Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,870,786	(C)5→4	coding (519/1050 nt)	truD ←	tRNA pseudouridine(13) synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,870,782	0	C	.	100.0%	206.8 / NA	48	coding (523/1050 nt)	truD	tRNA pseudouridine(13) synthase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (24/24);  total (24/24)

TTAACGTCTGCTTTTTTGAGGCGCTCAGCAACAATCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCGCCCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGATCAGACGTTGTTCAACGTCATCGCGATTGCTCACTTCGCGCAGAACCAG  >  NC_000913/2870655‑2870908                                                                                                                                |                                                                                                                               ttAACGTCTGCTTTTTTGAGGCGCTCAGCAACAATCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTg                                                                                                                   >  1:742230/1‑140 (MQ=255)  tAACGTCTGCTTTTTTGAGGCGCTCAGCAACAATCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGc                                                                                                                  >  1:508632/1‑140 (MQ=255)    aCGTCTGCTTTTTTGAGGCGCTCAGCAACAATCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTCTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTa                                                                                                                >  1:999432/1‑140 (MQ=255)      gTCTGCTTTTTTGAGGCGCTCAGCAACAATCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTAcc                                                                                                              >  2:801843/1‑140 (MQ=255)       tCTGCTTTTTTGAGGCGCTCAGCAACAATCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCg                                                                                                             >  2:256867/1‑140 (MQ=255)       tCTGCTTTTTTGAGGCGCTCAGCAACAATCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCg                                                                                                             >  2:1339907/1‑140 (MQ=255)          gCTTTTTTGAGGCGCTCAGCAACAATCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCa                                                                                                          >  2:1332573/1‑140 (MQ=255)          gCTTTTTTGAGGCGCTCAGCAACAATCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGAACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCa                                                                                                          >  2:886650/1‑140 (MQ=255)           cTTTTTTGAGGCGCTCAGCAACAATCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCaa                                                                                                         >  2:235438/1‑140 (MQ=255)           cTTTTTTGAGGCGCTCAGCAACAATCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCaa                                                                                                         <  2:1095295/140‑1 (MQ=255)                ttGAGGCGCTCAGCAACAATCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCa                                                                                                    >  2:789127/1‑140 (MQ=255)                          cAGCAACAATCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTggg                                                                                          <  2:1041603/140‑1 (MQ=255)                            gCAACAATCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCa                                                                                        <  1:62963/140‑1 (MQ=255)                            gCAACAATCTGATTAAACAACGCACTGCGGGCTGCCGACAACC‑AAACCTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCAc                                                                                       <  2:965219/140‑1 (MQ=255)                                caaTCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCAc                                                                                       <  2:1111144/137‑1 (MQ=255)                                caaTCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCAc                                                                                       >  1:1111144/1‑137 (MQ=255)                                  aTCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAag                                                                                  <  1:801843/140‑1 (MQ=255)                                   tCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAagt                                                                                 >  2:1364257/1‑140 (MQ=255)                                     tGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTGTTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAagtag                                                                               >  2:1147180/1‑140 (MQ=255)                                       aTTAAACAACGCACTGCGGGTTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGtt                                                                             >  2:102433/1‑140 (MQ=255)                                       aTTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGtt                                                                             <  1:256867/140‑1 (MQ=255)                                       aTTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGtt                                                                             <  1:1339907/140‑1 (MQ=255)                                           aacaacGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGt                                                                         <  1:158454/140‑1 (MQ=255)                                               acGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTGTTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTacac                                                                     <  1:1147180/140‑1 (MQ=255)                                                cGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACAcc                                                                    >  2:324968/1‑140 (MQ=255)                                                 gCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCt                                                                   >  2:109902/1‑140 (MQ=255)                                                 gCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGACCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTc                                                                            >  2:1383868/1‑131 (MQ=255)                                                 gCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGACCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTc                                                                            <  1:1383868/131‑1 (MQ=255)                                                     tGCGGGCTGCCGACAACC‑AAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTAc                                                              >  2:649886/1‑140 (MQ=255)                                                      gCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTAc                                                              >  2:556811/1‑140 (MQ=255)                                                        gggCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGc                                                            <  1:109902/140‑1 (MQ=255)                                                        gggCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGc                                                            <  1:909229/140‑1 (MQ=255)                                                        gggCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGc                                                            <  1:235438/140‑1 (MQ=255)                                                                 aCAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGa                                                   <  1:556811/140‑1 (MQ=255)                                                                     ccAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGATCAg                                               <  1:1327630/140‑1 (MQ=255)                                                                           aCTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGATCAGACgttg                                         <  1:649886/140‑1 (MQ=255)                                                                                        cGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGATCAGACGTTGTTCAACGTCATcg                            <  1:886650/140‑1 (MQ=255)                                                                                              cgcACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGATCAGACGTTGTTCAACGTCATcgcg                          >  1:367517/1‑136 (MQ=255)                                                                                              cgcACCGGAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGATCAGACGTTGTTCAACGTCATcgcg                          <  2:367517/136‑1 (MQ=255)                                                                                                     gAGTATTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGATCAGACGTTGTTCAACGTCATCGCGATTGCTCACtt               <  1:1008111/140‑1 (MQ=255)                                                                                                         aTTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGATCAGACGTTGTTCAACGTCATCGCGATTGCTCACTTcgcg           <  2:508632/140‑1 (MQ=255)                                                                                                         aTTGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGATCAGACGTTGTTCAACGTCATCGCGATTGCTCACTTcgcg           <  1:102433/140‑1 (MQ=255)                                                                                                           tGGTTTGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGATCAGACGTTGTTCAACGTCATCGCGATTGCTCACTTCGCGCa         >  2:465478/1‑140 (MQ=255)                                                                                                               ttGCGCCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGATCAGACGTTGTTCAACGTCATCGCGATTGCTCACTTCGCGCAGAAc     <  1:1237037/140‑1 (MQ=255)                                                                                                                  cgcCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGATCAGACGTTGTTCAACGTCATCGCGATTGCTCACTTCGCGCAGAAc     >  2:34661/1‑137 (MQ=255)                                                                                                                  cgcCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGATCAGACGTTGTTCAACGTCATCGCGATTGCTCACTTCGCGCAGAAc     <  1:34661/137‑1 (MQ=255)                                                                                                                  cgcCCAGCGCTGCG‑CCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGATCAGACGTTGTTCAACGTCATCGCGATTGCTCACTTCGCGCAGAACCAg  >  1:1042891/1‑140 (MQ=255)                                                                                                                  cgcCCAGCGCTGCG‑CCCCTACAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGATCAGACGTTGTTCAACGTCATCGCGATTGCTCACTTCGCGCAGAACCAg  >  1:1403074/1‑140 (MQ=255)                                                                                                                                |                                                                                                                               TTAACGTCTGCTTTTTTGAGGCGCTCAGCAACAATCTGATTAAACAACGCACTGCGGGCTGCCGACAACCAAAAACTCCGTTTATTGCGATCGCGCACCGGAGTATTGGTTTGCGCCCAGCGCTGCGCCCCCTGCAAGTTGCTACCGCCAATCCCAAAACGTTGGGCACCGAAGTAGTTCGGTACACCTTTTACGCAAATATCGATCAGACGTTGTTCAACGTCATCGCGATTGCTCACTTCGCGCAGAACCAG  >  NC_000913/2870655‑2870908

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑