Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,466,841	T→G	22.2%	intergenic (‑16/+108)	PP_3081 ← / ← PP_5560	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,466,841	0	T	G	22.2%	75.6 / 11.6	48	intergenic (‑16/+108)	PP_3081/PP_5560	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (10/26);  new base G (6/5);  total (17/31)
Fisher's exact test for biased strand distribution p-value = 1.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGTACCTGCGGGCAGGTTGTCCCAGCTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGC‑GTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTCCTGGTCCTCGGCAGTGCCTCCGCTG  >  NC_002947/3466693‑3466985                                                                                                                                                       |                                                                                                                                                  gcgTACCTGCGGGCAGGTTGTCCCAGCTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCt                                                                                                                                                   >  2:228974/1‑149 (MQ=255)  cgTACCTGCGGGCAGGTTGTCCCAGCTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTg                                                                                                                                                  <  4:53575/149‑1 (MQ=255)   gTACCTGCGGGCAGGTTGTCCCAGCTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTgc                                                                                                                                                 <  3:247872/149‑1 (MQ=255)      ccTGCGGGCAGGTTGTCCCAGCTCAGTTGCGGGGTACCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTgcgg                                                                                                                                               >  1:48727/1‑149 (MQ=255)      ccTGCGGGCAGGTTGTCCCAGCTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTgcggc                                                                                                                                              <  4:90005/149‑1 (MQ=255)         gCGGGCAGGTTGTCCCAGCTCAGTTGCGGGGT‑CCGCTCTTCACCACCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCggcggc                                                                                                                                           >  1:229460/1‑149 (MQ=255)           gggCAGGTTGTCCCAGCTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCGCAGGCGGcc                                                                                                                                          >  5:138265/1‑148 (MQ=255)             gCAGGTTGTCCCAGCTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCGCAGGCGGCCaag                                                                                                                                       <  6:138265/149‑2 (MQ=255)             gCAGGTTGTCCCAGCTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCGCAGGCGGCCaag                                                                                                                                       <  7:20775/149‑2 (MQ=255)                 gTTGTCCCAGCTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGAATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCtg                                                                                                                                   <  2:229460/149‑1 (MQ=255)                     tCCCAGCTCAGTTGCGGGGG‑CCGCTCTTCACCGGCACCGCAGGCGGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTTAAAGACTAGTAACT‑CACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGc                                                                                                                                <  2:123915/148‑1 (MQ=255)                      cccAGCTCAGTTGGGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGCCCTGTTGCAGGGCAATTACCCCGCCATCAGTTAAACACGAGGAAATACACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCa                                                                                                                               <  1:228974/149‑1 (MQ=255)                       ccAGCTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCGTTGGCCGCCGCAGGCGGCCAAGGcgcgatg                                                                                                                               >  3:52800/1‑141 (MQ=255)                       ccAGCTCAGTGGCGGGGG‑CCGCTCTACCCCGGCCCCGCATGCGGGGTCCTGGCCGACCTGTTGCTGGGCAATGACGCCGCCATCAGTCAACGACGCGCAACT‑CACCGACATCGCGGGTTGGCCGCCGCAGGCGGCCAAGGcgcgatg                                                                                                                               <  4:52800/147‑7 (MQ=255)                        cAGCTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGCATGTCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAggg                                                                                                                            <  1:218091/149‑1 (MQ=255)                        cAGCTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCAGCGGCGGCCAACCCTGTTCAggg                                                                                                                            >  4:63612/1‑149 (MQ=255)                        cAGCTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCCCCGGCGGCGGCCCACCCAGTGCAggg                                                                                                                            >  2:147839/1‑149 (MQ=255)                         aGCTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAggg                                                                                                                            >  8:67881/1‑148 (MQ=255)                         aGCTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCGGCGGCGGCCAACGCTGTGCAGGgc                                                                                                                           >  3:187500/1‑149 (MQ=255)                           cTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCGGCGGCGGCCCACCCGGTGGAGGggag                                                                                                                         >  2:190365/1‑149 (MQ=255)                                   cGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAagcag                                                                                                                 <  1:190365/149‑1 (MQ=255)                                   cGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAagca                                                                                                                  <  2:198034/148‑1 (MQ=255)                                      ggT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGa                                                                                                              <  2:48727/149‑1 (MQ=255)                                          ccGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACa                                                                                                           <  7:67881/149‑1 (MQ=255)                                           cGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAg                                                                                                          >  1:34000/1‑149 (MQ=255)                                                ttCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGcggcgg                                                                                                                                            >  3:210785/1‑110 (MQ=255)                                                ttCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGcggcgg                                                                                                                                            <  4:210785/110‑1 (MQ=255)                                                   aCCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCCACGCAGTGCAGGGCAGCAAAGCAGCGAACAGCCAgtgtg                                                                                                  >  6:92987/1‑148 (MQ=255)                                                     ggaccccGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTg                                                                                                <  8:83722/144‑1 (MQ=255)                                                                 ccGGGTCCTGGCCGACCTGTTGCAGGGAAATGACGCCGCAATCTGTCAAATCCGAGCAACT‑GACCGACATCGCGCCTTGGCCGCCGGCGGGGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGt                                                                                     <  4:161224/148‑1 (MQ=255)                                                                  cGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCa                                                                                   <  5:92987/149‑1 (MQ=255)                                                                   gggTCCTGGCCGACCTGTTGCTGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAagcagc                                                                                                                <  2:249320/119‑1 (MQ=255)                                                                    ggTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCtgtg                                                                                                                                 >  4:214733/1‑101 (MQ=255)                                                                    ggTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCtgtg                                                                                                                                 <  3:214733/101‑1 (MQ=255)                                                                        gtgcccGACGTGTTCCAGGGCTAGTACGCCCCCAACAGTGACCCACGCGTAACT‑GCCCGACTTCGCGCCTTGGCCGCCTGCGGGGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCtt                                                                             <  8:262579/145‑1 (MQ=255)                                                                             ctaCCTGTTGCAGGGCAATGAGGCCGCCATCAGTGAAATACGCGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAg                                                                        <  4:228262/147‑1 (MQ=255)                                                                                ccTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGc                                                                     <  3:116610/149‑1 (MQ=255)                                                                                    ttGCAGGGCAATGACGCCGCCATCAGTCAAAGACGAGCAACT‑GACCGACAGCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGC‑GTc                                                                 <  1:147839/148‑1 (MQ=255)                                                                                     tGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGC‑GTCAc                                                               >  7:249388/1‑149 (MQ=255)                                                                                      gCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGC‑GTCAc                                                               <  2:77040/148‑1 (MQ=255)                                                                                      gCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGC‑GTCAc                                                               >  1:77040/1‑148 (MQ=255)                                                                                         gggCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGC‑GTCACGGCt                                                           <  4:187500/149‑1 (MQ=255)                                                                                           gCATTGACTCCGCCATCAGTTAAAGACGAGGAACT‑GACCTACATCTCGCCTTGTCCGCCTGCGGCGGCCAACGCTGTGCAGTGCATCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGC‑GTCACGGCTCa                                                         <  6:302480/149‑1 (MQ=255)                                                                                                              tGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGGCGCCGGCGGCCGCCAACCCGGTGGACGGCAGCAAAGCAGCGAACAGCCAGGGTGTGAGGGGCATGGGCAAAACAAGGGAGGGCGGGCAC‑GCGCAGTGTAGACCACGTCTGcgt                                      >  4:17217/1‑147 (MQ=255)                                                                                                                 aaGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGC‑GTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAg                                   <  8:249388/149‑1 (MQ=255)                                                                                                                    aCGAGCAAGT‑GACCGACATCGCGCGTTGGCCGCGGGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGC‑GTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCgg                                <  3:140242/149‑1 (MQ=255)                                                                                                                                    aCATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGC‑GTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTCCTGGTCCTCg                 <  2:34000/149‑1 (MQ=255)                                                                                                                                                ggCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCATGGCAGGGC‑GTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTCCTGGTCCTCGGCAGTGCCTCCg     >  3:313855/1‑149 (MQ=255)                                                                                                                                                   cgccTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGC‑GTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTCCTGGTCCTCGGCAGTGCCTCCGCTg  <  3:63612/149‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                  GCGTACCTGCGGGCAGGTTGTCCCAGCTCAGTTGCGGGGT‑CCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACT‑GACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGC‑GTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTCCTGGTCCTCGGCAGTGCCTCCGCTG  >  NC_002947/3466693‑3466985

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: ‑