Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,992,311	C→T	L169L (TTG→TTA)	pgsA ←	phosphatidylglycerophosphate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,992,311	0	C	T	100.0%	73.5 / NA	22	L169L (TTG→TTA)	pgsA	phosphatidylglycerophosphate synthase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (15/7);  total (15/7)

TTTGATCGTTTGCTGAAAATTACGCCGAAACGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTGCAACATTGACCACAGAGTCAGTACCGCAGCCACAAAGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTCG  >  NC_000913/1992236‑1992384                                                                            |                                                                          tttGATCGTTTGCTGAAAATTACGCCGAAACGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTGTAACAt                                                                      >  2:339858/1‑81 (MQ=255) tttGATCGTTTGCTGAAAATTACGCCGAAACGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTGTAACAt                                                                      >  1:339852/1‑81 (MQ=255)   tGATCGTTTGCTGAAAATTACGCCGAAACGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTGTAACAtt                                                                     <  2:339825/80‑1 (MQ=255)       cGTTTGCTGAAAATTACGCCGAAACGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTATAACATTGACca                                                                >  2:339850/1‑81 (MQ=255)        gTTTGCTGAAAATTACGCCGAAACGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATAATGTAACATTGACca                                                                >  1:339848/1‑80 (MQ=255)                aaaaTTACGCCGAAACGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTGTAACATTGACCACAGAGTCAg                                                       >  1:339849/1‑81 (MQ=255)                       cGCCGAAACGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTGTAACATTGACCACAGAGTCAGTACCg                                                  >  2:339860/1‑79 (MQ=255)                       cGCCGAAACGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTGTAACATTGACCACAGAGTCAGTACCGCa                                                <  1:339826/81‑1 (MQ=255)                        gCCGAAACGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTGTAACATTGACCACAGAGTCAGTACCGCAg                                               >  2:339853/1‑81 (MQ=255)                          cGAAACGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTGTAACATTGACCACAGAGTCAGTACCGCAGc                                              >  2:339855/1‑80 (MQ=255)                           gAAACGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTGTAACATTGACCACAGAGTCAGTACCGCAGCca                                            <  1:339827/81‑1 (MQ=255)                             aaCGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTGTAACATTGACCACAGAGTCAGTACCGCAGCcaca                                          <  1:405379/81‑1 (MQ=255)                               cGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTGTAACATTGACCACAGAGTCAGTACCGCAGCcaca                                          >  2:339845/1‑79 (MQ=255)                               cGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTGTAACATTGACCACAGAGTCAGTACCGCAGCcaca                                          >  1:339863/1‑79 (MQ=255)                               cGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTGTAACATTGACCACAGAGTCAGTACCGCAGCCACaaa                                        <  2:339828/81‑1 (MQ=255)                                    aCTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTGTAACATTGACCACAGAGTCAGTACCGCAGCCACAAAGaa                                     >  2:339864/1‑79 (MQ=255)                                               aaaTCTGCACGCGCAGCGCTCAAATATTGTAACATTGACCACAGAGTCAGTACCGCAGCCACAAAGAAAAGTGCAATACCg                        >  2:339857/1‑81 (MQ=255)                                                         gcgcAGCGCTCAAATATTGTAACATTGACCACAGAGTCAGTACCGCAGCCACAAAGAAAAGTGCAATACCGGCGTACTCaa              >  1:339870/1‑81 (MQ=255)                                                              gcgcTCAAATATTGTAACATTGACCACAGAGTCAGTACCGCAGCCACAAAGAAAAGTGCAATACCGGCGTACTCAACCCaa         <  1:339829/81‑1 (MQ=255)                                                                gcTCAAATATTGTAACATTGACCACAGAGTCAGTACCGCAGCCACAAAGAAAAGTGCAATACCGGCGTACTCAACCCAAAt       >  1:339859/1‑81 (MQ=255)                                                                    aaaTATTGTAACATTGACCACAGAGTCAGTACCGCAGCCACAAAGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTc   >  2:339872/1‑81 (MQ=255)                                                                     aaTATTGTAACATTGACCACAGAGTCAGTACCGCAGCCACAAAGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTCg  <  1:339830/81‑1 (MQ=255)                                                                            |                                                                          TTTGATCGTTTGCTGAAAATTACGCCGAAACGATCACTGATCAAGCAAATCTGCACGCGCAGCGCTCAAATATTGCAACATTGACCACAGAGTCAGTACCGCAGCCACAAAGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTCG  >  NC_000913/1992236‑1992384

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: ‑