Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,278,746	G→A	12.8%	R111Q (CGG→CAG)	PP_3749 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,278,746	0	G	A	12.8%	112.6 / 8.2	47	R111Q (CGG→CAG)	PP_3749	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (24/17);  new base A (3/3);  total (27/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.99e-01

GGCGGGCCATTTCAGAGCATATGAAAGCTTCGACGGTTGAAGGCGTGCGCATCAAGCGCAACCGCAACGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGCCGCAAAGGCCTGGCCGATCAGC  >  NC_002947/4278608‑4278893                                                                                                                                           |                                                                                                                                                    ggcgggcCATTTCAGAGCATATGAAAGCTTCGACGGTTGAAGGCGTGCGCATCAAGCGCAACCGCAACGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTgagcgg                                                                                                                                          >  2:768137‑M2/1‑144 (MQ=255)       ccATTTCAGAGCATATGAAAGCTTCGACGGTTGAAGGCGTGCGCATCAAGCGCAACCGCAACGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCt                                                                                                                                    >  2:468236/1‑150 (MQ=255)        cATTTCAGAGCATATGAAAGCTTCGACGGTTGAAGGCGTGCGCATCAAGCGCAACCGCAACGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCAGAGCCgagcggtgctgac                                                                                                                                   <  1:1419971‑M2/150‑14 (MQ=255)             cAGAGCATATGAAAGCTTCGACGGTTGAAGGCGTGCGCATCAAGCGCAACCGCAACGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCAGAGCCgagcggtgctgacggtga                                                                                                                              >  2:1419971‑M2/1‑132 (MQ=255)                  cATATGAAAGCTTCGACGGTTGAAGGCGTGCGCATCAAGCGCAACCGCAACGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCAGAGCCgagcggtgctgacggtgatatag                                                                                                                         <  2:1360267‑M2/150‑24 (MQ=255)                      tGAAAGCTTCGACGGTTGAAGGCGTGCGCATCAAGCGCAACCGCAACGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGc                                                                                                                     >  1:611277/1‑150 (MQ=255)                       gAAAGCTTCGACGGTTGAAGGCGTGCGCATCAAGCGCAACCGCAACGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGcc                                                                                                                    >  1:903813/1‑150 (MQ=255)                        aaaGCTTCGACGGTTGAAGGCGTGCGCATCAAGCGCAACCGCAACGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCt                                                                                                                   <  1:452345/150‑1 (MQ=255)                          aGCTTCGACGGTTGAAGGCGTGCGCATCAAGCGCAACCGCAACGCGCCGGAAGTCGATACCGTGAGACGCATTGCAATGGAAGAAAACGGCTATATGGCCGGCGTCAGTGGTTGCGTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCtgt                                                                                                                 <  1:739117/150‑1 (MQ=255)                               cGACGGTTGAAGGCGTGCGCATCAAGCGCAACCGCAACGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCAGAGCCgagcggtgctgacggtgatatagcctttttctgcca                                                                                                            >  1:1360267‑M2/1‑114 (MQ=255)                                 aCGGTTGAAGGCGTGCGCATCAAGCGCAACCGCAACGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGc                                                                                                          <  2:611277/150‑1 (MQ=255)                                     ttGAAGGCGTGCGCATCAAGCGCAACCGCAACGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCt                                                                                                      <  2:107205/150‑1 (MQ=255)                                       gAAGGCGTGCGCATCAAGCGCAACCACACCGCGGCTCTTCCGGTATCCTTGATACGCATTGCCCTGGCAGAACAATGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGa                                                                                                    <  1:1385041/150‑1 (MQ=255)                                             gTGCGCATCAAGCGCAACCGCAACGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCa                                                                                              <  1:468236/150‑1 (MQ=255)                                                            aaccgcaacGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTc                                                                                                                                   <  2:849683/98‑1 (MQ=255)                                                            aaccgcaacGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTc                                                                                                                                   >  1:849683/1‑98 (MQ=255)                                                            aaccgcaacGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAg                                                                                                   <  2:443411/130‑1 (MQ=255)                                                            aaccgcaacGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAg                                                                                                   >  1:443411/1‑130 (MQ=255)                                                               cgcaacGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGa                                                                            <  2:231289/150‑1 (MQ=255)                                                               cgcaacGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGa                                                                            <  2:1250289/150‑1 (MQ=255)                                                                              gACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCAGAGCCgagcggtgctgacgg                                                                                                                                 >  2:1348525‑M2/1‑67 (MQ=255)                                                                              gACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCAGAGCCgagcggtgctgacgg                                                                                                                                 <  1:1348525‑M2/82‑16 (MQ=255)                                                                               aCGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTTGGCCGCTGTGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCcttcgctccg                                                            >  1:798519/1‑150 (MQ=255)                                                                                cGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCgg                                                           >  1:478965/1‑150 (MQ=255)                                                                                 gAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGc                                                                                                                                <  1:672166/80‑1 (MQ=255)                                                                                 gAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGc                                                                                                                                >  2:672166/1‑80 (MQ=255)                                                                                         gATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCa                                                  <  1:1276882/150‑1 (MQ=255)                                                                                            aCGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATgg                                               >  2:1263510/1‑150 (MQ=255)                                                                                                aTTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACt                                           <  2:1359868/150‑1 (MQ=255)                                                                                                aTTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACt                                           >  2:425861/1‑150 (MQ=255)                                                                                                    cccTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGcac                                       >  1:765650/1‑150 (MQ=255)                                                                                                         gCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCg                                  >  1:553085/1‑150 (MQ=255)                                                                                                             aaaaaGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTg                              <  2:1207022/150‑1 (MQ=255)                                                                                                                   gCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGc                        >  2:505779/1‑150 (MQ=255)                                                                                                                   gCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGc                        >  1:438268/1‑150 (MQ=255)                                                                                                                   gCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGc                        >  2:295228/1‑150 (MQ=255)                                                                                                                    cTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGcc                       >  2:826526/1‑150 (MQ=255)                                                                                                                     tataTCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGCCg                      >  1:918518/1‑150 (MQ=255)                                                                                                                         tCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGCCGCaaa                  >  1:96258/1‑150 (MQ=255)                                                                                                                         tCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGCCGCaaa                  <  1:425861/150‑1 (MQ=255)                                                                                                                            ccGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGCCGCAAAGGc               <  1:295228/150‑1 (MQ=255)                                                                                                                             cGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGCCGCAAAGGcc              >  1:1218459/1‑150 (MQ=255)                                                                                                                               tCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCTCCTGGAGGGCCGCAAAGGCCTg            >  1:705793/1‑150 (MQ=255)                                                                                                                                  gCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGCCGCAAAGGCCTGGcc         >  2:998337/1‑150 (MQ=255)                                                                                                                                    aCCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGCCGCAAAGGCCTGGCCGa       >  2:1165752/1‑150 (MQ=255)                                                                                                                                    aCCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAACCTGTGACAAGCAGCTGAGTCGCAGCCAATCCGCTATCCTGGCGAAGCTTCGGCTCCTGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGCCGCAAAGGCCTGGCCGa       >  1:1390857/1‑150 (MQ=255)                                                                                                                                         tCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGCCGCAAAGGCCTGGCCGATCAGc  <  1:826526/150‑1 (MQ=255)                                                                                                                                           ggCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGCCGCAAAg                 <  2:782197/133‑1 (MQ=255)                                                                                                                                           ggCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGCCGCAAAg                 >  1:782197/1‑133 (MQ=255)                                                                                                                                           |                                                                                                                                                    GGCGGGCCATTTCAGAGCATATGAAAGCTTCGACGGTTGAAGGCGTGCGCATCAAGCGCAACCGCAACGCGCCGGAAGACGAAACCGTGATACGCATTGCCCTGGCAGAAAAAGGCTATATCACCGTCAGCACCGCTCGGCTCTGAGCGGTTGGCTCGGCCTCTTGGTAGCCTGTGACAAGCACCTGAGTCGCAGCCAATCCGCTATCCTGAGCAATCCTCCGCTCCGGACCCGCCCATGGAACTGCACATTCGCCTGGAGGGCCGCAAAGGCCTGGCCGATCAGC  >  NC_002947/4278608‑4278893

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑