Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,189,970	A→T	13.3%	I227N (ATC→AAC)	PP_2799 ←	class III aminotransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,189,970	0	A	T	13.3%	113.1 / 9.5	45	I227N (ATC→AAC)	PP_2799	class III aminotransferase
Reads supporting (aligned to +/- strand):  ref base A (19/20);  new base T (4/2);  total (23/22)
Fisher's exact test for biased strand distribution p-value = 6.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01

CGTACAACTGAGAGCCGAACATTGTGCCAAGCCTGCCAAAGCCGGTGATGATTTCGTCGATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGATTCTCCTGGCCGAGCAAATCGGTAGAAGTTCGGGCAGGTCAG  >  NC_002947/3189824‑3190112                                                                                                                                                     |                                                                                                                                               cGTACAACTGAGAGCCGAACATTGTGCCAAGCCTGCCAAAGCCGGTGATGATTTCGTCGATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCTCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGAtt                                                                                                                                              <  1:70853/149‑1 (MQ=255)   tACAACTGAGAGCCGAACATTGTGCCAAGCCTGCCAAAGCCGGTGATGATTTCGTCGATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTAc                                                                                                                                            >  3:242641/1‑149 (MQ=255)    aCAACTGAGAGCCGAACATTGTGCCAAGCCTGCCAAAGCCGGTGATGATTTCGTCGATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTAcc                                                                                                                                           >  1:297531/1‑149 (MQ=255)      aaCTGAGAGCCGAACATTGTGCCAAGCCTGCCAAAGCCGGTGATGATTTCGTCGATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCgg                                                                                                                                         <  2:297531/149‑1 (MQ=255)      aaCTGAGAGCCGAACATTGTGCCAAGCCTGCCAAAGCCGGTGATGATTTCGGCGATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCgg                                                                                                                                         <  3:124510/149‑1 (MQ=255)               ccGAACATTGTGCCAAGCCTGCCAAAGCCGGTGATGATTTCGTCGATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGAt                                                                                                                                <  3:131531/149‑1 (MQ=255)                 gAACATTGTGCCAAGCCTGCCAAAGCCGGTGATGATTTCGTCGATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATg                                                                                                                               >  7:271114/1‑148 (MQ=255)                     aTTGTGCCAAGCCTGCCAAAGCCGGTGATGATTTCGTCGATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAAcgc                                                                                                                          <  7:43165/149‑1 (MQ=255)                                    ccAAAGCCGGTGATGATTTCGTCGATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGCCGCTGGTTTCCgg                                                                                                           >  8:112261/1‑149 (MQ=255)                                           cGGTGATGATTTCGTCGATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCg                                                                                                    >  2:193459/1‑149 (MQ=255)                                                atgatTTCGTCGATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAg                                                                                               >  5:6053/1‑149 (MQ=255)                                                 tgatTTCGTCGATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACGCCCCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCaa                                                                                                <  1:92644/149‑1 (MQ=255)                                                  gatTTCGTCGATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGTTCATCGGCGAGCCGGTAATCgcggcagg                                                                                                                    >  6:65518/1‑123 (MQ=37)                                                  gatTTCGTCGATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGTTCATCGGCGAGCCGGTAATCgcggcagg                                                                                                                    <  5:65518/126‑4 (MQ=37)                                                           gATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGtt                                                                                    >  5:290956/1‑149 (MQ=255)                                                                ccacGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAgt                                                                               <  4:305709/149‑1 (MQ=255)                                                                       gATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGttcgttcg                                                                        >  4:103833/1‑149 (MQ=255)                                                                         tGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGcc                                                                      <  1:193459/149‑1 (MQ=255)                                                                                  gTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGAcc                                                             >  5:163378/1‑149 (MQ=255)                                                                                   tttGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCg                                                            <  6:6053/149‑1 (MQ=255)                                                                                     tGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAATGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCAAGACGGACCGt                                                           >  1:147758/1‑148 (MQ=255)                                                                                     tGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATAGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGt                                                           >  4:114995/1‑148 (MQ=255)                                                                                        acacCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAg                                                       <  8:271114/149‑1 (MQ=255)                                                                                          acCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGTGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGTTTTCCGGCCCTTCGGCAAGTATATAGCGTTCCAGTTCGTTCGCCAGACGTACCGTAAAGGc                                                     <  2:17175/149‑1 (MQ=255)                                                                                          acCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAgttc                                                                             >  3:209717/1‑125 (MQ=255)                                                                                          acCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAgttc                                                                             <  4:209717/125‑1 (MQ=255)                                                                                                     cgccgcCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGAt                                           >  4:16269/1‑148 (MQ=255)                                                                                                           ccAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGATTCTCCTg                                    <  2:222319/149‑1 (MQ=255)                                                                                                           ccAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGATTCTCCTg                                    <  2:50258/149‑1 (MQ=255)                                                                                                                    tgtgGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAg                                                       <  8:43619/121‑1 (MQ=255)                                                                                                                    tgtgGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAg                                                       >  7:43619/1‑121 (MQ=255)                                                                                                                    tgtgGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGATTCTCCTGGCCGAGCa                            >  2:258059/1‑148 (MQ=255)                                                                                                                              tggATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCTATGGTTTCCGGCCCTTCGGCAATGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGATTCTCCTGGCCGAGCAAATCTGTAGaa                 <  7:182241/148‑1 (MQ=255)                                                                                                                               ggATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGATTCTCCTGGCCGAGCAAATCGGTAGAAg                >  6:276803/1‑149 (MQ=255)                                                                                                                                gATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGATTCTCCTGGCCGAGCAAATCGGTAGAAGt               >  2:176829/1‑149 (MQ=255)                                                                                                                                    aCG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGATTCTCCTGGCCGAGCAAATCGGTAGAAGTTCgg           >  8:112638/1‑149 (MQ=255)                                                                                                                                    aCG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGATTCTCCTGGCCGAGCAAATCGGTAGAAGTTCg            <  4:242641/148‑1 (MQ=255)                                                                                                                                     cG‑‑CCACCTGCCGCGATTACCTGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCg                                             <  5:563/114‑1 (MQ=255)                                                                                                                                     cG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCg                                             >  6:563/1‑114 (MQ=255)                                                                                                                                     cG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGATTCTCCTGGCCGAGCAAATCGGTAGAAGTACggg          <  3:16269/149‑1 (MQ=255)                                                                                                                                          ccatcgCCGCGTTCATCGGCGAGCCGGTAATCGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGATTCTCCTGGCCGAGCAAATCGGTAGAAGTTCGGGcag       >  3:163606/6‑149 (MQ=38)                                                                                                                                           catcgCCGCGTTCATCGGCGAGCCGGTAATCGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGATTCTCCTGGCCGAGCAAATCGGTAGAAGTTCGGGc         <  3:247031/142‑1 (MQ=38)                                                                                                                                           catcgCCGCGTTCATCGGCGAGCCGGTAATCGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGATTCTCCTGGCCGAGCAAATCGGTAGAAGTTCGGGc         >  4:247031/5‑146 (MQ=38)                                                                                                                                            atcgCCGCGTTCATCGGCGAGCCGGTAATCGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGATTCTCCTGGCCGAGCAAATCGGTAGAAGTTCGGGcaggt     >  3:144539/4‑149 (MQ=38)                                                                                                                                                ccGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGATTCTCCTGGCCGAGCAAATCGGTAGAAGTTCGGGcaggtcag  <  7:112638/148‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                               CGTACAACTGAGAGCCGAACATTGTGCCAAGCCTGCCAAAGCCGGTGATGATTTCGTCGATCACCACGAGGATGTCGTAGCGTTTGCACACCGCCTGGATCGCCGCCCAGTAGCCTGTGGGAGGAGGGATCACG‑‑CCACCTGCCGCGATTACCGGCTCGCCGATGAACGCGGCGATGGTTTCCGGCCCTTCGGCAAGGATATAGCGTTCCAGTTCGTTCGCCAGACGGACCGTAAAGGCCTCTTGCGATTCTCCTGGCCGAGCAAATCGGTAGAAGTTCGGGCAGGTCAG  >  NC_002947/3189824‑3190112

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: ‑