Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,073,996	Δ1 bp	coding (16/1149 nt)	rutA ←	pyrimidine oxygenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,073,993	0	G	.	100.0%	119.2 / NA	29	coding (19/1149 nt)	rutA	pyrimidine oxygenase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (9/20);  total (9/20)

AGCCGTTGTTGCCAATAGGTACGAATACGCCAATTTTCATCATCAACCTCTCTTCGTCTCGTAAAGTGAAAGTCAGACGGGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGATGCCAGTTTTTAAAAAGT  >  NC_000913/1073915‑1074068                                                                               |                                                                            agccGTTGTTGCCAATAGGTACGAATACGCCAATTTTCATCATCAACCTCTCTTCGTCTCATAAAGTGAAAGTCAGACggg                                                                           <  1:217992/81‑1 (MQ=255)         ttgCCAATAGGTACGAATACGCCAATTTTCATCATCAACCTCTCTTCGTCTCGTAAAGTGAAAGTCAGAC‑GGGCGCTGCAt                                                                  <  1:217993/81‑1 (MQ=255)            ccAATAGGTACGAATACGCCAATTTTCATCATCAACCTCTCTTCGTCTCGTAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCt                                                               >  2:218028/1‑81 (MQ=255)              aaTAGGTACGAATACGCCAATTTTCATCATCAACCTCTCTTCGTCTCGTAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCTg                                                              >  1:218035/1‑80 (MQ=255)                  ggTACGAATACGCCAATTTTCATCATCAACCTCTCTTCGTCTCGTAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCTGCatat                                                         <  1:217994/81‑1 (MQ=255)                     aCGAATACGCCAATTTTCATCATCAACCTCTCTTCGTCTCGTAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCt                                                      >  2:218029/1‑81 (MQ=255)                            cGCCAATTTTCATCATCAACCTCTCTTCGTCTCGTAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAg                                                <  1:217995/80‑1 (MQ=255)                               cAATTTTCATCATCAACCTCTCTTCGTCTCGTAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCcgc                                            <  1:217996/81‑1 (MQ=255)                                    ttCATCATCAACCTCTCTTCGTCTCGTAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTAtt                                       >  2:218032/1‑81 (MQ=255)                                    ttCATCATCAACCTCTCTTCGTCTCGTAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTAt                                        <  1:217997/80‑1 (MQ=255)                                             aaCCTCTCTTCGTCTCGTAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGttt                              <  1:217998/81‑1 (MQ=255)                                                ctctctTCGTCTCGTAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCa                           <  1:217999/81‑1 (MQ=255)                                                  ctctTCGTCTCGTAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCa                           >  1:218033/1‑79 (MQ=255)                                                      tCGTCTCGTAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCg                      >  2:218036/1‑80 (MQ=255)                                                       cGTCTCGTAAAGTGAAAGTCAGAC‑AGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCgg                     <  1:218000/80‑1 (MQ=255)                                                        gTCTCGTAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGAt                   <  2:218001/81‑1 (MQ=255)                                                          ctcGTAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGATGc                 >  2:218044/1‑81 (MQ=255)                                                             gTAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGATGc                 <  1:218002/78‑1 (MQ=255)                                                              tAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGATGCCAGt             <  2:218004/81‑1 (MQ=255)                                                              tAAAGTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGATGCCAGt             <  1:218003/81‑1 (MQ=255)                                                                aaGTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGATGCCAGtt            <  2:218005/80‑1 (MQ=255)                                                                  gTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGATGCCAGttttt         <  1:218007/81‑1 (MQ=255)                                                                  gTGAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGATGCCAGttttt         <  1:218006/81‑1 (MQ=255)                                                                    gAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGATGCCAGTTTTTa        >  1:218040/1‑80 (MQ=255)                                                                    gAAAGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGATGCCAGTTTTTa        >  1:218037/1‑80 (MQ=255)                                                                      aaGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGATGCCAGTTTTTaaaa     <  2:218008/81‑1 (MQ=255)                                                                       aGTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGATGCCAGTTTTTaaaaa    <  1:401056/81‑1 (MQ=255)                                                                        gTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGATGCCAGTTTTTAAAAAg   <  2:218009/81‑1 (MQ=255)                                                                        gTCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGATGCCAGTTTTTAAAAAg   <  2:218010/81‑1 (MQ=255)                                                                         tCAGAC‑GGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGATGCCAGTTTTTAAAAAGt  <  2:218011/81‑1 (MQ=255)                                                                               |                                                                            AGCCGTTGTTGCCAATAGGTACGAATACGCCAATTTTCATCATCAACCTCTCTTCGTCTCGTAAAGTGAAAGTCAGACGGGGCGCTGCATCCTGCATATCCTTTTCAGCCGCGTATTGGCTTGTTTGCAAAGCGGATGCCAGTTTTTAAAAAGT  >  NC_000913/1073915‑1074068

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑