Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,088,257	T→C	intergenic (+397/‑27)	metK → / → galP	S‑adenosylmethionine synthetase/D‑galactose transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,088,257	0	T	C	98.0%	171.0 / ‑6.6	49	intergenic (+397/‑27)	metK/galP	S‑adenosylmethionine synthetase/D‑galactose transporter
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (24/24);  total (25/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAATAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTACTCTTTGGCCTGGATATCGGTGTAATTG  >  NC_000913/3088126‑3088392                                                                                                                                    |                                                                                                                                        tCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATTTTAGTGTAAGCGATTACACTGATGTGATTTGCTTAACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAAt                                                                                                                                  <  2:325386/139‑1 (MQ=255) tCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAAt                                                                                                                                  <  1:679196/139‑1 (MQ=255)     tgatgaTATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAAcc                                                                                                                              >  1:2953/1‑139 (MQ=255)     tgatgaTATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAAcc                                                                                                                              <  2:199936/139‑1 (MQ=255)      gatgatATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCa                                                                                                                             <  2:2953/139‑1 (MQ=255)          atatAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATAtt                                                                                                                         <  1:736261/139‑1 (MQ=255)           tataACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAATTAACCATATTg                                                                                                                        >  1:1300007/1‑139 (MQ=255)              aaCTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAg                                                                                                                     <  1:140392/139‑1 (MQ=255)                cTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAggg                                                                                                                   >  2:309645/1‑139 (MQ=255)                cTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAggg                                                                                                                   >  2:242019/1‑139 (MQ=255)                  cAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGca                                                                                                                 >  1:941621/1‑139 (MQ=255)                             aTGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACTATATTGGAGGGCATCATGCCTGAc                                                                                                      >  2:983182/1‑139 (MQ=255)                                          aTAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAgg                                                                                         <  1:309645/139‑1 (MQ=255)                                                  gATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAgg                                                                                                                    <  1:46836/104‑1 (MQ=255)                                                  gATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAgg                                                                                                                    >  2:46836/1‑104 (MQ=255)                                                           tAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCa                                                                        >  2:284428/1‑139 (MQ=255)                                                             gtgtAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAAt                                                                      >  1:863134/1‑139 (MQ=255)                                                                  aGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGt                                                                 >  1:166836/1‑139 (MQ=255)                                                                      aTTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAATAAAAAATAACCATATTGGAGGGCATCATGCCTGa                                                                                                       >  1:705255/1‑97 (MQ=255)                                                                      aTTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGa                                                                                                       <  2:705255/97‑1 (MQ=255)                                                                       ttACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTc                                                            >  2:846630/1‑139 (MQ=255)                                                                        tACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACaaaa                                                                                                                                     >  1:357811/1‑65 (MQ=255)                                                                        tACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACaaaa                                                                                                                                     <  2:357811/65‑1 (MQ=255)                                                                        tACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCg                                                           >  1:514886/1‑139 (MQ=255)                                                                             tGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGc                                                      >  1:401121/1‑139 (MQ=255)                                                                             tGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGc                                                      >  2:107077/1‑139 (MQ=255)                                                                                    aTTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCgg                                                                                    >  1:1083924/1‑102 (MQ=255)                                                                                    aTTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCgg                                                                                    <  2:1083924/102‑1 (MQ=255)                                                                                    aTTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTg                                               >  2:333404/1‑139 (MQ=255)                                                                                    aTTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTg                                               <  2:863134/139‑1 (MQ=255)                                                                                         cTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGcc                                                                                                          >  2:828018/1‑75 (MQ=255)                                                                                         cTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGcc                                                                                                          <  1:828018/75‑1 (MQ=255)                                                                                         cTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGa                                                                                                       >  2:568159/1‑78 (MQ=255)                                                                                         cTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGa                                                                                                       <  1:568159/78‑1 (MQ=255)                                                                                         cTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGct                                          <  2:166836/139‑1 (MQ=255)                                                                                             acaTCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTgg                                      <  1:983182/139‑1 (MQ=255)                                                                                             acaTCTTTTTACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTgg                                      <  1:846630/139‑1 (MQ=255)                                                                                                   ttttACGTCGTACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGAt                                >  1:1164999/1‑139 (MQ=255)                                                                                                         gtcgtACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTActct                          <  2:941621/139‑1 (MQ=255)                                                                                                            gtACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCg                                            <  1:1053165/118‑1 (MQ=255)                                                                                                            gtACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCg                                            >  2:1053165/1‑118 (MQ=255)                                                                                                             tACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCt                                                 >  1:911344/1‑112 (MQ=255)                                                                                                             tACTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCGAGAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCt                                                 <  2:911344/112‑1 (MQ=255)                                                                                                              aCTCACCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTACTCTTTGGc                     <  1:284428/139‑1 (MQ=255)                                                                                                                  aCCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTgg                                      >  2:102353/1‑118 (MQ=255)                                                                                                                  aCCTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTgg                                      <  1:102353/118‑1 (MQ=255)                                                                                                                    cTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTActct                          >  2:1086033/1‑128 (MQ=255)                                                                                                                    cTATCTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTActct                          <  1:1086033/128‑1 (MQ=255)                                                                                                                       gcTTAATTCACGACAAGAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGTGCCGGTCAATGAAGGCAATGACGTGTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGTTTACTCTTTGGCCTGGATATc            <  2:1300007/138‑1 (MQ=255)                                                                                                                        cTTAATTCACAACAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTACTCTTTGGCCTGGATATCg           <  1:333404/139‑1 (MQ=255)                                                                                                                                 caacaaAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTACTCTTTGGCCTGGATATCGGTGTAATTg  >  2:706453/1‑139 (MQ=255)                                                                                                                                 caacaaAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTACTCTTTGGCCTGGATATCGGTGTAATTg  >  2:723508/1‑139 (MQ=255)                                                                                                                                    |                                                                                                                                        TCTATGATGATATAACTCAATTATTTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGTAAGCGATTACACTGATGTGATTTGCTTCACATCTTTTTACGTCGTACTCACCTATCTTAATTCACAATAAAAAATAACCATATTGGAGGGCATCATGCCTGACGCTAAAAAACAGGGGCGGTCAAACAAGGCAATGACGTTTTTCGTCTGCTTCCTTGCCGCTCTGGCGGGATTACTCTTTGGCCTGGATATCGGTGTAATTG  >  NC_000913/3088126‑3088392

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑