Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,808,039	G→T	12.9%	L62L (CTG→CTT)	slmA →	nucleoid occlusion factor, anti‑FtsZ division inhibitor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,808,039	0	G	T	12.9%	88.2 / 3.5	31	L62L (CTG→CTT)	slmA	nucleoid occlusion factor, anti‑FtsZ division inhibitor
Reads supporting (aligned to +/- strand):  ref base G (12/15);  new base T (2/2);  total (14/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.26e-01

ATAACATAGCCGCAAACATTTCGTTTGCGGTCATAGCGTGGGTGCCGCCTGGCAAGTGCTTATTTTCAGGGGTATTTTGTAACATGGCAGAAAAACAAACTGCGAAAAGGAACCGTCGCGAGGAAATACTTCAGTCTCTGGCGCTGATGCTGGAATCCAGCGATGGAAGCCAACGTATCACGACGGCAAAACTGGCCGCCTCTGTCGGCGTTTCCGAAGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGACACCACAGCGCGCCTGCGTCTGATTGTGTTGCTGCTTCTCGGTTTTGGTGAGCGTAATCCTGGCCTGACCCGCATCCTCACTGGTCATGCGCTAATGTTTGAACAGGATCGCCTGCAAGGGCGCATCAACCAGCTGTTCGAGCGTATTGAAGCGCAGCTGCGCCAGGTATTGCGTGAAAAGAGAATGCGTGAGGGT  >  CP009273/3807771‑3808297                                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                                                   aTAACATAGCCGCAAACATTTCGTTTGCGGTCATAGCGTGGGTGCCGCCTGGCAAGTGCTTATTTTCAGGGGTATTTTGTAACATGGCAGAAAAACAAACTGCGAAAAGGAACCGTCGCGAGGAAATACTTCAGTCTCTGGCGCTGATGCTGGAATCCAGCGATGGAAGCCAACGTATCACGACGGACAACCTGGCCGCCCCTTTCGGCGTTTCCGAAGCGGCCCGTTATCGCCACTTCCACCGTAAGACCCGCCTGTTCGACCACCTGAttcac                                                                                                                                                                                                                                                              >  2:28997/1‑272 (MQ=255)           gccAAACATGTNTTTTGCGTTCATAGCGGGGGTGCCGCCTGGCAAGTGCTTATTTTCTGGGTTATTTTGTCACATGGCAGAAAAACAAACGGCGAAAAGGAACCGTCGCGAGGAAATACTTCGGTCTCTGGCGCTGATGCTGGAATCCAGCGATGGAAGCCAACGTATCACGACGGCAAAACTGGCCGCCTCTGTCGGCGTTTCCGAAGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGAGTTTATCGAAg                                                                                                                                                                                                                                                    <  2:51529/273‑1 (MQ=255)             cAAACATTTCGTTTGCGGTCATAGCGTGGGTGCCGCCTGGCAAGTGCTTATTTTCAGGGGTATTTTGTAACATGGCAGAAAAACAAACTGCGAAAAGGAACCGTCGCGAGGAAATACTTCAGTCTCTGGCGCTGATGCTGGAATCCAGCGATGGAAGCCAACGTATCACGACGGCAAAACTGGCAGCCTCTGTCGGCGTTTCAGAAGCGGCACTGTAACGCCACCTCCCCCGTAAGACCCCACTGTTCGATAGCCTGATTGGTNTTATCGacgc                                                                                                                                                                                                                                                   >  2:68248/1‑271 (MQ=255)                                         gttGCCTCCTTGCAAGTGCTTATTGTCAGGGTTATTTTGTAACATGGAAGAAAAACAAACTGCGAAAAGGAAACGTCGCGAGGAAATACTTCAGTCTCTGGCGCTGATGCTGGAATCCAGCGATGGAAGCCAACGTATCACGACGGCAAAACTGGCCGCCTCTGTCGGCGTTTCCGAAGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTc                                                                                                                                                                                                                      <  1:68248/273‑1 (MQ=255)                                                                                tAACATGGCAGAAAAACAACCTGCGAAAAGGCACCGTAGCGAGGAAATACTTCAGTCTCTGGCGCTGATGCTGGAATCCAGCCATGGAAGCCAACGTATCACGACGGCAAAACTGGCCGCCTCTGTCGGCGTGTCCTAAGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGTATGTTCGATAGCCTGATTGAGTTGATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGAt                                                                                                                                                                                                              <  1:27255/244‑1 (MQ=255)                                                                                aggcATGGCNAAAAAACAACCGCCGAAAATGACCCGTCGCGAGGAAATGCTTCAGTCTCTGGCGCTGATGCTGGAATCCAGCGATGGAAGCCAACGTATCACGACGGCAAAACTGGCCGCCTCTGTCGGCGTTTCCGAAGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCCGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGACACCACAGCGCGCCTGCGTCTGa                                                                                                                                                                               <  2:201573/272‑1 (MQ=255)                                                                                     tGGCAGAAAAACAAACTGCGAAAAGGAACCGTCGCGAGGAAATACTTCAGTCTCTGGCGCTGATGCTGGAATCCAGCGATGGAAGCCAACGTATCACGACGGCAAAACTGGCCGCCTCTGTCGGCGTTTCCGAAGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGCGTTTATCGAAGATAGCCTGCTTACTCGCATCAACCTGATTCTGAAAGAGGAGAAAGACACCACAGCACGCCTTNTTCTGCCtgtg                                                                                                                                                                          >  2:62244/1‑275 (MQ=255)                                                                                                                   gTCGCGAGGAAATACTTCAGTCTCTGGCGCTGATGCTGGAATCCAGCGATGGAAGCCAACGTATCACGACGGCAAAACTGGCCGCCTCTGTCGGCGTTTCCGAAGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGACACCACAgcgcg                                                                                                                                                                                          >  2:84826/1‑229 (MQ=255)                                                                                                                     cgcgAGGCAATACGTCCGTCTCTGGGGCTGATGCTGGAAGCCAGCGTTTGAAGCCAACGTATCACGACGGCAAAACTGGCCGCCTCTGTCGGCGTTTCCGAAGCGGCACTGGATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGACACCACAGCGCGCCTGCGTCTGATTGTGTTGCTGCTTCTCGGTTTTGGTGAGCGTAATc                                                                                                                                           <  1:15373/274‑1 (MQ=255)                                                                                                                       cgAGGAAATACTTCAGTCTCTGGCGCTGATGCTGGAATCCAGCGATGGAAGCCAACGTATCACGACGGCAAAACTGGCCGCCTCTGTCGGCGTTTCCGAAGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGACACCACAGCGCGCCTg                                                                                                                                                                                      <  1:84827/229‑1 (MQ=255)                                                                                                                                    caatttctGGCGGTGAGGCTGGAATCCAGCGATGGAAGCCAACGTATCACGACGGCAAAACTGGCCGCCTCTGTCGGCGTTTCCGAAGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGACACCACAGCGCGCCTGCGTCTGATTGTGTTGCTGCTTCTCGGTTTTGGTGAGCGTAATCCTGGCCTGACCCGCAt                                                                                                                           <  2:422726/270‑1 (MQ=255)                                                                                                                                                   aTGCTGGAATCCAGCGATGGAAGCCAACGTATCACGACGGCAAAACTGGCCGCCTCTGTCGGCGTTTCCGAAGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAANACAACACAGCGCGCCTGCGTCTGATTGTGTTGCTGCTTCTCGGTTTTGGTGAGCGTAATCCTGGCCTGACCCGCAACCTCACTCGTCATgc                                                                                                            >  1:393201/1‑275 (MQ=255)                                                                                                                                                                 cGATGGAAGCCAACGTATCACGACGGCAAAACTGGCCGCCTCTGTCGGCGATTCCGAAGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTg                                                                                                                                                                                                                    >  2:76822/1‑157 (MQ=255)                                                                                                                                                                     ggAAGCCAACGTATCACGACGGCAAAACTGGCCGCCTCTGTCGGCGATTCCGAAGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAg                                                                                                                                                                                                                <  1:76823/157‑1 (MQ=255)                                                                                                                                                                              cGTATCACGACGGCAAAACTGGCCGCCTCTGTCGGCGTTTCCGAAGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGAtt                                                                                                                                                                                                                                                                 >  2:318176/1‑99 (MQ=255)                                                                                                                                                                                  tCACGACGGCAAAACTGGCCGCCTCTGTCGGCGTTTCCGAAGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGAGt                                                                                                                                                                                                                                                             <  1:318188/99‑1 (MQ=255)                                                                                                                                                                                                                     tCCGAAGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGACACCACAgc                                                                                                                                                                                             >  1:80877/1‑128 (MQ=255)                                                                                                                                                                                                                         aaGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGACACCACAgcgcgc                                                                                                                                                                                         <  2:80876/128‑1 (MQ=255)                                                                                                                                                                                                                                         acACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTTATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGACACCACAgc                                                                                                                                                                                             >  2:137688/2‑108 (MQ=255)                                                                                                                                                                                                                                            cTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGACACCACAGCGCGCCTGCGTCTGATTGTGTTGCTGCTTCTCGGTTTTGGTGAGCGTAATCCTGGCCTGACCCGCATCCTCACTGGTCATGCGCTAATGTTTGAAc                                                                                              >  2:55485/1‑200 (MQ=255)                                                                                                                                                                                                                                             ttCCCCAGTAAGACCCGCATGTTCGATAGCCTTATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGACACCACAgcgcgc                                                                                                                                                                                         <  1:137690/108‑1 (MQ=255)                                                                                                                                                                                                                                              tCCCCAGTAAGACCCGCATGTTCGATAGCCTGAtt                                                                                                                                                                                                                                                                 >  1:429273/1‑35 (MQ=255)                                                                                                                                                                                                                                              tCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGAGt                                                                                                                                                                                                                                                             >  2:27956/1‑39 (MQ=255)                                                                                                                                                                                                                                                cccAGTAAGACCCGCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGACACCACAGCGCGCCTGCGTCTGATTGTGTTGCTGCTTCTCGGTTTTGGTGAGCGTAATCCTGGCCTGACCCGCATCCTCACTGGTCATGCGCTAATGTTTGAACAGGa                                                                                          <  1:55485/200‑1 (MQ=255)                                                                                                                                                                                                                                                  cAGTAAGACCCGCATGTTCGATAGCCTGATTGAGt                                                                                                                                                                                                                                                             <  2:429258/35‑1 (MQ=255)                                                                                                                                                                                                                                                  cAGTAAGACCCGCATGTTCGATAGCCTGATTGAGTTTAt                                                                                                                                                                                                                                                         <  1:27956/39‑1 (MQ=255)                                                                                                                                                                                                                                                       aGACCCGCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGACACCACAGCGCGCCTGCGTCTGATTGTGTTGCTGCTTCTCGGTTTTGGTg                                                                                                                                                    >  2:267752/1‑135 (MQ=255)                                                                                                                                                                                                                                                           ccGCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGACACCACAGCGCGCCTGCGTCTGATTGTGTTGCTGCTTCTCGGTTTTGGTGAGCg                                                                                                                                                <  1:267763/135‑1 (MQ=255)                                                                                                                                                                                                                                                             gCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGACACCCCAGCGCGCCTGCGTCTGATTTTGTTGCTGCTTCTCGGTTTTGGTGAGCGTAATCCTGGCCTGACCCGCATCCTCACTGGTCATGCGCTAATGTTTGAACAGGATCGCCTGCAAGGGCGCATCAACCAGCTGTTCGAGCGTATTGAAGCGCAGCTGCGCCAGGTATTGCGTGAAAAGAGAATGCGTGAGGGt  <  1:62244/275‑1 (MQ=255)                                                                                                                                                                                                                                                              cATGTTCGATAGCCTTATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATgaga                                                                                                                                                                                                          >  1:151256/1‑74 (MQ=255)                                                                                                                                                                                                                                                                  ttCGATAGCCTTATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGa                                                                                                                                                                                                      <  2:151253/74‑1 (MQ=255)                                                                                                                                                                                                                                                                             gATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATg                                                                                                                                                                                                             >  1:183300/1‑56 (MQ=255)                                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                                                   ATAACATAGCCGCAAACATTTCGTTTGCGGTCATAGCGTGGGTGCCGCCTGGCAAGTGCTTATTTTCAGGGGTATTTTGTAACATGGCAGAAAAACAAACTGCGAAAAGGAACCGTCGCGAGGAAATACTTCAGTCTCTGGCGCTGATGCTGGAATCCAGCGATGGAAGCCAACGTATCACGACGGCAAAACTGGCCGCCTCTGTCGGCGTTTCCGAAGCGGCACTGTATCGCCACTTCCCCAGTAAGACCCGCATGTTCGATAGCCTGATTGAGTTTATCGAAGATAGCCTGATTACTCGCATCAACCTGATTCTGAAAGATGAGAAAGACACCACAGCGCGCCTGCGTCTGATTGTGTTGCTGCTTCTCGGTTTTGGTGAGCGTAATCCTGGCCTGACCCGCATCCTCACTGGTCATGCGCTAATGTTTGAACAGGATCGCCTGCAAGGGCGCATCAACCAGCTGTTCGAGCGTATTGAAGCGCAGCTGCGCCAGGTATTGCGTGAAAAGAGAATGCGTGAGGGT  >  CP009273/3807771‑3808297

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑