Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,388,295	A→T	13.8%	M338L (ATG→TTG)	pyrD →	dihydroorotate dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,388,295	0	A	T	13.8%	75.3 / 4.4	29	M338L (ATG→TTG)	pyrD	dihydroorotate dehydrogenase
Reads supporting (aligned to +/- strand):  ref base A (12/13);  new base T (2/2);  total (14/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.38e-01

GTTGCCGATCATTGCCGCCGGGGGCATTACCGAAGGCCGCCATGCTGCCGAGAAGATCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCTGATGAGGTTTGCCAAGGCATAAAAAAGGGCCCCTTCAAGGGGCCCCTGGGCCTTCGCCCGCCGCCCGGATGGGGCGTGCATGGTAAATCGAATTCA  >  NC_002947/2388147‑2388439                                                                                                                                                     |                                                                                                                                                 gTTGCCGATCATTGCCGCCGGGGGCATTACCGAAGGCCGCCATGCTGCCGAGAAGATCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAAt                                                                                                                                                 <  2:297526/150‑1 (MQ=255)  ttGCCGATCATTGCCGCCGGGGGCATTACCGAAGGCCGCCATGCTGCCGAGAAGATCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAATg                                                                                                                                                <  1:445931/150‑1 (MQ=255)   tGCCGATCATTGCCGCCGGGGGCATTACCGAAGGCCGCCATGCTGCCGAGAAGATCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGAGCTTCATCTACAAAGGGCGGGCGCTGATTCGAGAAGCGGGGGATGCTGTCGCGTCAATgg                                                                                                                                               >  1:124292/1‑149 (MQ=255)                        gCATTACCGAAGGCCGCCATGCTGCCGAGAAGATCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCt                                                                                                                          >  2:555743/1‑150 (MQ=255)                          aTTACCGAAGGCCGCCATGCTGCCGAGAAGATCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCtgt                                                                                                                        >  2:387899/1‑150 (MQ=255)                           ttACCGAAGGCCGCCATGCTGCCGAGAAGATCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCtgtg                                                                                                                       >  1:333421/1‑150 (MQ=255)                               cGAAGGCCGCCATGCTGCCGAGAAGATCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCATTGCcgcgat                                                                                                                                         >  2:206364/1‑126 (MQ=255)                               cGAAGGCCGCCATGCTGCCGAGAAGATCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCATTGCcgcgat                                                                                                                                         <  1:206364/128‑3 (MQ=255)                                        ccATGCTGCCGAGAAGATCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCgggtgg                                                                                                          <  2:379653/150‑1 (MQ=255)                                         cATGCTGCCGAGAAGATCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCgggtggg                                                                                                         <  2:333421/150‑1 (MQ=255)                                               gcCGAGAAGATCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGc                                                                                                   >  1:210890/1‑150 (MQ=255)                                                  gagaAGATCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCtga                                                                                                <  2:358455/150‑1 (MQ=255)                                                  gagaAGATCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCtga                                                                                                >  2:193002/1‑150 (MQ=255)                                                     aagaTCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGAGGTGGATGCTATCGCGGCAATGCAGCGGTGACCAGCCCGCCCCTGTGGGGGGGGGGGTGGGGGCCGCtgatga                                                                                             >  1:87622/1‑150 (MQ=255)                                                        aTCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCTGATGAGGt                                                                                          >  1:340335/1‑150 (MQ=255)                                                                           tGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCTGATGAGGTTTGCCAAGGCATAAAAAAg                                                                       <  2:210890/150‑1 (MQ=255)                                                                                        cTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCTGATGAGGTTTGCCAAGGCATAAAAAAGGGCCCCTTCAAgg                                                          >  1:559542/1‑150 (MQ=255)                                                                                             gCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCTGATGAGGTTTGCCAAGGCATAAAAAAGGGCCCCTTCAAGGGGccc                                                     <  1:193002/150‑1 (MQ=255)                                                                                                           gggCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCTGATGAGGTTTGCCAAGGCATAAAAAAGGGCCCCTTCAAGGGGCCCCTGGGCCTTcgccc                                       >  2:30669/1‑150 (MQ=255)                                                                                                                             gAAGCGGTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCTGATGAGGTTTGCCAAGGCATAAAAAAGGGCCCCTTCAAGGGGCCCCTGGGCCTTCGCCCGCCGCCCGGATGGGGCGt                     <  1:555743/150‑1 (MQ=255)                                                                                                                                   gTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCTGATGAGGTTTGCCAAGGCATAAAAAAGGGcccc                                                                 <  1:91001/100‑1 (MQ=255)                                                                                                                                   gTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCTGATGAGGTTTGCCAAGGCATAAAAAAGGGcccc                                                                 >  2:91001/1‑100 (MQ=255)                                                                                                                                      gATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCTGATGAGGTTTGCCAAGGCATAAAAAAGGGCCCCTTCAAGGGGCCCCTGGGCCTTCGCCCGCCGCCCGGATGGGGCGTGCATGGTaa            >  1:98579/1‑150 (MQ=255)                                                                                                                                            aTCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCTGATGAGGTTTGCCAAGGCATAAAAAAGGGCCCCTTCAAGGGGCCCCTGGGCCTTCGCCCGCCGCCCGGATGGGGCGTGCATGGTAAATCGaa      <  1:387899/150‑1 (MQ=255)                                                                                                                                             ccgcgGCATTGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCTGATGAGGTTTGCCAAGGCATAAAAAAGGGCCCCTTCAAGGGGCCCCTGGGCCTTcgc                                         <  1:50852/113‑1 (MQ=255)                                                                                                                                             ccgcgGCATTGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCTGATGAGGTTTGCCAAGGCATAAAAAAGGGCCCCTTCAAGGGGCCCCTGGGCCTTcgc                                         >  2:50852/2‑114 (MQ=255)                                                                                                                                                cgGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCTGATGAGGTTTGCCAAGGCATAAAAAAGGGCCCCTTCAAGGGGCCCCTGGGCCTTCGCCCGCCGCCCGGATGGGGCGTGCATGGTAAATCGAATTCa  <  1:151008/150‑1 (MQ=255)                                                                                                                                                cgGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCTGATGAGGTTTGCCAAGGCATAAAAAAGGGCCCCTTCAAGGGGCCCCTGGGCCTTCGCCCACCGCCCGGATGGGGCGTGCATGGTAAATCGAATTCa  <  2:340335/150‑1 (MQ=255)                                                                                                                                                cgGCAATGCCGCGGTGACCAGCCCGCCCCTGGGGGGGGGCGGGTTGGTGCAGCTGATGAGGTTTGCCAAGGCATAAAAAAGGGCCCCTTCAAGGCGCCCCTGGGCCCTCGCCCGCCGCCCGGATGGGGCGTTCATGGTAAATCGAATTCa  <  2:87622/150‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                 GTTGCCGATCATTGCCGCCGGGGGCATTACCGAAGGCCGCCATGCTGCCGAGAAGATCGCGGCCGGGGCGAGCCTGGTGCAGATATACTCGGGCTTCATCTACAAAGGGCCGGCGCTGATTCGCGAAGCGGTGGATGCTATCGCGGCAATGCCGCGGTGACCAGCCCGCCCCTGTGGGGGGGCGGGTGGGTGCAGCTGATGAGGTTTGCCAAGGCATAAAAAAGGGCCCCTTCAAGGGGCCCCTGGGCCTTCGCCCGCCGCCCGGATGGGGCGTGCATGGTAAATCGAATTCA  >  NC_002947/2388147‑2388439

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑