Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,068,276	Δ1 bp	intergenic (+22/+235)	ymdF → / ← rutG	KGG family protein/pyrimidine permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,068,276	0	G	.	100.0%	262.6 / NA	61	intergenic (+22/+235)	ymdF/rutG	KGG family protein/pyrimidine permease
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (30/31);  total (30/31)

TGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAA  >  NC_000913/1068155‑1068387                                                                                                                          |                                                                                                                tGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCg                                                                                              >  1:658095/1‑139 (MQ=255)   gACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGT‑AAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCa                                                                                           >  1:607424/1‑139 (MQ=255)           agcGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGcc                                                                                    >  1:283741/1‑139 (MQ=255)             cGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCAt                                                                                  >  2:33897/1‑139 (MQ=255)                           aGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTAcc                                                                    <  2:283741/139‑1 (MQ=255)                             aaTGACCCGCTGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                  <  1:186416/139‑1 (MQ=255)                               tGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCggt                                                                >  2:1219202/1‑139 (MQ=255)                               tGACCCGCAGCGCGCATCTGAAGCAGGT‑AAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCggtg                                                               <  2:607424/139‑1 (MQ=255)                                gACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCggtg                                                               >  1:1291113/1‑139 (MQ=255)                                       aGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATa                                                        >  2:750856/1‑139 (MQ=255)                                       aGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATa                                                        <  2:1291113/139‑1 (MQ=255)                                       aGCGCGCATCTGAAGCA‑GTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATAc                                                       >  2:997240/1‑139 (MQ=255)                                        gcgcgcATCTGAAGCA‑GTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACt                                                      <  1:997240/139‑1 (MQ=255)                                           cgcATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CAttt                                                                                                            <  1:1124887/84‑1 (MQ=39)                                           cgcATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CAttt                                                                                                            >  2:1124887/1‑84 (MQ=255)                                           cgcATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGcc                                                                                    >  2:216526/1‑107 (MQ=255)                                           cgcATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGcc                                                                                    <  1:216526/107‑1 (MQ=255)                                           cgcATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                  >  2:706847/1‑125 (MQ=255)                                           cgcATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                  <  1:706847/125‑1 (MQ=255)                                           cgcATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACtga                                                    >  2:807644/1‑139 (MQ=255)                                                         gTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGc                                      <  1:1219202/139‑1 (MQ=255)                                                          tAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTAcc                                                                    >  2:886727/1‑108 (MQ=255)                                                          tAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTAcc                                                                    <  1:886727/108‑1 (MQ=255)                                                          tAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                  >  2:565307/1‑110 (MQ=255)                                                          tAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                  <  1:565307/110‑1 (MQ=255)                                                          tAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACtgatga                                                 <  1:796713/127‑1 (MQ=255)                                                          tAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAAt                                            >  2:284018/1‑132 (MQ=255)                                                          tAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAAt                                            <  1:284018/132‑1 (MQ=255)                                                          tAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCt                                     >  2:444682/1‑139 (MQ=255)                                                          tAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCt                                     >  2:172908/1‑139 (MQ=255)                                                          tAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCATCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACtgatga                                                 >  2:796713/1‑127 (MQ=255)                                                           aaaaaaGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCtt                                    <  1:750856/139‑1 (MQ=255)                                                                   tggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                  <  1:873558/101‑1 (MQ=255)                                                                   tggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                  >  2:873558/1‑101 (MQ=255)                                                                    ggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCAccgc                                                                            <  1:789858/90‑1 (MQ=255)                                                                    ggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCAccgc                                                                            >  2:789858/1‑90 (MQ=255)                                                                    ggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTAcc                                                                    >  2:760436/1‑98 (MQ=255)                                                                    ggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTAcc                                                                    <  1:760436/98‑1 (MQ=255)                                                                     gtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                          <  2:658095/139‑1 (MQ=255)                                                                              gTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTa                 <  1:444682/139‑1 (MQ=255)                                                                               tCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTAcc                                                                    <  2:64390/87‑1 (MQ=255)                                                                               tCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTAcc                                                                    >  1:64390/1‑87 (MQ=255)                                                                                cACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATc               <  2:1079606/139‑1 (MQ=255)                                                                                          gCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCa     <  1:33897/139‑1 (MQ=255)                                                                                             aCAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCagaa  <  1:807644/139‑1 (MQ=255)                                                                                                    accGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTAcc                                                                    >  2:573406/2‑66 (MQ=255)                                                                                                    accGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTAcc                                                                    <  1:573406/65‑1 (MQ=255)                                                                                                    accGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGAt                             >  1:110802/2‑105 (MQ=255)                                                                                                    accGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGAt                             <  2:110802/104‑1 (MQ=255)                                                                                                     ccGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAgg            <  1:1306286/121‑1 (MQ=255)                                                                                                     ccGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAgg            >  2:1306286/1‑121 (MQ=255)                                                                                                        ggCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTAcc                                                                    >  2:610109/1‑62 (MQ=255)                                                                                                        ggCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTAcc                                                                    <  1:610109/62‑1 (MQ=255)                                                                                                            aaTCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                  >  2:884599/1‑60 (MQ=255)                                                                                                            aaTCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                  <  1:884599/60‑1 (MQ=255)                                                                                                             aTCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATc               >  1:1300016/1‑110 (MQ=255)                                                                                                             aTCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATc               <  2:1300016/110‑1 (MQ=255)                                                                                                                   gACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                          >  1:1137584/1‑93 (MQ=255)                                                                                                                   gACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                          <  2:1137584/93‑1 (MQ=255)                                                                                                                    aCGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATg                     <  1:923173/97‑1 (MQ=255)                                                                                                                    aCGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATg                     >  2:923173/1‑97 (MQ=255)                                                                                                                          |                                                                                                                TGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAA  >  NC_000913/1068155‑1068387

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑