGCGTTGCCCGGCGAAGCTGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGccac                                                                                                            >  5:224417/1‑149 (MQ=255)                                        gACAGCTGGCGCAGGGCCTGGCTGCGTTGCCCGGCGAAGCTGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCcaccac                                                                                                         >  7:4959/1‑148 (MQ=255)                                                         cttgCTTCGTTGCCCGGCGAAGCTGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGATGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAg                                                                                       <  2:88979/146‑1 (MQ=255)                                                         cTGGCTGCGTTGCCCGGCGAAGCTGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAg                                                                                       <  6:224417/149‑1 (MQ=255)                                                            gCTGCGTTGCCCGGCGAAGCTGTAGCTGCCGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGa                                                                                    >  1:227718/1‑149 (MQ=255)                                                                      ccGGCGAAGCTGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAggg                                                                          >  1:289707/1‑149 (MQ=255)                                                                            aaGCTGTAGCTGACGCTTAGGTCGGGGACCTCGATGAGGGGTGACTGGCTCATCTGGCATGCTCCTCG‑GCGCTTGGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGtg                                                                    <  2:31947/149‑1 (MQ=255)                                                                                tGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGtgat                                                                  >  5:153624/1‑147 (MQ=255)                                                                                 gTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGcccc                                                                                               >  7:186389/1‑117 (MQ=255)                                                                                 gTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGcccc                                                                                               <  8:186389/117‑1 (MQ=255)                                                                                  tAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAgg                                                              <  4:223514/149‑1 (MQ=255)                                                                                  tAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAg                                                               <  8:109962/148‑1 (MQ=255)                                                                                    gCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAac                                                                                                                       >  2:32826/1‑90 (MQ=255)                                                                                    gCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAac                                                                                                                       <  1:32826/90‑1 (MQ=255)                                                                                    gCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAgg                                                              >  5:193327/1‑147 (MQ=255)                                                                                        aCGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGa                                                        <  4:14488/149‑1 (MQ=255)                                                                                              aGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGACGGc                                                    <  6:193327/147‑1 (MQ=255)                                                                                                gTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGACGGCCGtt                                                <  2:289707/149‑1 (MQ=255)                                                                                                   gcgGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGACGGCCGTTGGc                                             >  6:46369/1‑149 (MQ=255)                                                                                                    cgGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGa                                                        >  2:160907/1‑137 (MQ=255)                                                                                                    cgGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGa                                                        <  1:160907/137‑1 (MQ=255)                                                                                                            gATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGACGGCCGTTGGCGATCAGCGt                                    >  1:293989/1‑149 (MQ=255)                                                                                                                       aCTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGACGGCCGTTGGCGATCAGCGTGCCCCATTcc                          <  8:4959/148‑1 (MQ=255)                                                                                                                       aCTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGACGGCCGTTGGCGATCAGCGTGCCCCATTCcg                         >  1:48145/1‑149 (MQ=255)                                                                                                                            cTCATCGGGCATTCTCATCG‑TCGCTGCGAGACAGGTGTTTGAGGCTGAACACCACGGCCACCACTAACAGCACCTGTAGCAGTGATAGACAAGGGGCTGTGATGAGGAAGTGACGGCCGTTGGCGATCAGCGTGCCCCATTCCgcggc                     <  1:203354/148‑1 (MQ=255)                                                                                                                               aTCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGACGGCCGTTGGCGATCAGCGTGCCCCATTCCGCGGCggg                  <  2:227718/148‑1 (MQ=255)                                                                                                                                   ggCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGACGGCCGTTGGCGATCAGCGTGCCCCATTCCGCGGCGGGTGgcg             >  2:125090/1‑149 (MQ=255)                                                                                                                                        gCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTCAACACCACGGCCCCCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGACGGCCGTTGGCGCTCAGCGTGCCCCATTCCCCGGCGGGTGgcgccgcg        >  8:48450/1‑149 (MQ=255)                                                                                                                                         ctcctcG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGACGGCCGTTGGCGATCAGCGTGCCCCATTCCGCGGCGGGTGgcgccgcgc       <  6:153624/149‑1 (MQ=255)                                                                                                                                            ctcG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGACGGCCGTTGGCGATCAGCGTGCCCCATTCCGCGGCGGGTGGCGCCGCGCCa     >  1:5168/1‑148 (MQ=255)                                                                                                                                               g‑gCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGACGGCCGTTGGCGATCAGCGTGCCCCATTCCGCGGCGGGTGGCGCCGCGCCAAAg  <  2:48145/148‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                    CCCACCACCGCCAGGGTCTCGCCCTGGACCAGGCTGAACGACAGCTGGCGCAGGGCCTGGCTGCGTTGCCCGGCGAAGCTGTAGCTGACGCTTAGGTCGCGGACCTCGATCAGGGGTGACTGGCTCATCGGGCATGCTCCTCG‑GCGCTGCGCGCCAGGTGGTTGAGGCTGAACACCACGGCCACCACGAACAGCCCCGGTAGCAGGGATAGCCAAGGGGCGGTGATGAGGAAGTGACGGCCGTTGGCGATCAGCGTGCCCCATTCCGCGGCGGGTGGCGCCGCGCCAAAG  >  NC_002947/3656265‑3656554

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑