Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,969,741	C→T	A35V (GCG→GTG)	wzxE →	lipid III flippase WzxE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,969,741	0	C	T	100.0%	102.4 / NA	31	A35V (GCG→GTG)	wzxE	lipid III flippase WzxE
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (16/15);  total (16/15)

TTGCGACTTTGTTGAACTACTTTTCCTGATATGTCGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGCGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGCCCAGTACCATGATAATCC  >  NZ_CP009273/3969608‑3969855                                                                                                                                      |                                                                                                                   ttGCGACTTTGTTGAACTACTTTTCCTGATATGTCGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGc                                                                                                               >  1:210609/1‑139 (MQ=255) ttGCGACTTTGTTGAACTACTTTTCCTGATATGTCGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGc                                                                                                               >  1:488981/1‑139 (MQ=255)      aCTTTGTTGAACTACTTTTCCTGATATGTCGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTggg                                                                                                          >  2:417558/1‑139 (MQ=255)                    ctTTTCCTGATATGTCGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAAttt                                                                                            >  1:564500/1‑139 (MQ=255)                              tatGTCGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGtt                                                                                   >  1:87497/1‑138 (MQ=255)                                tGTCGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGa                                                                                 <  1:417558/138‑1 (MQ=255)                                   cGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTAc                                                                             >  2:435351/1‑139 (MQ=255)                                                gTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTg                                                                <  2:450859/139‑1 (MQ=255)                                                      gtgGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGc                                                           <  1:435351/138‑1 (MQ=255)                                                              cggcCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGCGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTTCGCCAGTTGATTACCGTGCTCGGCGCGCTTGCCGGGGCTgg                                                  >  1:76902/1‑139 (MQ=255)                                                               ggcCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGc                                                 <  2:420645/139‑1 (MQ=255)                                                                            gTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGgtg                                    >  2:442228/1‑139 (MQ=255)                                                                            gTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGgtg                                    <  1:219548/139‑1 (MQ=255)                                                                               aaGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTaa                                 >  1:310346/1‑139 (MQ=255)                                                                                      gTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATa                          >  1:402241/1‑139 (MQ=255)                                                                                      gTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATa                          >  1:2514/1‑139 (MQ=255)                                                                                      gTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATa                          >  2:431407/1‑139 (MQ=255)                                                                                       tGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATAc                         >  2:120869/1‑139 (MQ=255)                                                                                         ccGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACg                        <  1:440793/138‑1 (MQ=255)                                                                                         ccGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACg                        <  1:120869/138‑1 (MQ=255)                                                                                             gTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGcc                   <  2:87497/139‑1 (MQ=255)                                                                                             gTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGcc                   <  2:488981/139‑1 (MQ=255)                                                                                             gTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGcc                   <  2:310346/139‑1 (MQ=255)                                                                                             gTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGcc                   <  2:165520/139‑1 (MQ=255)                                                                                             gTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGcc                   <  1:442228/139‑1 (MQ=255)                                                                                                    gTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGCCCAGTa              <  2:515937/137‑1 (MQ=255)                                                                                                    gTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGCCCAGTAc             <  2:476980/138‑1 (MQ=255)                                                                                                      cGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGCCCAGTACCAt          >  1:284374/1‑139 (MQ=255)                                                                                                              tGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGCCCAGTACCATGATAATcc  >  1:97893/1‑139 (MQ=255)                                                                                                                                 tCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTaa                                         >  2:155398/1‑81 (MQ=255)                                                                                                                                 tCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTaa                                         <  1:155398/81‑1 (MQ=255)                                                                                                                                      |                                                                                                                   TTGCGACTTTGTTGAACTACTTTTCCTGATATGTCGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGCGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGCCCAGTACCATGATAATCC  >  NZ_CP009273/3969608‑3969855

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑