Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,671,509	C→A	15.4%	G68C (GGC→TGC)	yhjG ←	putative inner membrane‑anchored periplasmic AsmA family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,671,509	0	C	A	15.4%	106.1 / 3.9	39	G68C (GGC→TGC)	yhjG	putative inner membrane‑anchored periplasmic AsmA family protein
Reads supporting (aligned to +/- strand):  ref base C (15/18);  new base A (3/3);  total (18/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.70e-01

ACGGCTTTGCATTCGCGTCTTTGTTATCATCGTTGGCAAGATTAAACGTCCAGTTATTGTTCTTTTCAGAGAGGCGAATCAGGCGCGCGTCGGGCTTTTCGAGCTTGATCCACGGCAGCCAGACCGTTTTGGTCAGCAGCGCCAGCGGGGCCAGCGTTGCCTCTACGCGTGGCAAATGCACCATCGTGACTTCGGGAATATCCGGTGGATTGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAACTCCGCAGAGACTTTCTGGTTGATAGTCGGTTTGAGTCGATTCCAGTCAAAAGTTGCAATCAAAATGATCGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCTCATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCG  >  CP009273/3671242‑3671765                                                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                                  aCGGCTTTGCATTCGCGTCTTTGTTATAATCGTTGGCAAGATTAAACGTCAAGTTATTGTTCTTTTCAGAGAGGCGAATCAGGCGCGCGTCGGGCTTTTCGAGCTTGATCCACGGCAGCCAGACCGTTTTGGTCAGCAGCGCCAGCGGGGCCAGCGTTGCCTCTACGCGTGGCAAATGCACCATCGTGACTTCGGGAATATCCGGTGGATTGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTc                                                                                                                                                                                                                                                             >  1:35247/1‑274 (MQ=255)       ttGCATTCGCGTCTTTGTTATCATCGTTGGCAAGATTAAACGTCCAGTTATTGTTCTTTTCAGAGAGGCGAATCAGGCGCGCGTCGGGCTTTTCGAGCTTGATCCACGGCAGCCAGACCGTTTTGGTCAGCAGCGCCAGCGGGGCCAGCGTTGCCTCTACGCGTGGCAAATGCACCATCGTGCCTTCGGGAATATCCGGTGGATTGCCAAGAATGATGTCTTCCGCGTGTACAAGGGGCCACGGCACCCAGCGGCGCCAGCCCGTTTCGTGgtt                                                                                                                                                                                                                                                       >  2:610374/1‑274 (MQ=255)           atgggctgtgttGTTTTCATCGTTGGCAAGATGAAACGTCCCTTTTTTGTTCTTTTCCGAGGGGCGAATCAGGCGCGCGTCGTGCTTTTCGAGCTTGATCCACGGCAGCCAGACCGTTTTGGTCAGCAGCGCCAGCGGGGCCAGCGTTGCCTCTACGCGTGGCAAATGCACCATCGTGACTTCGGGAATATCCGGTGGATTGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGcc                                                                                                                                                                                                                                                  <  2:628920/265‑1 (MQ=255)                                                                                        cgTCGGGCTTTTCGAGCTTGATCCACGGCAGCCAGACCGTTTTGGTCAGCAGCGCCAGCGGGGCCAGCGTTGCCTCTACGCGTGGCAAATGCACCATCGTGACTTCGGGAATATCNGGTGGATTGCTTAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAACTCCGCAGAGACTTTCTGGTTGATAGt                                                                                                                                                                     <  1:610385/274‑1 (MQ=255)                                                                                         gTCGGGCTTTTCTAGCTTGATCCACGGCAGCCAGACCGTTTTGTTCAGCAGCGCCAGCGGGGCCAGCGTTGCCTCTACGCGTGGCAAATGCACCATCGTGACTTCGGGAATATCCGGTGGATTGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGc                                                                                                                                                                                                                                                   <  1:581669/196‑1 (MQ=255)                                                                                                                               ttttGGTCAGCAGCGCCAGCGGGGCCAGCGTTGCCTCTACGCGTGGCAAATGCACCATCGTGACTTCGGGAATATCCGGTGGATTGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCAAGTTTCTTGttt                                                                                                                                                                                                                                                       >  2:567833/1‑154 (MQ=255)                                                                                                                                ttttGTCAGCAGCGCCAGCGGGGCCAGCGTTGCCTCTACGCGTGGCAAATGCACCATCGTGACTTCGGGAATATCCGGTGGATTGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGttt                                                                                                                                                                                                                                                       >  1:636257/1‑153 (MQ=255)                                                                                                                                   ggTCAGCAGCGCCAGCGGGGCCAGCGTTGCCTCTACGCGTGGCAAATGCACCATCGTGACTTCGGGAATATCCGGTGGATTGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCAAGTTTCTTGTTTTTGc                                                                                                                                                                                                                                                   <  1:567844/154‑1 (MQ=255)                                                                                                                                    gTCAGCAGCGCCAGCGGGGCCAGCGTTGCCTCTACGCGTGGCAAATGCACCATCGTGACTTCGGGAATATCCGGTGGATTGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGc                                                                                                                                                                                                                                                   <  2:636246/153‑1 (MQ=255)                                                                                                                                                                     aCGCGTGGCAAATGCACCATCGTGACTTCGGGAATATCCGGTGGATTGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCAAGTTTCTTGTTTTTGCCGCTCCcac‑a                                                                                                                                                                                                                                        >  2:649927/1‑130 (MQ=255)                                                                                                                                                                         gTGGCAAATGCACCATCGTGACTTCGGGAATATCCGGTGGATTGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCAAGTTTCTTGTTTTTGCCGCTCCCAc‑accac                                                                                                                                                                                                                                    <  1:649938/130‑1 (MQ=255)                                                                                                                                                                                     ccATCGTGACTTCGGGAATATCCGGTGGATTGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCa                                                                                                                                                                                                                               >  1:645243/1‑123 (MQ=255)                                                                                                                                                                                         cGTGACTTCGGGAATATCCGGTGGATTGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATc                                                                                                                                                                                                                           <  2:645232/123‑1 (MQ=255)                                                                                                                                                                                                  gggAATATCCGGTGGATTGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCca                                                                                                                                                                                                                                           >  1:107423/1‑99 (MQ=255)                                                                                                                                                                                                      atatCCGGTGGATTGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAc‑acc                                                                                                                                                                                                                                      <  2:107422/99‑1 (MQ=255)                                                                                                                                                                                                              tGGATTGCCAAGAATGCTGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGttt                                                                                                                                                                                                                                                       >  2:128117/1‑75 (MQ=255)                                                                                                                                                                                                                  ttGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGttt                                                                                                                                                                                                                                                       >  2:357303/1‑71 (MQ=255)                                                                                                                                                                                                                  ttGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGc                                                                                                                                                                                                                                                   <  1:128118/75‑1 (MQ=255)                                                                                                                                                                                                                   tGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCca                                                                                                                                                                                                                                           >  2:425144/1‑82 (MQ=255)                                                                                                                                                                                                                   tGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGATAGCGAACGGACGAtt                                                                                                                                                                                                   >  2:188527/1‑121 (MQ=255)                                                                                                                                                                                                                      cAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGc                                                                                                                                                                                                                                                   <  1:357308/71‑1 (MQ=255)                                                                                                                                                                                                                       aagaaagaTGTCTTCCGCGTGTGCATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAACTCCGCAGAGACTTTCTGGTTGATAGTCGGTTTGAGTCGATTCCAGTCAAAAGTTGCAATCAAAATGATCGCCACGACAATcaaca                                                                                                          <  2:496658/206‑1 (MQ=255)                                                                                                                                                                                                                       aaGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAc‑acc                                                                                                                                                                                                                                      <  1:425150/82‑1 (MQ=255)                                                                                                                                                                                                                       aaGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAAc                                                                                                                                                                                               <  1:188531/121‑1 (MQ=255)                                                                                                                                                                                                                               tgTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAAc                                                                                                                                                                                               >  2:564515/1‑113 (MQ=255)                                                                                                                                                                                                                               tgTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAACTCCGCAGAGACTTTCTGGTTg                                                                                                                                                                          >  1:333582/1‑134 (MQ=255)                                                                                                                                                                                                                                   ttCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAACTCCg                                                                                                                                                                                           <  1:564526/113‑1 (MQ=255)                                                                                                                                                                                                                                   ttCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAACTCCGCATAGACTTTCTGGTTGATAg                                                                                                                                                                      <  2:333577/134‑1 (MQ=255)                                                                                                                                                                                                                                        cgTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAACTCCGCAGAGACTTTCTGGTTGATAGTCGGTTTGAGTCGATTCCAGTCAAAAGTTGCAATCaa                                                                                                                                 >  1:537969/1‑166 (MQ=255)                                                                                                                                                                                                                                            tACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAACTCCGCAGAGACTTTCTGGTTGATAGTCGGTTTGAGTCGATTCCAGTCAAAAGTTGCAATCAAAATg                                                                                                                             <  2:537958/166‑1 (MQ=255)                                                                                                                                                                                                                                            tACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAACTCCGCAGAGACTTTCTGGTTGATAGTCGGTTTGAGTCGATTCCAGTCAAAAGTTGCAATCAAAATGATCGCCACGACAATc                                                                                                              <  1:210840/181‑1 (MQ=255)                                                                                                                                                                                                                                                    gCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGcc                                                                                                                                                                                                                        >  1:78964/1‑67 (MQ=255)                                                                                                                                                                                                                                                        cGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACgg                                                                                                                                                                                                                    <  2:78964/67‑1 (MQ=255)                                                                                                                                                                                                                                                        cGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAACTCCGCAGAGACTTTCTGGTTGATAGTCGGTTTGAGTCGATTCCAGTCAAAAGTTGCAATCAAAATGATCGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTg                                                              >  2:480132/1‑217 (MQ=255)                                                                                                                                                                                                                                                           cACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAACTCCGCAGAGACTTTCTGGTTGATAGTCGGTTTGAGTCGATTCCAGTCAAAAGTTGCAATCAAAATGATCGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCTCATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCg  <  1:140198/274‑1 (MQ=255)                                                                                                                                                                                                                                                            aCCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAACTCCGCAGAGACTTTCTGGTTGATAGTCGGTTTGAGTCGATTCCAGTCAAAAGTTGCAATCAAAATGATCGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCTCa                                                          <  1:480140/217‑1 (MQ=255)                                                                                                                                                                                                                                                             cccAGCTGCGCCAGCAAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCa                                                                                                                                                                                                                       >  1:7982/1‑59 (MQ=255)                                                                                                                                                                                                                                                                 gCTGCGCCAGCAAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGa                                                                                                                                                                                                                   <  2:7982/59‑1 (MQ=255)                                                                                                                                                                                                                                                                  cTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCAc                                                                                                                                                                                                                      >  2:608326/1‑55 (MQ=255)                                                                                                                                                                                                                                                                      gccagccaGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGAt                                                                                                                                                                                                                  <  1:608337/55‑1 (MQ=255)                                                                                                                                                                                                                                                                       ccagccagTTTCTTGTTTTTGCCGCTCCCACAACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAACTCCGCAGAGACTTTCTGGTTGATAGTCGGTTTGAGTCGATTCCAGTCAAAAGTTGCAATCAAAATGATCGCCGCGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCTCATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTa                     >  1:599194/1‑244 (MQ=255)                                                                                                                                                                                                                                                                           ccagTTTCTTGTTTTTGCCGCTCCCACAACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAACTCCGCAGAGACTTTCTGGTTGATAGTCGGTTTGAGTCGATTCCAGTCAAAAGTTGCAATCAAAATGATCGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCTCATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGa                 <  2:599183/244‑1 (MQ=255)                                                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                                  ACGGCTTTGCATTCGCGTCTTTGTTATCATCGTTGGCAAGATTAAACGTCCAGTTATTGTTCTTTTCAGAGAGGCGAATCAGGCGCGCGTCGGGCTTTTCGAGCTTGATCCACGGCAGCCAGACCGTTTTGGTCAGCAGCGCCAGCGGGGCCAGCGTTGCCTCTACGCGTGGCAAATGCACCATCGTGACTTCGGGAATATCCGGTGGATTGCCAAGAATGATGTCTTCCGCGTGTACATGGGGCCACGGCACCCAGCTGCGCCAGCCAGTTTCTTGTTTTTGCCGCTCCCAC‑ACCACGCCCAGATCGCCACGGATAGCGAACGGACGATTCAACTCCGCAGAGACTTTCTGGTTGATAGTCGGTTTGAGTCGATTCCAGTCAAAAGTTGCAATCAAAATGATCGCCACGACAATCAACAACAAGAAAGCCCCTGAAATCGCAGCGGTTATTTTGCCTGCCTTGCTCATCGTTCGCTTCCTCATATTCTTCCTGTGCCAGTCCTAAAGATAGTCCAGCCAGGCG  >  CP009273/3671242‑3671765

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑