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	97.0%	111.6 / ‑4.0	34	A35V (GCG→GTG)	wzxE	lipid III flippase WzxE
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (12/20);  total (13/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.26e-01

CGACTTTGTTGAACTACTTTTCCTGATATGTCGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGCGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGCCCAGTACCATGATAATCCGCAACAGCTGCGCCGC  >  NZ_CP009273/3969611‑3969871                                                                                                                                   |                                                                                                                                   cGACTTTGTTGAACTACTTTTCCTGATATGTTGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTg                                                                                                                            >  1:463833/1‑139 (MQ=255)       tgttgAACTACTTTTCCTGATATGTCGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTgg                                                                                                                      >  1:593190/1‑139 (MQ=255)                 ctTTTCCTGATATGTCGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAAtt                                                                                                             <  2:674212/138‑1 (MQ=255)                       cTGATATGTCGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCa                                                                                                      <  1:335437/139‑1 (MQ=255)                       cTGATATGTCGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCa                                                                                                      <  1:679830/139‑1 (MQ=255)                          atatGTCGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGtt                                                                                                   <  2:743282/139‑1 (MQ=255)                             tGTCGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGa                                                                                                 <  1:455481/138‑1 (MQ=255)                                    ggCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTg                                                                                         >  2:502007/1‑139 (MQ=255)                                                   gtgGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGcc                                                                          >  1:715740/1‑139 (MQ=255)                                                   gtgGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGcc                                                                          >  1:572482/1‑139 (MQ=255)                                                   gtgGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGc                                                                           <  2:722459/138‑1 (MQ=255)                                                    tgGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGcc                                                                          <  2:359606/138‑1 (MQ=255)                                                           cggcCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTAc                                                                                             <  1:215200/112‑1 (MQ=255)                                                           cggcCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTAc                                                                                             >  2:215200/1‑112 (MQ=255)                                                           cggcCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTgg                                                                  >  2:100135/1‑139 (MQ=255)                                                           cggcCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTgg                                                                  >  2:289533/1‑139 (MQ=255)                                                            ggcCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGc                                                                 <  2:649996/139‑1 (MQ=255)                                                            ggcCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGc                                                                 <  2:463833/139‑1 (MQ=255)                                                                         gTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTTCGCCAGTTGGTTACCGTGCTCGGCGTGCTTGCCGGGGCTGGAATCTTTTACGgtg                                                    >  2:269044/1‑139 (MQ=255)                                                                         gTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGgtg                                                    <  1:562669/139‑1 (MQ=255)                                                                            aaGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTa                                                  <  1:100135/138‑1 (MQ=255)                                                                            aaGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGGGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTaa                                                 >  2:286879/1‑139 (MQ=255)                                                                                   gTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCCTCTTTAACGGGGTAACCCAATa                                          >  2:528904/1‑139 (MQ=255)                                                                                      ccGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACg                                        <  1:354791/138‑1 (MQ=255)                                                                                          gTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGcc                                   <  2:568385/139‑1 (MQ=255)                                                                                          gTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGAATCTTTAACGGTGTAACCAAATACGTTGcc                                   <  1:269044/139‑1 (MQ=255)                                                                                           ttACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGccc                                  <  2:419093/139‑1 (MQ=255)                                                                                           ttACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGccc                                  <  1:493583/139‑1 (MQ=255)                                                                                              cTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGCCCAg                                >  1:230688/1‑138 (MQ=255)                                                                                              cTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGCCCAg                                <  1:528904/138‑1 (MQ=255)                                                                                                     gTAAGTTGCTGGCGGTGTCATTTGGTCCGGCGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGCCCAGTACCATGa                        <  2:578437/139‑1 (MQ=255)                                                                                                                    tgtCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGCCCAGTACCATGATAATCCGc                >  2:257320/1‑132 (MQ=255)                                                                                                                    tgtCATTTGGTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGCCCAGTACCATGATAATCCGc                <  1:257320/132‑1 (MQ=255)                                                                                                                            ggTCCGGTGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGCCCAGTACCATGATAATCCGCAACAGCTGcgccgc  <  1:492804/138‑1 (MQ=255)                                                                                                                                   |                                                                                                                                   CGACTTTGTTGAACTACTTTTCCTGATATGTCGTTGGCAAAAGCGTCCTTGTGGACGGCGGCCAGTACACTGGTCAAGATTGGTGCCGGGTTACTGGTCGGTAAGTTGCTGGCGGTGTCATTTGGTCCGGCGGGGCTTGGGCTGGCGGCAAATTTCCGCCAGTTGATTACCGTGCTCGGCGTGCTTGCCGGGGCTGGCATCTTTAACGGTGTAACCAAATACGTTGCCCAGTACCATGATAATCCGCAACAGCTGCGCCGC  >  NZ_CP009273/3969611‑3969871

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑