Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,088,010	2 bp→TT	intergenic (+150/‑273)	metK → / → galP	methionine adenosyltransferase/galactose:H(+) symporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,088,010	0	C	T	91.7%	58.8 / ‑3.1	25	intergenic (+150/‑274)	metK/galP	methionine adenosyltransferase/galactose:H(+) symporter
Reads supporting (aligned to +/- strand):  ref base C (2/0);  new base T (12/10);  total (14/11)
Fisher's exact test for biased strand distribution p-value = 4.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*	NC_000913	3,088,011	0	C	T	92.0%	57.4 / ‑3.2	25	intergenic (+151/‑273)	metK/galP	methionine adenosyltransferase/galactose:H(+) symporter
Reads supporting (aligned to +/- strand):  ref base C (2/0);  new base T (12/11);  total (14/11)
Fisher's exact test for biased strand distribution p-value = 4.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGCGCAGCTGCTGCGCGATGCTGCCGGTCTGAAGTAATCTTTCTTCACCTGCGTTCAAAGGCCAGCCTCGCGCTGGCCTTTTTCTTTTGGATAGGCGTTCACGCCGCATCCGGCAAAAAAACCGCCCGCACAATAACATCATTCTTCCTGATCACGTTTCACCGCAGATTATCATCACAACTGAAACCGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAATTGCAGATAACAGCGTTTAATCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGT  >  NC_000913/3087823‑3088234                                                                                                                                                                                            ||                                                                                                                                                                                                                                aaGCGCAGCGGCGGCGCGATGCTGCCGGTCGGAAGTAATCGTTCTTCACCTGCGTTAAAAGGCCAGCCTCGCTGTGGCTTTTTTCTTTTGTATAGGCGTTCTCGCCGCATCCTGCAAAAAATCCGCCCGCACAATAACATCATTCTGCCGGATCACGTTTCACCGCAGATTATCATCACAACTGAAATTGATTACaccaacc                                                                                                                                                                                                                    <  1:338286/202‑1 (MQ=255)              gcgcGATGCTGCCGGTCTGAAGTAATCTTTCTTCACCTGCGTTCAAAGGCCAGCCTCGCGCTGGCCTTTTTCTTTTGGATAGGCGTTCACGCCGCATCCGGCAAAAAAACCGCCCGCACAATAACATCATTCTTCCTGATCACGTTTCACCGCAGATTATCATCACAACTGAAATTGATTACACCAACCACAACAGAAAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACAttt                                                                                                                                                      >  1:438404/1‑251 (MQ=255)               ngcgATGCTGCCGGTCTGAAGTAATCTTTCTTCACCTGCGTTCAAAGGCCAGCCTCGCGCTGGCCTTTTTCTTTTGGATAGGCGTTCACGCCGCATCCGGCAAAAAAACCGCCCGCACAATAACATCATTCTTCCTGATCACGTTTCACCGCAGATTATCATCACAACTGAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTc                                                                                                                                                     >  1:45748/2‑251 (MQ=255)                                                              gCCAGCCTCGCGCTGGCCTTTTTCTTTTGGATAGGCGTTCACGCCGCATCCGGCAAAAAAACCGCCCGCACAATAACATCATTCTTCCTGATCACGTTTCACCGCAGATTATCATCACAACTGAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTcac                                                                                                                                                                   >  1:31173/1‑190 (MQ=255)                                                              gCCAGCCTCGCGCTGGCCTTTTTCTTTTGGATAGGCGTTAACGCCGCATCCGGCAAAAACACCGCCCGCACAATAACATCATTCTTCATGATCACGTTTCACCGCAGATTATCATCACAACTGAACTTGATTACACCAACCACCACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTc                                                                                                                                                     >  1:294028/1‑204 (MQ=255)                                                                       gcgcTGGCCTTTTTCTTTTGGATAGGCGTTCACGCCGCATCCGGCAAAAAAACCGCCCGCACAATAACATCATTCTTCCTGCTCACGTTTCACCGACGATTATCATCACAACTGAAACCGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAATTGCAGATAACAGCGTTTAATCTATGATGATATAACTc                                                                                             >  1:273988/1‑251 (MQ=255)                                                                       gcgcTGGCCTTTTTCTTTTGGATAGGCGTTCACGCCGCATCCGGCAAAAAAACCGCCCGCACAATAACATCATTCTTCCTGATCACGTTTCACCGCAGATTATCATCACAACTGAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATGATTCGGTTTTCACAGTTGGTACATTTCTTTGCATTAAAGTCTTAATTGCAGATAACAGCGTTTAATCTATGATGATATAACtn                                                                                             <  1:54765/251‑2 (MQ=255)                                                                              ccTTTTTCTTTTGGATAGGCGTTCACGCCGCATCCGGCAAAAAAACCGCCCGCACAATAACATCATTCTTCCTGATCACGTTTCACCGCAGATTATCATCACAACTGAAAGTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTcac                                                                                                                                                                   <  1:375834/174‑1 (MQ=255)                                                                              ccTTTNNCTNNNGGNNAGGCGTTCACGCCGCATCCGGCANAAAAACCGCCCGCACAATAACATCATTCTNCNTNATCANNTTTNACCGCAGATTNTCATCACAACTGAAATTGATTACACCAACCACAACCGACAAAGATTTGNANTATTTTCATATTATTATTCGGTTTTcac                                                                                                                                                                   >  2:375834/1‑174 (MQ=255)                                                                                                      aCGCCGCATCCGGCAAAAAAACCGCCCGCACAATAACATCATTCTTCCTGATCACGTTTCACCGCAGATTATCATCACAACTGAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAATTGCAGATAACAGCGTTTAATCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTa                                                               >  1:464388/1‑250 (MQ=255)                                                                                                       cgccgcATCCGGCAAAAAAACCGCCCGCACAATAACATCATTCTTCCTGATCACGTTTCACCGCAGATTATCATCACAACTGAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTGCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAATTGCAGATAACAGCGTGTAAGCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAg                                                             <  1:476258/251‑1 (MQ=255)                                                                                                         ccgcATCCGGCAAAAAAACCGCCCGCACAATAACATCATTCTTCCTGATCACGTTTCACCGCAGATTATCATCACAACTGAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAATTGCAGATAACAGCGTTTAATCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTa                                                               >  1:197844/1‑247 (MQ=255)                                                                                                           gcATCAGGCAAAAAAACCGCCCGCACAATAACATCATTATTCCTGATCACGTTTCACCGCAGATTATCATCCCACCTGCAATTGATTACACCAACCACAACAGACAAAGATTTGTCATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAAt                                                                                                                                  >  1:376022/1‑178 (MQ=255)                                                                                                            cATCCGGCAAAAAAACCGCCCGCACAATAACATCATTCTTCCTGATCACGTTTCACCGCAGATTATCATCACAACTGAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAATTGCAGATAACAGCGTTTAATCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATaa                                                         >  1:116902/1‑250 (MQ=255)                                                                                                                cGGCAAAAAAACCGCCCGCACAATAACATCATTCTTCCTGATCACGTTTCACCGCATATTATCATCACAACTGAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAATTGCAg                                                                                                                             <  1:38957/178‑1 (MQ=255)                                                                                                                   cAAAAAAACCGCCCGCACAATAACATCATTCTTCCTGATCACGTTTCACCGCAGATTATCATCACAACTGAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAATTGCa                                                                                                                              >  1:426294/1‑174 (MQ=255)                                                                                                                    aaaaaaaCCGCCCGCACAATAACATCATTCTTCCTGCTTACGTTTCACCGCAGATTATCATCACAACTGAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAATTGCAGATAACAGCGTTTAATCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAgtg                                                >  1:427760/1‑251 (MQ=255)                                                                                                                             gcccgcACAATAACATCATTCTTCCTGATCACGTTTCACCGCAGATTATCATCACAACTGAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAATTGCAGATAACAGCGTTTAATCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGAtt                                       >  1:255345/1‑251 (MQ=255)                                                                                                                                 gcACAATAACATCATTCTTCCTGATCACGTTTCACCGCAGATTATCATCACAACTAAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAATTGCAGATAACAGCGTTTAATCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAg                                                  <  1:68224/236‑1 (MQ=255)                                                                                                                                                   tcCTGATCACGTTTCACCGCAGATTATCATCACAACTGAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAATTGCAGATAACAGCGTTTAATCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGGTAGTGTAAGCGATTACACTGATGTGATTTGCtta                   <  1:64719/249‑2 (MQ=255)                                                                                                                                                       gATCACGTTTCACCGCAGATTATCATCACAACTGAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAATTGCAGATAACAGCg                                                                                                                    <  1:251498/148‑1 (MQ=255)                                                                                                                                                            cGTTTCNNCGCAGATTATCATCACAACTGAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTcac                                                                                                                                                                   <  2:31173/96‑1 (MQ=255)                                                                                                                                                                  aCCGCAGATTATCATCACAACTGAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAATTGCAGATAACAGCGTTTAATCTATGATGATATAACTCAATGATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTAcgtcgt  <  1:220138/251‑1 (MQ=255)                                                                                                                                                                        gATTATCATCACAACTGAAATTGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCAAATTATTATTCGGTTTTCACAGTTGTTACATTGCTTTTCAGTAAAGTCTTAATTGCAGATAACAGCGTTTAATCTATGATGATATAACTGAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACt                                  <  1:505500/213‑1 (MQ=255)                                                                                                                                                                                   caACTGAAACCGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAATTGCAGATAACAGCGTTTAATCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGAt                                        >  1:28643/1‑196 (MQ=255)                                                                                                                                                                                            ||                                                                                                                                                                                                                                AAGCGCAGCTGCTGCGCGATGCTGCCGGTCTGAAGTAATCTTTCTTCACCTGCGTTCAAAGGCCAGCCTCGCGCTGGCCTTTTTCTTTTGGATAGGCGTTCACGCCGCATCCGGCAAAAAAACCGCCCGCACAATAACATCATTCTTCCTGATCACGTTTCACCGCAGATTATCATCACAACTGAAACCGATTACACCAACCACAACAGACAAAGATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGTCTTAATTGCAGATAACAGCGTTTAATCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGT  >  NC_000913/3087823‑3088234

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑