Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,734,543	(C)8→9	coding (492/732 nt)	pgeF ←	polyphenol oxidase YfiH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,734,535	1	.	C	80.0%	61.1 / 11.6	25	coding (500/732 nt)	pgeF	polyphenol oxidase YfiH
Reads supporting (aligned to +/- strand):  ref base . (3/2);  new base C (12/8);  total (15/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.23e-01

GACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGCATGAGCGGCGGC  >  NC_000913/2734431‑2734674                                                                                                          |                                                                                                                                            gACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGc                                                                                                           <  1:478758/140‑1 (MQ=255)                 cTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCg                                                                                           <  1:523109/140‑1 (MQ=255)                  tGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCCCCCCCCACTTCGAACGCTCGTGGACCAATTGCCGGCCCTAACCAGGCga                                                                                          >  1:177256/1‑140 (MQ=255)                  tGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCga                                                                                          >  1:576256/1‑140 (MQ=255)                          atCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATAttt                                                                                  >  1:116273/1‑140 (MQ=255)                           tCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATAtttt                                                                                 >  2:163550/1‑140 (MQ=255)                             cGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTcc                                                                               <  1:738181/140‑1 (MQ=255)                               ccAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGa                                                                            <  1:19555/140‑1 (MQ=255)                                              cATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAAATGCCGGCCCCAAGCTGTGGACAATATTTTCCAGATTATCTGCAAAACa                                                              >  2:353915/1‑140 (MQ=255)                                               aTGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAgg                                                            >  2:539330/1‑140 (MQ=255)                                                tGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑‑CCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGaa                                                          >  1:639948/1‑140 (MQ=255)                                                  cTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGaa                                                          <  2:576256/140‑1 (MQ=255)                                                   tgaatgaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGaaa                                                         <  2:116273/140‑1 (MQ=255)                                                     aatgaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATAGTTTACGGATTATCTGCAAAACAGGAAAcc                                                       >  1:302630/1‑140 (MQ=255)                                                     aatgaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCTCTAACCAGACGAGATTATTTTCCGGATTATCTGCAAAACAGGAAACCg                                                      >  2:338749/1‑140 (MQ=255)                                                       tgaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGt                                                     <  1:693118/140‑1 (MQ=255)                                                           aGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAgg                                                            >  1:462956/1‑129 (MQ=255)                                                           aGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAgg                                                            <  2:462956/129‑1 (MQ=255)                                                               gCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTGTCCGGATGTTCAGCGAAACAGAAAACCGTCTCTTCCa                                             >  1:206977/1‑140 (MQ=255)                                                                cACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAg                                            >  1:412312/1‑140 (MQ=255)                                                                          aGCGTCTACTGCCATAAACGCCTCGCGAACCT‑‑CCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca                                <  2:639948/140‑1 (MQ=255)                                                                           gCGTCTACTGCCATATACGCCTAGCTAACGT‑CCCCCCTCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca                                <  1:338749/140‑1 (MQ=255)                                                                            cGTCTACTGCCATAAACGCCTCCCGAACCTCCCCCCCCCTCTTCGAACCCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca                                <  2:302630/140‑1 (MQ=255)                                                                                               cTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACgccagcc                 <  2:94372/136‑1 (MQ=255)                                                                                               cTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACgccagcc                 >  1:94372/1‑136 (MQ=255)                                                                                               cTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGCa             >  1:512757/1‑140 (MQ=255)                                                                                               cTCGCGAACCTCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGCa             >  1:125081/1‑140 (MQ=255)                                                                                                         t‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGCATGAgcggcggc  <  1:539330/140‑1 (MQ=255)                                                                                                          |                                                                                                                                            GACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGCATGAGCGGCGGC  >  NC_000913/2734431‑2734674

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑