Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	402,171	T→A	L142Q (CTG→CAG)	phoA →	alkaline phosphatase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	402,171	0	T	A	100.0%	97.5 / NA	28	L142Q (CTG→CAG)	phoA	alkaline phosphatase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (19/9);  total (19/9)

AACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACG  >  NC_000913/402096‑402248                                                                            |                                                                              aaCCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCAGGGCg                                                                          >  1:77948/1‑81 (MQ=255)   ccGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCAGGGCGTc                                                                        <  1:77922/81‑1 (MQ=255)   ccGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCAGGGCGTc                                                                        <  2:77923/81‑1 (MQ=255)     ggACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCAGGGCGTCGa                                                                      >  1:77950/1‑81 (MQ=255)       aCTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCAGGGCGTCGata                                                                    >  1:77955/1‑81 (MQ=255)            gTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCAGGGCGTCGATATTCAc                                                               >  2:412990/1‑81 (MQ=255)                ccGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCAGGGCGTCGATATTCACGaa                                                            >  2:77964/1‑80 (MQ=255)                            cATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCaa                                               <  1:77924/81‑1 (MQ=255)                             aTCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAAc                                              >  1:77949/1‑81 (MQ=255)                             aTCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAAc                                              >  1:77951/1‑81 (MQ=255)                             aTCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAAc                                              >  2:77972/1‑81 (MQ=255)                                 gCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAACGAtt                                          >  2:77956/1‑81 (MQ=255)                                  cAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTc                                         >  1:77952/1‑81 (MQ=255)                                   aaCCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCt                                        >  2:77954/1‑81 (MQ=255)                                           ggTCAACCGGTGTCAAAACCTATAACGGCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATgg                                >  1:77945/1‑81 (MQ=255)                                             tCAACCGGTGTCAAAACCTATAACGGCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCa                              <  2:77925/81‑1 (MQ=255)                                               aaCCGGTGTCAAAACCTATAACGGCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCaa                             <  1:77926/80‑1 (MQ=255)                                                 ccGGTGTCAAAACCTATAACGGCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAg                          <  2:77927/81‑1 (MQ=255)                                                          aaaCCTATAACGGCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTc                 >  2:77973/1‑81 (MQ=255)                                                           aaCCTATAACGGCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCt                >  1:77958/1‑81 (MQ=255)                                                                ataACGGCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGa           >  2:77957/1‑81 (MQ=255)                                                                    cGGCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCgg       >  2:77960/1‑81 (MQ=255)                                                                     ggCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCgg       >  1:77962/1‑80 (MQ=255)                                                                     ggCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGt      <  2:77928/81‑1 (MQ=255)                                                                     ggCGCGCAGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGt      <  1:77929/81‑1 (MQ=255)                                                                        gcgcAGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAAc   >  1:77974/1‑81 (MQ=255)                                                                         cgcAGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACg  <  2:77930/81‑1 (MQ=255)                                                                         cgcAGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACg  >  2:77946/1‑81 (MQ=255)                                                                            |                                                                              AACCGGACTACGTCACCGACTCGGCTGCATCAGCAACCGCCTGGTCAACCGGTGTCAAAACCTATAACGGCGCGCTGGGCGTCGATATTCACGAAAAAGATCACCCAACGATTCTGGAAATGGCAAAAGCCGCAGGTCTGGCGACCGGTAACG  >  NC_000913/402096‑402248

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: ‑