Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,640,548	T→C	intergenic (+3/‑314)	uspA → / → dtpB	universal stress global response regulator/dipeptide and tripeptide permease B

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,640,548	0	T	C	100.0%	94.8 / NA	27	intergenic (+3/‑314)	uspA/dtpB	universal stress global response regulator/dipeptide and tripeptide permease B
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (11/16);  total (11/16)

TTCTGGAGCAAACTGATGTCTTCCGCACGTCAGCTGATCAACACCGTTCACGTTGATATGCTGATTGTTCCGCTGCGCGACGAAGAAGAATAATCTTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCTTGTTACCTGATCAGCGTAAACACCTTATCTGGCCTACGGTCTGCGTACGCAATCAAAATCCCCAGCCAATACA  >  NC_000913/3640453‑3640682                                                                                                |                                                                                                                                       ttCTGGAGCAAACTGATGTCTTCCGCACGTCAGCTGATCAACACCGTTCACGTTGATATGCTGATTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGtt                                                                                             <  1:235333/139‑1 (MQ=255)      gAGCAAACTGATGTCTTCCGCACGTCAGCTGATCAACACCGTTCACGTTGATATGCTGAGTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCt                                                                                        <  2:384255/139‑1 (MQ=255)                  gTCTTCCGCACGTCAGCTGATCAACACCGTTCACGTTGATATGCTGATTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGcc                                                                            <  1:182887/139‑1 (MQ=255)                  gTCTTCCGCACGTCAGCTGATCAACACCGTTCACGTTGATATGCTGATTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGcc                                                                            <  1:450243/139‑1 (MQ=255)                     ttCCGCACGTCAGCTGATCAACACCGTTCACGTTGATATGCTGATTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCtt                                                                          <  2:248750/138‑1 (MQ=255)                     ttCCGCACGTCAGCTGATCAACACCGTTCACGTTGATATGCTGATTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCtt                                                                          >  1:248750/1‑138 (MQ=255)                      tCCGCACGTCAGCTGATCAACACCGTTCACGTTGATATGCTGATTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCTTGt                                                                        >  2:582814/1‑139 (MQ=255)                               cAGCTCATCAACACGGTTCACGTTGGTATGCTGATTGTACCGCTGCGCGACGAAGAAAAATAAAGCCCCCTCTACGACGGGTGCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCGTTGTTACCTGGTc                                                               <  2:617765/139‑1 (MQ=255)                                               ttCACGTTGATATGCTGATTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGgcg                                                                                >  1:208693/1‑106 (MQ=255)                                               ttCACGTTGATATGCTGATTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGgcg                                                                                <  2:208693/106‑1 (MQ=255)                                               ttCACGTTGATATGCTGATTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCTTGTTACCTGATCAGCGTAAACACCTTAt                                               <  2:491512/139‑1 (MQ=255)                                               ttCACGTTGATATGCTGATTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCTTGTTACCTGATCAGCGTAAACACATTAt                                               >  1:223066/1‑139 (MQ=255)                                                 cACGTTGATATGCTGATTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCTTGTTACCTGATCAGCGTa                                                         >  1:344528/1‑127 (MQ=255)                                                 cACGTTGATATGCTGATTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCTTGTTACCTGATCAGCGTa                                                         >  1:360097/1‑127 (MQ=255)                                                 cACGTTGATATGCTGATTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCTTGTTACCTGATCAGCGTa                                                         <  2:360097/127‑1 (MQ=255)                                                 cACGTTGATATGCTGATTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCTTGTTACCTGATCAGCGTa                                                         <  2:344528/127‑1 (MQ=255)                                                              tGATTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCg                                                                                               >  2:550129/1‑76 (MQ=255)                                                              tGATTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCg                                                                                               <  1:550129/76‑1 (MQ=255)                                                                aTTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGcc                                                                            <  2:101442/93‑1 (MQ=255)                                                                aTTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGcc                                                                            >  1:101442/1‑93 (MQ=255)                                                                aTTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGcc                                                                            <  1:483696/93‑1 (MQ=255)                                                                aTTGTTCCGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGcc                                                                            >  2:483696/1‑93 (MQ=255)                                                                       cGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCtt                                                                          <  1:98406/88‑1 (MQ=255)                                                                       cGCTGCGCGACGAAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCtt                                                                          >  2:98406/1‑88 (MQ=255)                                                                               gacgaAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCTTGTTACCTGATCAGCGTAAACACCTTATCTGGCCTACGGTCTGCGTACGCAATCAAAATc               >  2:300065/1‑139 (MQ=255)                                                                                acgaAGAAGAATAATCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCTTGTTACCTGATCAGCGTAAACACCTTATCTGGCCTACGGTCTGCGTACGCAATCAAAATcc              <  1:512404/139‑1 (MQ=255)                                                                                           taatCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCTTGTTACCTGATCAGCGTAAACACCTTATCTGGCCTACGGTCTGCGTACGCAATCAAAATCCCCAGCCAATac   <  1:140225/139‑1 (MQ=255)                                                                                            aatCCTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCTTGTTACCTGATCAGCGTAAACACCTTATCTGGCCTACGGTCTGCGTACGCAATCAAAATCCCCAGCCAATaca  <  1:86535/139‑1 (MQ=255)                                                                                                |                                                                                                                                       TTCTGGAGCAAACTGATGTCTTCCGCACGTCAGCTGATCAACACCGTTCACGTTGATATGCTGATTGTTCCGCTGCGCGACGAAGAAGAATAATCTTCCCTCTACGACGTGTTCCTGAACGCCCGCATATGCGGGCGTTTTGCTTTTTGGCGCGCCTTGTTACCTGATCAGCGTAAACACCTTATCTGGCCTACGGTCTGCGTACGCAATCAAAATCCCCAGCCAATACA  >  NC_000913/3640453‑3640682

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑