Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,871,206	Δ1 bp	coding (99/1050 nt)	truD ←	tRNA pseudouridine(13) synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,871,204	0	C	.	100.0%	107.7 / NA	26	coding (101/1050 nt)	truD	tRNA pseudouridine(13) synthase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (18/8);  total (18/8)

CATCCGCCACAAAACGGGTATTGCAGCCGTTTTTGAGGATTCTAACCAGAATATGCTCACCTTCACCATCAGGCTCAAAGCCCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTGGAGG  >  NC_000913/2871124‑2871278                                                                                 |                                                                           cATCCGCCACAAAACGGGTATTGCAGCCGTTTTTGAGGATTCTAACCAGAATATGCTCACCTTCACCATCAGGCTCAAAGc                                                                            <  2:466020/81‑1 (MQ=255)     cGCCACAAAACGGGTATTGCAGCCGTTTTTGAGGATTCTAACCAGAATATGCTCACCTTCACCATCAGGCTCAAAGccaa                                                                         <  1:466021/80‑3 (MQ=255)           aaaaCGGGTATTGCAGCCGTTTTTGAGGATTCTAACCAGAATATGCTCACCTTCACCATCAGGCTCAAAG‑CCAAATCTTc                                                                  >  2:466022/1‑80 (MQ=255)           aaaaCGGGTATTGCAGCCGTTTTTGAGGATTCTAACCAGAATATGCTCACCTTCACCATCAGGCTCAAAG‑CCAAATCTTc                                                                  >  1:466048/1‑80 (MQ=255)             aaCGGGTATTGCAGCCGTTTTTGAGGATTCTAACCAGAATATGCTCACCTTCACCATCAGGCTCAAAG‑CCAAATCTTccac                                                               >  1:466045/1‑81 (MQ=255)                gggTATTGCAGCCGTTTTTGAGGATTCTAACCAGAATATGCTCACCTTCACCATCAGGCTCAAAG‑CCAAATCTTccaccac                                                            >  2:466046/1‑81 (MQ=255)                 ggTATTGCAGCCGTTTTTGAGGATTCTAACCAGAATATGCTCACCTTCACCATCAGGCTCAAAG‑CCAAATCTTccaccac                                                            >  2:584349/1‑80 (MQ=255)                             gTTTTTGAGGATTCTAACCAGAATATGCTCACCTTCACCATCAGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTcc                                               >  1:466047/1‑81 (MQ=255)                                 ttGAGGATTCTAACCAGAATATGCTCACCTTCACCATCAGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGAt                                           >  2:466061/1‑81 (MQ=255)                                  tGAGGATTCTAACCAGAATATGCTCACCTTCACCATCAGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGAtt                                          >  1:466053/1‑81 (MQ=255)                                  tGAGGATTCTAACCAGAATATGCTCACCTTCACCATCAGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGAt                                           <  1:466023/80‑1 (MQ=255)                                     ggATTCTAACCAGAATATGCTCACCTTCACCATCAGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGc                                       >  1:466051/1‑81 (MQ=255)                                          cTAACCAGAATATGCTCACCTTCACCATCAGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCttt                                    >  2:466057/1‑79 (MQ=255)                                               cAGAATATGCTCACCTTCACCATCAGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCagcagc                             >  2:466049/1‑81 (MQ=255)                                                aGAATATGCTCACCTTCACCATCAGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGcc                            >  2:466066/1‑81 (MQ=255)                                                       gCTCACCTTCACCATCAGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGcc                     >  2:466062/1‑81 (MQ=255)                                                           aCCTTCACCATCAGGCTCAAAG‑CCAAATCTTCCACCACCATAAAGACTTCCGGATTGGCTTTCAGCAGTCCGGTGCCTTGc                 >  1:466068/1‑81 (MQ=255)                                                              ttCACCATCAGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGt              >  1:466058/1‑81 (MQ=255)                                                                cACCATCAGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGtt             >  2:466063/1‑80 (MQ=255)                                                                 aCCATCAGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGttt            <  1:466024/80‑1 (MQ=255)                                                                 aCCATCAGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGttt            <  1:466025/80‑1 (MQ=255)                                                                    aTCAGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCg        >  1:466050/1‑81 (MQ=255)                                                                     tCAGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGt       <  1:466026/81‑1 (MQ=255)                                                                      cAGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTg      >  1:466064/1‑81 (MQ=255)                                                                       aGGCTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTg      <  2:466027/80‑1 (MQ=255)                                                                          cTCAAAG‑CCAAATCTTCCACCGCCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTGGAgg  <  1:466028/81‑1 (MQ=255)                                                                          cTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTGGAgg  <  2:466030/81‑1 (MQ=255)                                                                          cTCAAAG‑CCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTGGAgg  <  1:466029/81‑1 (MQ=255)                                                                                 |                                                                           CATCCGCCACAAAACGGGTATTGCAGCCGTTTTTGAGGATTCTAACCAGAATATGCTCACCTTCACCATCAGGCTCAAAGCCCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTGGAGG  >  NC_000913/2871124‑2871278

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑