Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,408,058	G→A	15.6%	V162V (GTC→GTT)	PP_3021 ←	LysE family transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,408,058	0	G	A	15.6%	69.2 / 5.8	32	V162V (GTC→GTT)	PP_3021	LysE family transporter
Reads supporting (aligned to +/- strand):  ref base G (12/15);  new base A (2/3);  total (14/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.14e-01

CGCACCTTGCAACAAGTCAGCCCCGGGCCAGATGCAGCAACAACGCCCCCGCCAACATCACCAGCATGACCCCCGAGGCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGCCAGGCTGGCATAGAACAGCGCGTTCTTGGGGTTGAGGATGCCAGACAAGAAGCCCATGC  >  NC_002947/3407913‑3408206                                                                                                                                                   |                                                                                                                                                      cgcACCTTGCAACAAGTCAGCCCCGGGCCAGATGCAGCAACAACGCCCCCGCAAACATCACCAGCATGACCCCCGAGGCCCGCTCCAGCCACGCCATGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGAc                                                                                                                                                     <  2:66499/148‑1 (MQ=255)  gcACCTTGCAACAAGTCAGCCCCGGGCCAGATGCAGCAACAACGCCCCCGCCAACATCACCAGCATGACCCCCGAGGCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGAc                                                                                                                                                     >  1:74054/1‑147 (MQ=255)   cACCTTGCAACAAGTCAGCCCCGGGCCAGATGCAGCAACAACGCCCCCGCCAACATCACCAGCATGACCCCCGAGGCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAg                                                                                                                                                  <  2:191276/149‑1 (MQ=255)      cTTGCAACAAGTCAGCCCCGGGCCAGATGCAGCAACAACGCCCCCGCCAACATCACCAGCATGACCCCCGAGGCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTCGCCG‑TGGCCATCGGCAACCAGcgg                                                                                                                                               <  1:267916/149‑3 (MQ=255)         ccaacaaGTCAGCCCCGGGCCAGATGCAGCAACAACGCCCCCGCCAACATCACCAGCATGACCCCCGAGGCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAg                                                                                                                                              <  8:141954/146‑1 (MQ=255)             caaGTCAGCCCCGGGCCAGATGCAGCAACAACGCCCCCGCCAACATCACCAGCATGACCCCCGAGGCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCag                                                                                                                                        <  2:74054/149‑1 (MQ=255)                   aGCCCCGGGCCAGATGCAGCACCAACGCCCCCGCCAACAACACCAGCATGACCCCCGAGCCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCTCCTCAGTACCCGCTGGTTGCCGATTGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAg                                                                                                                                  <  4:265436/148‑1 (MQ=255)                            ccAGATGCAGCAACAACGCCCCCGCCAACATCACCAGCATGACCCCCGAGGCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCt                                                                                                                         >  6:9752/1‑148 (MQ=255)                                             gCCCCCGCCAACATCACCAGCATGACCCCCGAGGCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGACGCAGGACGATGCTGAACATCCATAGCGCGt                                                                                                        <  1:26877/149‑1 (MQ=255)                                                      aaCATCACCAGCATGACCCCCGAGGCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGtttt                                                                                              <  8:161536/149‑1 (MQ=255)                                                           cACCAGCATGACCCCCGAGGCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGc                                                                                         >  3:178416/1‑149 (MQ=255)                                                              cAGCATGACCCCCGAGGCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCgg                                                                                      >  5:145271/1‑149 (MQ=255)                                                                       ccccGAGGCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGAAGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGc                                                                             >  7:131724/1‑149 (MQ=255)                                                                       ccccGAGGCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGAAGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGc                                                                             >  3:8328/1‑149 (MQ=255)                                                                          cGAGGCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTgg                                                                          <  5:9752/149‑1 (MQ=255)                                                                             ggCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGAAGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGa                                                                       <  8:131724/149‑1 (MQ=255)                                                                             ggCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGAAGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGa                                                                       <  4:8328/149‑1 (MQ=255)                                                                                ccGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCa                                                                    >  4:47774/1‑149 (MQ=255)                                                                                       aGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGc                                                             >  2:256305/1‑149 (MQ=255)                                                                                       aGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGc                                                             >  8:20835/1‑149 (MQ=255)                                                                                                aGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGCCAGGCTgg                                                     >  2:6126/1‑148 (MQ=255)                                                                                                          cGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGCCAGGCTGGCATAGAACAgc                                          <  3:47774/149‑1 (MQ=255)                                                                                                                     aGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGCCAGGCTGGCATAGAACAGCGCGTTCTTggg                               <  8:251837/149‑1 (MQ=255)                                                                                                                          ttgCTGGTCGCCG‑TGGCCATCGGCAACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGCCAGGCTGGCATAGAACAGCGCGTTCTTGGGGtt                            >  4:191048/3‑147 (MQ=255)                                                                                                                            gCTGGTCGCCG‑TGGCCATCGGCAACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGCCAGGCTGGCATAGAACAGCGCGTTCTTGGGGTTGa                          <  3:191048/147‑1 (MQ=255)                                                                                                                              tGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGCCAGGCTGGCATAGAACAGCGCGTTCTTGGGGTTGAGGAt                      <  6:145271/149‑1 (MQ=255)                                                                                                                                     cGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGCCAGGCTGGCATAGAACAGCGCGTTCTTGGGGTTGAGGATGCCa                  <  7:113750/146‑1 (MQ=255)                                                                                                                                     cGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGCCAGGCTGGCATAGAACAGCGCGTTCTTGGGGTTGAGGATGCCa                  >  8:113750/1‑146 (MQ=255)                                                                                                                                           ccA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGCCAGGCTGGCATAGAACAGCGCGTTCTTGGGGTTGAGGATGCCAGACaagaag         <  7:20835/149‑1 (MQ=255)                                                                                                                                            catcGGCAACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGCCAGGCTGGCATAGAACAGCGCGTTCTTgggg                              <  5:140984/125‑1 (MQ=255)                                                                                                                                            catcGGCAACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGCCAGGCTGGCATAGAACAGCGCGTTCTTgggg                              >  6:140984/4‑128 (MQ=255)                                                                                                                                            cA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGCCAGGCTGGCATAGAACAGCGCGTTCTTGGGGTTGAGGATGCCAGACAAGAAGc        >  4:125399/1‑149 (MQ=255)                                                                                                                                                   gACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGCCAGGCTGGCATAGAACAGCGCGTTCTTGGGGTTGAGGATGCCAGACAAGAAGCCCATGc  <  1:256305/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                      CGCACCTTGCAACAAGTCAGCCCCGGGCCAGATGCAGCAACAACGCCCCCGCCAACATCACCAGCATGACCCCCGAGGCCCGCTCCAGCCACGCCAGGCTGCGGGCGAAGCGCCGCAGTACCCGCTGGTTGCCGATGGCCA‑CGGCGACCAGCAAGTCCCAGA‑GCAGGACGATGCTGAACATCCATAGCGCGTAGGCCGTTTTCCAGCCGGGGCTGACGCTGGCGACCATGCTGGCCAGGCTGGCATAGAACAGCGCGTTCTTGGGGTTGAGGATGCCAGACAAGAAGCCCATGC  >  NC_002947/3407913‑3408206

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: ‑