Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,256,865	T→A	9.1%	intergenic (+17/+28)	PP_5703 → / ← PP_4634	type III effector protein HopJ/alpha/beta family hydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,256,865	0	T	A	9.1%	120.5 / 3.4	44	intergenic (+17/+28)	PP_5703/PP_4634	type III effector protein HopJ/alpha/beta family hydrolase
Reads supporting (aligned to +/- strand):  ref base T (21/19);  new base A (2/2);  total (23/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.92e-01

CGGCGAGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGCCAAT  >  NC_002947/5256722‑5257009                                                                                                                                                 |                                                                                                                                                 cGGCGAGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCg                                                                                                                                              <  3:99837/148‑1 (MQ=255)    cGAGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCgg                                                                                                                                             <  4:136580/146‑1 (MQ=255)        cACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCAAAGCGGccccggc                                                                                                                                      <  5:294983/149‑4 (MQ=255)            aCCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATcc                                                                                                                                  >  7:15344/1‑149 (MQ=255)                tGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTgcg                                                                                                                              >  8:257072/1‑149 (MQ=255)                tGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTgcg                                                                                                                              <  1:78241/149‑1 (MQ=255)                tGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTgcg                                                                                                                              <  7:257072/149‑1 (MQ=255)                          gCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTc                                                                                                                     >  6:125694/1‑148 (MQ=255)                            cACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAAt                                                                                                                  >  6:284129/1‑149 (MQ=255)                            cACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCACAAAGCGGccc                                                                                                                                          >  6:103909/1‑125 (MQ=255)                            cACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCACAAAGCGGccc                                                                                                                                          <  5:103909/125‑1 (MQ=255)                               gCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCCGGGGGCCGGTTTG‑GGCCCCACCATACGGCCCCCCCCCACaaaac                                                                                                                >  2:288127/1‑145 (MQ=255)                                        tctcGACCATGGAAACATCCGTGCACTTATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTg                                                                                                       <  3:304352/145‑1 (MQ=255)                                          gCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTgc                                                                                                                               >  7:278545/1‑122 (MQ=255)                                          gCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTgc                                                                                                                               <  8:278545/122‑1 (MQ=255)                                          gCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCa                                                                                                    <  4:66098/149‑1 (MQ=255)                                          gCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGACGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGc                                                                                                      >  2:26865/1‑147 (MQ=255)                                            gACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCCGCCCCCCGAACCAGCCCCCACCCTCAAACCATGATGGTGcaaat                                                                                                  >  4:304352/1‑145 (MQ=255)                                             aCCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGc                                                                                                 >  3:270413/1‑149 (MQ=255)                                                        aTCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTc                                                                                      <  5:125694/149‑1 (MQ=255)                                                            gTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCATTGCGGCCCCAACCACCAGCCCCCCCCCCCAAAGCCTGATGGTTCCCGGCccccccccatgcctc                                                                                  >  8:164133/1‑142 (MQ=255)                                                               cACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTc                                                                               <  5:284129/149‑1 (MQ=255)                                                                   gATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGCCAGCTTTGCGGCCACACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGc                                                                                                 >  5:72393/1‑127 (MQ=255)                                                                    aTCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTg                                                                          >  5:77628/1‑149 (MQ=255)                                                                     acaaccccGGTCTGGCGGGCGTCAAGTTGCCTGCGCAGCCGCTTGCGCGCAAGGCTGGAGAGGCCC‑GGGGCCGCTTTCCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGc                                                                         <  3:167868/142‑1 (MQ=255)                                                                       aaaCACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCAAGATCCTGCGCCCACCCACAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCg                                                                       >  5:283340/1‑149 (MQ=255)                                                                                   gcgggcgTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGc                                                             <  1:269807/147‑1 (MQ=255)                                                                                   gcgggcgTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGc                                                             >  6:69112/1‑147 (MQ=255)                                                                                   gcgggcgTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAACCTCCCCTGCCGCAACCACTGc                                                             <  1:26865/147‑1 (MQ=255)                                                                                            aaGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGccccc                                                                                             >  5:275865/1‑106 (MQ=255)                                                                                            aaGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGccccc                                                                                             <  6:275865/106‑1 (MQ=255)                                                                                             aGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCgg                                                  <  7:44012/148‑1 (MQ=255)                                                                                               tttGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACAGCAAGGCCCCCCGCca                                               >  4:290226/1‑149 (MQ=255)                                                                                                    tgcGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGc                                          >  5:93856/1‑149 (MQ=255)                                                                                                                     gcAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTACCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAAACGGTCa                         >  6:147224/1‑149 (MQ=255)                                                                                                                       aaGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAAcc                              <  4:193262/142‑1 (MQ=255)                                                                                                                       aaGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAAcc                              >  3:193262/1‑142 (MQ=255)                                                                                                                               agaTTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAAcg               <  5:69112/149‑1 (MQ=255)                                                                                                                                    gCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATGCATGATGGTGCCAGGCCCCCCCCCATCCAGCCTCCCCTGCCGCAACCACGGCAAGGCCACCCGCCACCGGCTTTCGCGAAACCGGTCATGGaaaaaaagaacg          >  6:94728/1‑142 (MQ=255)                                                                                                                                    gCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGaaaaa                 <  5:94728/142‑1 (MQ=255)                                                                                                                                      c‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATg        <  8:15344/149‑1 (MQ=255)                                                                                                                                       tggggCCGCAAAGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGGCATGGAAAAACGCGAAATg        >  1:322068/2‑149 (MQ=255)                                                                                                                                             cGCTTTGCGGCCCCACGATCCTGCGCCCTCCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCCCTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCAGGGAAAAACGCGAAATGGCCAAt  >  1:183798/1‑149 (MQ=255)                                                                                                                                             cGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGCCAAt  <  2:269179/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                 CGGCGAGCACTACCGTGATGTGTTGGCCACGCCTGAGGGTAGCGACCATGGCAACATCCGTGCACTGATCAAACACGGTCTGGCGGGCGTGAAGTTTGCTGCGCAGCCGCTTGCGCGCAAGGCTTGAGATTGCC‑GGGGCCGCTTTGCGGCCCCACGATCCTGCGCCCACCCTCAATCCATGATGGTGCCAGGCCCCCCGCCTTCCAGCCTCCCCTGCCGCAACCACTGCAAGGCCACCGGCCACAGGCTTTCGCGAAACCGGTCATGGAAAAACGCGAAATGGCCAAT  >  NC_002947/5256722‑5257009

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: ‑