Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,050,045	G→A	18.4%	intergenic (+17/‑124)	PP_2662 → / → PP_2663	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,050,045	0	G	A	18.4%	60.7 / 7.8	33	intergenic (+17/‑124)	PP_2662/PP_2663	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (9/17);  new base A (4/2);  total (14/19)
Fisher's exact test for biased strand distribution p-value = 1.94e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.24e-01

GTTCCATGACATCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCGAATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCTCATAACGACGGTG  >  NC_002947/3049899‑3050193                                                                                                                                                      |                                                                                                                                                      ggtCCATGACATCCACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACAGCAGTGCGCACAACGAAGACACCGATACCT‑‑TTGCGTTGGGCGCGGTTTTGACCTGGTAAG‑CGGCCGGGGCCGCTAggc                                                                                                                                                     <  5:84191/147‑1 (MQ=255)  gtCCATGACCTCAACGACACCCTGAACCTGGTGGCCGAGTACCACCAGTTTTCCATCGACGGGCAGGACACCAGGGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCGGGTAAG‑CGGCCGGGGCCGCTAgg                                                                                                                                                      <  7:230860/146‑1 (MQ=255)       tGACATCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCCTAGCGGcccc                                                                                                                                               <  3:228856/149‑1 (MQ=255)          cttCAACGACATCCTTAATCTGGTTGCGGAGTACTACCTGTTTTCCATCTACGGGCTTGACTCCAGTGCGCAGAACTAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCGaa                                                                                                                                            <  2:295103/147‑1 (MQ=255)          cATCAACGACAACCTGTAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCGa                                                                                                                                             <  3:128293/148‑1 (MQ=255)          cATCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACGGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCGaa                                                                                                                                            <  8:319038/149‑1 (MQ=255)          cATCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGGCCCgga                                                                                                                                            >  7:92089/1‑147 (MQ=255)           aTCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGGCGGGGCCGCCTAGCGGCCCCggcc                                                                                                                                           <  1:113503/149‑4 (MQ=255)               aCGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCGAATGaca                                                                                                                                       <  6:41888/149‑1 (MQ=255)                                      ctcggccaCCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAGCCGGCCGGGGCCGCTAGGCGGCCCCGAATGACA‑CGGTCTTTTACGCCCATGGaa                                                                                                                 <  1:295990/141‑1 (MQ=255)                                       aGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGGCGCGAGGGGGGGCCGCATTCCA‑CGGGCGGTTAGGGCCATGGGAccc                                                                                                              >  4:233278/1‑148 (MQ=255)                                            aaCCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGGCGCTAGGCGGGCCCGACTGACA‑CGGGCTTTTACGCCCAATGAAcccccccc                                                                                                         >  2:61896/1‑147 (MQ=255)                                              ccAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCCAATGACA‑CGGTCTTTTACGCCCAAGGAAACGCCCAccc                                                                                                       >  6:188076/1‑149 (MQ=255)                                                   tttCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCGAATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTa                                                                                                   <  7:244853/148‑1 (MQ=255)                                                    ttCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTATGCGGCCCCCCCATACA‑CCGTGGTTTAAGGCCCAGGGACCGCCCAcccccgaac                                                                                                 >  3:377618/1‑143 (MQ=255)                                                              gggCATGACACCAGTGCGCAGAACGAAGACAACGATACCTTCTTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCGAATGACA‑Cg                                                                                                                                    <  1:310875/106‑1 (MQ=255)                                                                    gACACCAGTGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCGAATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTca                                                                                 >  3:114905/1‑149 (MQ=255)                                                                    gACACCAGTGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCAAGGCGGGCCCCAAAGAAA‑CCGTCTTTTTAGCCCATGGAACCGCCCACCCCCTAACCAAATATCATTAGTca                                                                                 >  7:229382/1‑149 (MQ=255)                                                                         cAGTGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGGCGCGAGGCGGCCCCCCAAGACACCGGGGTTTTA‑GCCCCAGGCACCCCCCCCCCCCGACCCAACTAGGCTTAGTaaccccc                                                                            >  3:193997/1‑147 (MQ=255)                                                                                  gAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCGAATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCAcctc                                                                   <  4:114905/149‑1 (MQ=255)                                                                                   aaCGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCGAATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCAcctcc                                                                  <  3:381763/149‑1 (MQ=255)                                                                                            acCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCGAATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGa                                                         >  1:52313/1‑149 (MQ=255)                                                                                             ccGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCGAATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGAt                                                        <  2:52313/149‑1 (MQ=255)                                                                                              cGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCGCCTGCCA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCGACCCAAGTAGCATTCGTCACCCACCACCCCCTCCTTAAAcggct                                                        >  7:80705/1‑144 (MQ=255)                                                                                              cGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCGAATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTa                                                                                                   <  3:351877/105‑1 (MQ=255)                                                                                                                ggCGCGGTGTTGACCTGTTAAG‑CGGCCGGGGCCGCTAGTCGGCCCCGAATGACA‑CGTTCTTTTACGCGCATGTAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCAACACCACCTCCTTAAACTGATCACTCAGCGACCCCGTg                                       <  4:377618/149‑1 (MQ=255)                                                                                                                 gcgcGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCGAATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGc                                      <  2:337294/149‑1 (MQ=255)                                                                                                                      gtgtTGACCTGGTAAT‑CGGGCGGGGCCGCTAGGCGGCCCCGAATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGgag                                 <  3:229309/149‑1 (MQ=255)                                                                                                                                       cGGCCGGGGCCGCTAGGCGGCCCCGGATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAgg                 <  8:92089/149‑1 (MQ=255)                                                                                                                                        attcGGGGCCGCCTAGCGGCCCCGGATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGc                >  7:238036/4‑149 (MQ=255)                                                                                                                                            ggggCCGCCTAGCGGCCCCGAATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCTCa             >  3:179072/1‑148 (MQ=255)                                                                                                                                            ggggCCGCCTAGCGGCCCCGAATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCTCa             >  3:178670/1‑148 (MQ=255)                                                                                                                                            ggggCCGCCTAGCGGCCCCGAATGACA‑CGGTCTTTTACGCCAATGGACCCGCCCACCCGCTACCCAAGTAGCATTCGTCAACCACAAGACCCTCAGGGAAAGGATCCCTCAGCCACCCCGAGCCGGCGACGACGAAGCAGCAGGCGCAt            >  6:238302/1‑149 (MQ=255)                                                                                                                                                  gCTAGGCGGCCCCGAATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCTCATAacgac      <  1:61896/149‑1 (MQ=255)                                                                                                                                                  gCTAGGCGGCCCCGAATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCTCATAacgac      <  8:80705/149‑1 (MQ=255)                                                                                                                                                      ggcggcCCCGAATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCTCATAACGACGgtg  >  1:242230/1‑149 (MQ=255)                                                                                                                                                      |                                                                                                                                                      GTTCCATGACATCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATGACACCAGTGCGCAGAACGAAGACACCGATACCT‑‑TTGCGGTGGGCGCGGTGTTGACCTGGTAAG‑CGGCCGGGGCCGCTAGGCGGCCCCGAATGACA‑CGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCTCATAACGACGGTG  >  NC_002947/3049899‑3050193

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: ‑