Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,903,164	G→T	10.2%	intergenic (‑128/‑140)	PP_5175 ← / → PP_5176	HlyD family secretion protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,903,164	0	G	T	10.2%	107.7 / 4.2	48	intergenic (‑128/‑140)	PP_5175/PP_5176	HlyD family secretion protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (14/29);  new base T (2/3);  total (16/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.66e-01

GACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCC  >  NC_002947/5903021‑5903308                                                                                                                                                   |                                                                                                                                                 gACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCTCGccc                                                                                                                                             <  3:193528/149‑1 (MQ=255)  aCGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCA‑TAGCGGGCGAGcccc                                                                                                                                            >  6:29663/1‑148 (MQ=255)      aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCTGGGGCCTCT‑TCGCGGGCGAGACcgcg                                                                                                                                          >  6:149703/1‑147 (MQ=255)      aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGaa                                                                                                                                        <  5:123497/149‑1 (MQ=255)      aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGaa                                                                                                                                        <  8:2457/149‑1 (MQ=255)      aTCAACGCCATCCTGGCTCATTGCTTGTGCACAAATGATTTGAGGGATGCGACTGTCAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCATGCGGGGGCCTAT‑TAGCCGGCGAGccccgca                                                                                                                                         >  4:104865/1‑144 (MQ=255)       tCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCcgcg                                                                                                                                          >  2:114928/1‑146 (MQ=255)        cAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAaga                                                                                                                                      <  1:114928/149‑1 (MQ=255)         aaCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAaga                                                                                                                                      <  4:49590/148‑1 (MQ=255)           cGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGGGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGc                                                                                                                                   <  3:202293/149‑1 (MQ=255)                      cTCCTTGCTTGTGCACAATTGATTTGTGGGATGCGACTGTGAGCGTTGTTCAGGGTTCGTTAATCATCAGTGAG‑GGGGGCCATCGT‑GGCTTTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGACCCCGCGAAGAGGCCTCCACAGCCa                                                                                                                        <  2:85921/149‑1 (MQ=255)                         cttgcgtgTGAACAAATGATTTGTGGGATGCGTCTGTGCGCGTTGTTCAGTGCGCGATAAACATCACTCCC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCAt                                                                                                                       <  2:310954/147‑1 (MQ=255)                             cttgTGCACAAATTTTTTGTGGGATGCGACTGTGTGCGTATTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCa                                                                                                                 <  8:94815/149‑1 (MQ=255)                                   cacaAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCTCGCCCGCGAag                                                                                                                                       <  7:309860/121‑1 (MQ=255)                                   cacaAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCTCGCCCGCGAag                                                                                                                                       >  8:309860/1‑121 (MQ=255)                                      aaaTGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTgg                                                                                                         >  3:346104/1‑147 (MQ=255)                                      aaaTGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGc                                                                                                         >  8:66021/1‑148 (MQ=255)                                              tgtgGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCa                                                                                                 <  2:248172/148‑1 (MQ=255)                                              tgggggAGGCGACGGGGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCGCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCa                                                                                                 <  8:287789/145‑1 (MQ=255)                                                         aCTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAgg                                                                                     <  5:29663/149‑1 (MQ=255)                                                              gAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGCGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TAGCGGGCGCGCCCGCCAAGAGGCCACACCAACCCAATATAACTATAAGCCAAATCCACAAACCAACacccaaag                                                                                >  4:139491/1‑142 (MQ=255)                                                               aGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCg                                                                                <  2:286445/148‑1 (MQ=255)                                                               aGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTAT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCgg                                                                               >  3:306875/1‑149 (MQ=255)                                                                gCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAACCCATCAGGCATCgg                                                                               <  7:333520/148‑1 (MQ=255)                                                                  gTAGTTTATGGTTGGATAAACATTAATTTCGGGGGGCCTTTCTCGGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCgg                                                                               <  1:329309/148‑1 (MQ=255)                                                                   tAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TAGCGGGCGGGCCCGGGAAGAGGCCGCCCCAGCCCTGTTTCAGTTTCTGGCATAGTCAGCAACCATCAGGGCTCGGccct                                                                           >  8:27464/1‑147 (MQ=255)                                                                     gTTCTGGTTTCTATAAACATAATTGAG‑GGGGGCATTTGT‑GGAATTTTTGGTGCGTGGGGGGGCGTCT‑TGGCGGGCGAGCCGGGGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAAGCATCGGCCATc                                                                          <  4:166270/148‑1 (MQ=255)                                                                      ttCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTAT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATATGCCATATACAGAAAACATCAGGCAACGGCCATacc                                                                        >  5:80527/1‑149 (MQ=255)                                                                                gttAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAAc                                                               <  3:139491/146‑1 (MQ=255)                                                                                caTAAACATCACTGCC‑GGGGGCCATCCT‑GGCATTTTTGGAGCCTGCGGGGGCCTCT‑TCGCGGGCGCGCCCGCGAAGAGGCCGCCACAGCCATGTATCCGTATCTGCCATATCCAGAAACCATCAGCCATCGGCCATCCCCGTTCCAAc                                                               <  3:44325/147‑1 (MQ=255)                                                                                           cTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTca                                                   <  4:118465/149‑1 (MQ=255)                                                                                            tGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCTGTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATACCCGTTCCAACCGCTACCtttaa                                                   >  1:278769/1‑147 (MQ=255)                                                                                              aC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAATAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAg                                                <  5:149703/149‑1 (MQ=255)                                                                                                 ggggtCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAggg                                              <  3:92070/149‑1 (MQ=255)                                                                                                    ggCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAgg                                           <  3:84311/149‑1 (MQ=255)                                                                                                    ggCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAgg                                           <  4:346104/149‑1 (MQ=255)                                                                                                     gCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGc                                          >  5:75536/1‑149 (MQ=255)                                                                                                     gCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGc                                          <  2:278769/149‑1 (MQ=255)                                                                                                       cATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTc                                        <  7:66021/149‑1 (MQ=255)                                                                                                         tGCT‑GGCATTTTTGGTGCCTGCGGGGGCTTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCTCAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTca                                                   <  3:239687/136‑1 (MQ=255)                                                                                                                            cTGCGGGGGCGTCT‑TCGCTGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATGCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCaaaa                    <  1:353717/149‑1 (MQ=255)                                                                                                                                      ctct‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGc          >  2:39964/1‑149 (MQ=255)                                                                                                                                         t‑tCGCGGGCTCGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGcc         <  7:107391/147‑1 (MQ=255)                                                                                                                                         t‑tCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCCTCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCg        >  5:330967/1‑148 (MQ=255)                                                                                                                                           tCGCGGGCTCGCCCGCGAAGAGGCCCCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGaa      >  8:313402/1‑149 (MQ=255)                                                                                                                                             gcgGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAAt     <  6:75536/148‑1 (MQ=255)                                                                                                                                              cgGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGc   <  3:104865/149‑1 (MQ=255)                                                                                                                                               gggCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGcc  <  4:306875/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                 GACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGAC‑GGGGGCCATGCT‑GGCATTTTTGGTGCCTGCGGGGGCCTCT‑TCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCC  >  NC_002947/5903021‑5903308

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑