Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,944,244	C→A	intergenic (+13/‑80)	rrlC → / → rrfC	23S ribosomal RNA/5S ribosomal RNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,944,244	0	C	A	100.0%	148.6 / NA	62	intergenic (+13/‑80)	rrlC/rrfC	23S ribosomal RNA/5S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (36/26);  total (36/26)

GGCTTAACCTTACAACGCCGAA‑GCTGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGG  >  NC_000913/3944221‑3944333                         |                                                                                          ggCTTAACCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAATATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCtgatg                      <  1:172218/93‑1 (MQ=9) ggCTTAACCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCtgatg                      <  1:4462472/93‑1 (MQ=14)  gCTTTACCTTTCAACGCCGAAGGATGTTTGGGCGG‑TGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCtgatga                     <  2:4243863/93‑1 (MQ=11)  gCTTAACCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCtgatga                     <  2:3300087/93‑1 (MQ=17)    ttAACCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGaaa                   <  1:1463650/93‑1 (MQ=18)    ttAACCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGaaa                   >  2:2429689/1‑93 (MQ=18)    ttAACCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGaaa                   >  1:5965024/1‑93 (MQ=18)    ttAACCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGaaa                   >  1:5965023/1‑93 (MQ=18)    ttAACCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGaaa                   >  2:4348490/1‑93 (MQ=18)     tAACCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAAc                  <  2:2824378/93‑1 (MQ=18)     tAACCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAAc                  >  1:1211629/1‑93 (MQ=18)      aaCCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACa                 <  1:5927185/93‑1 (MQ=18)      aaCCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACa                 <  1:2246309/93‑1 (MQ=18)      aaCCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACa                 >  1:5772861/1‑93 (MQ=18)      aaCCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACa                 >  2:165835/1‑93 (MQ=18)      aaCCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACa                 <  2:5400312/93‑1 (MQ=21)      aaCCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACa                 <  1:1735521/93‑1 (MQ=21)      aaCCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACa                 <  2:1021636/93‑1 (MQ=21)      aaCCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACa                 <  2:4877070/93‑1 (MQ=21)      aaCCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACa                 >  2:4734977/1‑93 (MQ=18)      aaCCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACa                 <  1:3741222/93‑1 (MQ=21)      aaCCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACa                 >  1:4043564/1‑93 (MQ=18)       aCCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAg                >  1:2042753/1‑93 (MQ=18)       aCCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAg                <  2:585616/93‑1 (MQ=18)       aCCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAg                >  1:1922652/1‑93 (MQ=18)       aCCTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAg                >  1:2501084/1‑93 (MQ=18)        ccTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGa               <  1:3873713/93‑1 (MQ=18)        ccTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGa               >  1:6059474/1‑93 (MQ=18)        ccTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGa               >  2:2761364/1‑93 (MQ=18)        ccTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGa               <  1:1499375/93‑1 (MQ=18)        ccTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGa               <  1:1499374/93‑1 (MQ=21)         cTTACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGaa              <  1:3876664/93‑1 (MQ=18)          ttACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAAt             >  1:3171825/1‑93 (MQ=18)          ttACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAAt             >  2:5314509/1‑93 (MQ=18)          ttACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAAt             <  1:3052328/93‑1 (MQ=21)          ttACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAAt             >  1:4707487/1‑93 (MQ=18)          ttACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAAt             >  2:2872609/1‑93 (MQ=18)           tACAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAAtt            <  2:5690735/93‑1 (MQ=21)            aCAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAAttt           >  1:3441569/1‑93 (MQ=18)            aCAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAAttt           >  1:3263200/1‑93 (MQ=18)            aCAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAAttt           <  2:2175126/93‑1 (MQ=18)             cAACGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTg          <  2:5629596/93‑1 (MQ=18)              aaCGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGc         <  1:2730641/93‑1 (MQ=18)               aCGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGcc        >  2:937616/1‑93 (MQ=18)               aCGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGcc        >  1:5334679/1‑93 (MQ=18)                cGCCGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCt       <  1:3277752/93‑1 (MQ=18)                  gcGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTgg     <  1:2632173/92‑1 (MQ=18)                  ccGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTgg     >  2:5783874/1‑93 (MQ=18)                  ccGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTgg     <  1:2989402/93‑1 (MQ=21)                   cGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggc    <  2:2273358/93‑1 (MQ=18)                   cGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggc    >  2:3182931/1‑93 (MQ=18)                   cGAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggc    >  2:4161165/1‑93 (MQ=18)                    gAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggcg   >  1:1515221/1‑93 (MQ=18)                    gAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggcg   <  1:1689957/93‑1 (MQ=18)                    gAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggcg   >  1:4331973/1‑93 (MQ=18)                    gAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggcg   >  1:4543836/1‑93 (MQ=18)                    gAA‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggcg   >  2:1812512/1‑93 (MQ=18)                     aa‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggcgg  >  1:3644907/1‑93 (MQ=18)                     aa‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggcgg  >  2:5020065/1‑93 (MQ=18)                     aa‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggcgg  >  1:3059473/1‑93 (MQ=18)                     aa‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggcgg  >  1:4264788/1‑93 (MQ=18)                     aa‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggcgg  >  1:2135480/1‑93 (MQ=18)                     aa‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggcgg  >  1:4850134/1‑93 (MQ=18)                     aa‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggcgg  <  2:5998650/93‑1 (MQ=21)                     aa‑GATGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTggcgg  >  2:6019172/1‑93 (MQ=18)                         |                                                                                          GGCTTAACCTTACAACGCCGAA‑GCTGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATGAAACAGAATTTGCCTGGCGG  >  NC_000913/3944221‑3944333

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑