Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,687,701	Δ1 bp	6.7%	coding (677/1074 nt)	PP_4148 →	ABC transporter permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,687,701	0	T	.	6.7%	189.6 / 7.1	60	coding (677/1074 nt)	PP_4148	ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base T (30/26);  new base . (2/2);  total (32/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01

CTGATCGTGCTGTTCGCCGGTGGCAGCTACTTCGACTGGTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGCCAAGGCCAAGGGCCTGAGCCGATCACGGGTGCTGTACGGCCACGTGTTCCGCAACGC  >  NC_002947/4687562‑4687842                                                                                                                                             |                                                                                                                                               ctgATCGTGCTGTTCGCCGGTGGCAGCTACTTCGACTGGTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCgg                                                                                                                                       <  2:179498/149‑1 (MQ=255) ctgATCGTGCTGTTCGCCGGTGGCAGCTACTTCGACTGGTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCg                                                                                                                                        <  5:15911/148‑1 (MQ=255)   gATCGTGCTGTTCGCCGGTGGCAGCTACTTCGACTGGTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGc                                                                                                                                      >  1:76963/1‑148 (MQ=255)          cTGTTCGCCGGTGGCAGCTACTTCGACTGGTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATGACCAGCGC‑GGTGATCGGCag                                                                                                                                    >  1:269310/1‑142 (MQ=39)          cTGTTCGCCGGTGGCAGCTACTTCGACTGGTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATGACCAGCGC‑GGTGATCGGCag                                                                                                                                    <  2:269310/143‑2 (MQ=39)           tGTTCGCCGGTGGCAGCTACTTCGACTGGTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGc                                                                                                                              >  7:222854/1‑148 (MQ=255)                  cGGTGGCAGCTACTTCGACTGGTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGa                                                                                                                      >  8:178423/1‑149 (MQ=255)                    gTGGCAGCTACTTCGACTGGTTCCCGCTGCGTGGCCGCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGAcc                                                                                                                    <  8:218974/149‑1 (MQ=255)                         aGCTACTTCGACTGGTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCctgct                                                                                                               >  5:171631/1‑149 (MQ=255)                                tCGACTGGTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATGACCAGCGC‑GGTGATCGGCag                                                                                                                                    <  7:54069/121‑2 (MQ=38)                                tCGACTGGTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATGACCAGCGC‑GGTGATCGGCag                                                                                                                                    >  8:54069/1‑120 (MQ=38)                                tCGACTGGTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGAcc                                                                                                           >  4:19350/1‑146 (MQ=255)                                  gACTGGTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGaa                                                                                                      >  8:72852/1‑149 (MQ=255)                                    cTGGTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACa                                                                                                    <  1:80795/149‑1 (MQ=255)                                       gTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGcca                                                                                                                            <  1:88656/122‑1 (MQ=255)                                       gTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGcca                                                                                                                            >  2:88656/1‑122 (MQ=255)                                       gTTACCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCT‑CTGACCAAGAACAGCtt                                                                                                >  7:284187/1‑149 (MQ=255)                                        ttCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAAc                                                                                                     <  8:55087/144‑1 (MQ=255)                                        ttCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAAc                                                                                                     >  7:55087/1‑144 (MQ=255)                                        ttCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCtt                                                                                                >  5:12264/1‑149 (MQ=255)                                            cGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTc                                                                                            <  8:222854/149‑1 (MQ=255)                                                        tCACCTCGAACAACTTCGACGAACTGAGCACCACCGTCAAGGTGCTGTACTACTTCTGGCACCTGGTGCTGGCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCT‑CTGACCAAGAACAGCTTCCTCCACGAAATcaaca                                                                               <  8:284187/149‑1 (MQ=255)                                                        tCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACtt                                                                                                                                 <  3:167552/100‑1 (MQ=255)                                                        tCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACtt                                                                                                                                 >  4:167552/1‑100 (MQ=255)                                                          aCCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATcaac                                                                                <  7:178423/147‑1 (MQ=255)                                                            cTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCaacaaac                                                                            <  3:19350/149‑1 (MQ=255)                                                               caacaaCTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTTGTCATCGGCAACTTCGCCACCATGACCCTGATGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGt                                                                         <  6:157898/149‑1 (MQ=255)                                                               caacaaCTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTc                                                                                            <  5:184498/130‑1 (MQ=255)                                                               caacaaCTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTc                                                                                            >  6:184498/1‑130 (MQ=255)                                                               caacaaCTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCaacaaaca                                                                           <  6:12264/147‑1 (MQ=255)                                                                aacaacTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGa                                                                                                             >  5:177011/1‑112 (MQ=255)                                                                aacaacTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGa                                                                                                             <  6:177011/112‑1 (MQ=255)                                                                        cgacgaACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑Ca                                                               >  1:221498/1‑149 (MQ=255)                                                                                tGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCgccaag                                                       >  1:273450/1‑149 (MQ=255)                                                                                    caccacCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTcgacg                                                                                        <  8:71597/113‑1 (MQ=255)                                                                                    caccacCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTcgacg                                                                                        >  7:71597/1‑113 (MQ=255)                                                                                       caccGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCt                                                                                                 <  5:246361/101‑1 (MQ=255)                                                                                       caccGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCt                                                                                                 >  6:246361/1‑101 (MQ=255)                                                                                       caccGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCaacaaa                                                                             <  4:194338/121‑1 (MQ=255)                                                                                       caccGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGccaaggccaagg                                                >  4:160974/1‑149 (MQ=255)                                                                                         ccGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGCCAAGGCCAAGGGc                                              >  8:90091/1‑149 (MQ=255)                                                                                            gCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGCCAAGGCCAAGGGCCt                                            >  1:14871/1‑148 (MQ=255)                                                                                              aaGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTAc                                                                       >  2:93046/1‑120 (MQ=255)                                                                                                    cTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGCCAAGGCCAAGGGCCTGAGCCGAt                                    <  2:76963/148‑1 (MQ=255)                                                                                                     tGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCAGACCAAGAACAGCTTCGAAGACGAAATAAACAAAAAGTAAGTGGTACACC‑CCAAAGCCAAGGGCCTGAGCCGAta                                   >  1:257326/1‑147 (MQ=37)                                                                                                       gACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGCCAAGGCCAAGGGCCTGAGCCGATCAc                                 <  6:171631/148‑1 (MQ=255)                                                                                                       gACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGCCAAGGCCAAGGGCCTGAGCCGATCAc                                 <  2:57668/148‑1 (MQ=255)                                                                                                          tactTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCgcc                                                          <  6:178431/120‑1 (MQ=255)                                                                                                          tactTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCgcc                                                          >  5:178431/1‑120 (MQ=255)                                                                                                            ctTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGCCAAGGCCAAGGGCCTGAGCCGATCACGGGTg                            <  7:72852/148‑1 (MQ=255)                                                                                                            ctTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGCCAAGGCCAAGGGCCTGAGCCGATCACGGGTg                            <  3:160974/148‑1 (MQ=255)                                                                                                             ttCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGCCAAGGCCAAGGGCCTGAGCCGATCACGGGTGCt                          >  8:762/1‑149 (MQ=255)                                                                                                                  gCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGCCAAGGCCAAGGGCCTGAGCCGATCACGGGTGCTGTACg                     >  6:271400/1‑149 (MQ=255)                                                                                                                    aCCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGCCAAGGCCAAGGGCCTGAGCCGATCACGGGTGCTGTACGGc                   >  1:122471/1‑149 (MQ=255)                                                                                                                      cTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGCCAAGGCCAAGGGCCTGAGCCGATCACGGGTGCTGTACGGCCa                 >  1:281446/1‑149 (MQ=255)                                                                                                                      cTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGCCAAGGCCAAGGGCCTGAGCCGATCACGGGTGCTGTACGGCCa                 >  8:84379/1‑149 (MQ=255)                                                                                                                             tgcCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGCCAAGGCCAAGGGCCTGAGCCGATCACGGGTGCTGTACGGCCACGTGTTc          >  2:100614/1‑149 (MQ=255)                                                                                                                                 gATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGt                                                                         <  3:121004/83‑1 (MQ=255)                                                                                                                                 gATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGt                                                                         >  4:121004/1‑83 (MQ=255)                                                                                                                                     aCC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGCCAAGGCCAAGGGCCTGAGCCGATCACGGGTGCTGTACGGCCACGTGTTCCGCAACGc  <  2:273450/149‑1 (MQ=255)                                                                                                                                             |                                                                                                                                               CTGATCGTGCTGTTCGCCGGTGGCAGCTACTTCGACTGGTTCCCGCTGCGTGGCCTCACCTCCAACAACTTCGACGAACTGAGCACCACCGGCAAGGTGCTGGACTACTTCTGGCACCTGGTGCTGCCGATCACC‑GCGCTGGTCATCGGCAACTTCGCCACCATGACCCTGCTGACCAAGAACAGCTTCCTCGACGAAATCAACAAACAGTACGTGGT‑CACCGCCAAGGCCAAGGGCCTGAGCCGATCACGGGTGCTGTACGGCCACGTGTTCCGCAACGC  >  NC_002947/4687562‑4687842

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: ‑