Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,508,798	G→T	intergenic (+56/+36)	rlhA → / ← yncJ	23S rRNA 5‑hydroxycytidine C2501 synthase/protein YncJ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,508,798	0	G	T	100.0%	154.7 / NA	45	intergenic (+56/+36)	rlhA/yncJ	23S rRNA 5‑hydroxycytidine C2501 synthase/protein YncJ
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (26/19);  total (26/19)

AAAATGCCGTTACCGGGAAGCGTAGTGGCATCCGTAAGTCCGGATGAGCTGCTGAAAACATTGCCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCGGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCCACAGCACGCAATTCATCGCTG  >  NC_000913/1508662‑1508933                                                                                                                                         |                                                                                                                                        aaaaTGCCGTTACCGGGAAGCGTAGTGGCATCCGTAAGTCCGGATGAGCTGCTGAAAACATTGCCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGt                                                                                                                                      >  2:51167/1‑140 (MQ=255)         gTTACCGGGAAGCGTAGTGGCATCCGTAAGACCGGATGAGCTGCTGAAAACATTGCCGAAGCGGAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGtt                                                                                                                              >  2:859990/1‑140 (MQ=255)           tACCGGGAAGCGTAGTGGCATCCGTAAGTCCGGATGAGCTGCTGAAAACATTGCCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTAc                                                                                                                            >  1:794870/1‑140 (MQ=255)                 gAAGCGTAGTGGCATCCGTAAGTCCGGATGAGCTGCTGAAAACATTGTCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCa                                                                                                                      >  1:464910/1‑140 (MQ=255)                  aaGCGTAGTGGCATCCGTAAGTCCGGATGAGCTGCTGAAAACATTGCCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCAt                                                                                                                     <  1:181354/140‑1 (MQ=255)                        aGTGGCATCCGTAAGTCCGGATGAGCTGCTGAAAACATTGCCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCa                                                                                                               <  1:484548/140‑1 (MQ=255)                             cATCCGTAAGTCCGGATGAGCTGCTGAAAACATTGCCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCaaa                                                                                                          <  1:256496/140‑1 (MQ=255)                               tCCGTAAGTCCGGATGAGCTGCTGAAAACATTGCCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATg                                                                                                        >  2:104676/1‑140 (MQ=255)                                ccGTAAGTCCGGATGAGCTGCTGAAAACATTGCCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGa                                                                                                       <  1:368455/140‑1 (MQ=255)                                  gTAAGTCCGGATGAGCTGCTGAAAACATTGTCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACt                                                                                                     <  2:464910/140‑1 (MQ=255)                                    aaGTCCGGATGAGCTGCTGAAAACATTGCCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCa                                                                                                   >  2:1293709/1‑140 (MQ=255)                                           gATGAGCTGCTGAAAACATTGCCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGt                                                                                            >  2:258413/1‑140 (MQ=255)                                                      gAAAACATTGCCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTcc                                                                                          >  2:753023/1‑131 (MQ=255)                                                      gAAAACATTGCCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTcc                                                                                          <  1:753023/131‑1 (MQ=255)                                                            aTTGCCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTgcg                                                                           <  2:62829/140‑1 (MQ=255)                                                            aTTGCCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTgcg                                                                           <  1:51167/140‑1 (MQ=255)                                                                    aGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGAttttt                                                                   <  2:185616/140‑1 (MQ=255)                                                                       gAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGcc                                                                <  2:631535/140‑1 (MQ=255)                                                                          aaGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGt                                                             >  1:110303/1‑140 (MQ=255)                                                                                  aaCGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGc                                                     <  2:473208/140‑1 (MQ=255)                                                                                                  ttACTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAAccagaag                                     <  2:647963/140‑6 (MQ=255)                                                                                                    aCTCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTccgcc                                   >  2:270880/1‑140 (MQ=255)                                                                                                      tCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGa                                 <  1:258413/140‑1 (MQ=255)                                                                                                      tCACAACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGa                                 >  1:794963/1‑140 (MQ=255)                                                                                                        acaACTTATTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGAct                               >  1:950615/1‑140 (MQ=255)                                                                                                               aTTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGc                        >  1:975355/1‑140 (MQ=255)                                                                                                               aTTGAATCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGc                        >  1:1174053/1‑140 (MQ=255)                                                                                                                   aaTCTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCcaca                    <  2:794870/140‑1 (MQ=255)                                                                                                                      cTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCcaca                    <  1:276490/137‑1 (MQ=255)                                                                                                                      cTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCcaca                    >  2:276490/1‑137 (MQ=255)                                                                                                                      cTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCCACAGCa                 >  2:440953/1‑140 (MQ=255)                                                                                                                      cTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCCACAGCa                 >  1:1303335/1‑140 (MQ=255)                                                                                                                      cTGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCCACAGCa                 >  1:359825/1‑140 (MQ=255)                                                                                                                       tGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCCACAGCAc                >  1:449460/1‑140 (MQ=255)                                                                                                                       tGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCCACAGCAc                >  2:238912/1‑140 (MQ=255)                                                                                                                       tGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCCACAGCAc                >  1:992831/1‑140 (MQ=255)                                                                                                                       tGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCCTCCGCCGACTCTTCCGCcac                     >  2:1071195/1‑135 (MQ=255)                                                                                                                       tGCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCCTCCGCCGACTCTTCCGCcac                     <  1:1071195/135‑1 (MQ=255)                                                                                                                        gCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCCACAGCACg               <  1:270880/140‑1 (MQ=255)                                                                                                                        gCATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCCACAGCACg               <  1:119532/140‑1 (MQ=255)                                                                                                                         cATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCCACAGCACGc              >  1:1009499/1‑140 (MQ=255)                                                                                                                         cATGATATTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCACCGACTCTTCAGCCACAGCACGc              >  2:1186215/1‑140 (MQ=255)                                                                                                                             atatTGCCTGCCTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCCACAGCACGCAAtt          <  1:1293709/140‑1 (MQ=255)                                                                                                                                 tgcctgccTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCCACAGCACGCAATTCATc      >  1:825574/1‑140 (MQ=255)                                                                                                                                   cctgcctgGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCCACAGCACGCAATTCATCGc    >  1:358455/1‑140 (MQ=255)                                                                                                                                   cctgcctgGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGAAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCCACAGCACGCAATTCATCGc    >  2:1269991/1‑140 (MQ=255)                                                                                                                                     tgccTGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCCACAGCACGCAATTCATCGCTg  >  2:565894/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                                        AAAATGCCGTTACCGGGAAGCGTAGTGGCATCCGTAAGTCCGGATGAGCTGCTGAAAACATTGCCGAAGCGAAAAGGGTAAAACGCCAGTTTTCTGGTTACTCACAACTTATTGAATCTGCATGATATTGCCTGCCGGGTAAGGCGTTACGCCGCATCCGGCATCAAATGACTCAACGTTGTCCCGCTTCTGGTTTGCGCGATTTTTGCCAGTAAAAATGCTCGCGCAAACCTTCCGCCGACTCTTCCGCCACAGCACGCAATTCATCGCTG  >  NC_000913/1508662‑1508933

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑