Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,211,078	C→T	intergenic (+82/‑29)	rpsU → / → dnaG	30S ribosomal subunit protein S21/DNA primase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,211,078	0	C	T	100.0%	182.1 / NA	52	intergenic (+82/‑29)	rpsU/dnaG	30S ribosomal subunit protein S21/DNA primase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (27/25);  total (27/25)

ACGTCACGCGAAGAAACTGGCTCGCGAAAACGCACGCCGCACTCGTCTGTACTAATTCCCCGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTCGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGGCACGCACTGACATCGTCGATCTGATCGATGCCCGTGTGAAGCTGAAAAAGCAGGG  >  NC_000913/3210942‑3211204                                                                                                                                         |                                                                                                                               aCGTCACGCGAAGAAACTGGCTCGCGAAAACGCACGCCGCACTCGTCTGTACTAATTCCCCGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGt                                                                                                                              >  2:243208/1‑139 (MQ=255)        gcgAAGAAACTGGCTCGCGAAAACGCACGCCGCACTCGTCTGTACTAATTCCCCGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGaa                                                                                                                       <  1:608275/139‑1 (MQ=255)         cgAAGAAACTGGCTCGCGAAAACGCACGCCGCACTCGTCTGTACTAATTCCCCGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAAt                                                                                                                      >  1:1008746/1‑139 (MQ=255)                      tCGCGAAAACGCACGCCGCACTCGTCTGTACTAATTCCCCGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCgg                                                                                                         >  2:1286490/1‑139 (MQ=255)                        gcgAAAACGCACGCCGCACTCGTCTGTACTAATTCCCCGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCgggg                                                                                                       >  1:587059/1‑139 (MQ=255)                         cgAAAACGCACGCCGCACTCGTCTGTACTAATTCCCCGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCg                                                                                                          >  1:388539/1‑135 (MQ=255)                         cgAAAACGCACGCCGCACTCGTCTGTACTAATTCCCCGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCg                                                                                                          <  2:388539/135‑1 (MQ=255)                         cgAAAACGCACGCCGCACTCGTCTGTACTAATTCCCCGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGc                                                                                                      <  2:587059/139‑1 (MQ=255)                              acgcacgcCGCACTCGTCTGTACTAATTCCCCGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATg                                                                                                 >  1:321070/1‑139 (MQ=255)                                 cacgcCGCACTCGTCTGTACTAATTCCCCGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCt                                                                                              <  2:294401/139‑1 (MQ=255)                                      cgcACTCGTCTGTACTAATTCCCCGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACg                                                                                         <  2:321070/139‑1 (MQ=255)                                           tCGTCTGTACTAATTCCCCGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATcc                                                                                    <  1:243208/139‑1 (MQ=255)                                                   aCTAATTCCCCGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTa                                                                            <  2:1031973/139‑1 (MQ=255)                                                          ccccGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATc                                                                                                           >  1:6166/1‑101 (MQ=255)                                                          ccccGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATc                                                                                                           <  2:6166/101‑1 (MQ=255)                                                                      tGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTgg                                                         <  2:1008746/139‑1 (MQ=255)                                                                      tGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCAC‑CGTATTCATTAATGATCTGCTGgc                                                        >  1:580511/1‑139 (MQ=255)                                                                       gCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCAC‑CGTATTCATTAATGATCTGCTGgca                                                       <  2:580511/139‑1 (MQ=255)                                                                                tCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGCCGAATCCCACGCGTATTCATGAATGATCTGCTGGCACGCACTGa                                               <  1:925690/139‑1 (MQ=255)                                                                                tCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGGCACGCACTGa                                               >  1:262935/1‑139 (MQ=255)                                                                                          ttgtagttgtaAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGGCACGCACTGACATCGTCGAt                                     >  1:607585/1‑139 (MQ=255)                                                                                                  gtaAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGgca                                                       <  2:934345/113‑1 (MQ=255)                                                                                                  gtaAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGgca                                                       >  1:934345/1‑113 (MQ=255)                                                                                                   taAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGGCACGCACTGACATCGTCGATCTGATCGAt                            >  1:169282/1‑139 (MQ=255)                                                                                                     aGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATctg                                                             >  1:556268/1‑104 (MQ=255)                                                                                                     aGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATctg                                                             <  2:556268/104‑1 (MQ=255)                                                                                                       gCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTAtt                                                                          >  2:690739/1‑89 (MQ=255)                                                                                                       gCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTAtt                                                                          <  1:690739/89‑1 (MQ=255)                                                                                                       gCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGgcacgcac                                                  >  2:948065/1‑113 (MQ=255)                                                                                                       gCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGgcacgcac                                                  <  1:948065/113‑1 (MQ=255)                                                                                                         cGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGaa                                                                                                                       >  2:223065/1‑42 (MQ=255)                                                                                                         cGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGaa                                                                                                                       <  1:223065/42‑1 (MQ=255)                                                                                                         cGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCa                                                                                  >  2:18063/1‑79 (MQ=255)                                                                                                         cGTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCa                                                                                  <  1:18063/79‑1 (MQ=255)                                                                                                          gTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGaa                                                                                                                       >  1:410759/1‑41 (MQ=255)                                                                                                          gTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGaa                                                                                                                       <  2:410759/41‑1 (MQ=255)                                                                                                          gTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGc                                                                                               <  2:288247/65‑1 (MQ=255)                                                                                                          gTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGc                                                                                               >  1:288247/1‑65 (MQ=255)                                                                                                          gTGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGGCACGCACTGACATCGTCGATCTGATCGATGCCCgtg                     >  2:298884/1‑139 (MQ=255)                                                                                                           tGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTa                                                                            <  1:745553/83‑1 (MQ=255)                                                                                                           tGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTa                                                                            >  2:745553/1‑83 (MQ=255)                                                                                                           tGCTTCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGGCACGCACTGACATCGTCGATCTGATCGATGCCCgtgt                    >  1:1093615/1‑139 (MQ=255)                                                                                                              ttCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGGCACGCACTGACATCGTCGATCTGATCGATGCCCGTGTGaa                 <  2:169282/139‑1 (MQ=255)                                                                                                              ttCCGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGGCACGCACTGACATCGTCGATCTGATCGATGCCCGTGTGaa                 <  1:1286490/139‑1 (MQ=255)                                                                                                                 cGAAAGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGGCACGCACTGACATCGTCGATCTGATCGATGCCCGTGTGAAGCt              >  2:1139171/1‑139 (MQ=255)                                                                                                                     aGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCg                                                                                                          >  1:1156048/1‑43 (MQ=255)                                                                                                                     aGGAATGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCg                                                                                                          <  2:1156048/43‑1 (MQ=255)                                                                                                                          tGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGGCACGCACTGACATCGTCGATc                                    <  1:326988/108‑1 (MQ=255)                                                                                                                          tGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGGCACGCACTGACATCGTCGATc                                    >  2:326988/1‑108 (MQ=255)                                                                                                                          tGCGCGGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGGCACGCACTGACATCGTCGATCTGATCGATGCCCGTGTGAAGCTGAAAAAGCa     >  1:389761/1‑139 (MQ=255)                                                                                                                            cgcgGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGGCACGCACTGACATCGTCGATCTGATCGATGCCCGTGTGAAGCTGAAAAAGCAgg   <  1:1139171/139‑1 (MQ=255)                                                                                                                             gcgGCTTATTTTTGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGGCACGCACTGACATCGTCGATCTGATCGATGCCCGTGTGAAGCTGAAAAAGCAggg  >  1:378715/1‑139 (MQ=255)                                                                                                                                         |                                                                                                                               ACGTCACGCGAAGAAACTGGCTCGCGAAAACGCACGCCGCACTCGTCTGTACTAATTCCCCGAGAGCGTTGCTCTCCGATCAGACCGAGTTGTAGTTGTAAGGCCGTGCTTCCGAAAGGAATGCGCGGCTTATTTTCGTTTATGAATTGCTAAAAATCGGGGCCTATGGCTGGACGAATCCCACGCGTATTCATTAATGATCTGCTGGCACGCACTGACATCGTCGATCTGATCGATGCCCGTGTGAAGCTGAAAAAGCAGGG  >  NC_000913/3210942‑3211204

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑