Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	1,469,551	G→T	16.6%	E51* (GAA→TAA)	ydbD →	PF10971 family putative periplasmic methylglyoxal resistance protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	1,469,551	0	G	T	16.6%	84.1 / 2.9	30	E51* (GAA→TAA)	ydbD	PF10971 family putative periplasmic methylglyoxal resistance protein
Reads supporting (aligned to +/- strand):  ref base G (11/14);  new base T (2/3);  total (13/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.26e-01

TATTTCGCGAGAATAACGAATATACAAAAGGGAAAGATGCATTTCCCTTTTTTTCTTTTTTAATGGCATGGAGTGCATATGTTGAAGGCCAGGAATTGCGGCTGGATACGTTTACTGCCCCTGTTTATGCTGAGTCTACCAGTACAGGCGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCGAACTGGAAAGTGCATCGTGGCGATTTAGTGGTAGAAGGTAATATAGAGAGTAATCAAAAATTGATTGTTCTTGGGAATTTGACAGTCAAAGGTAATATTTCCACTTTCTCTCTTTCTAATCCATGGGTTATTCTCGGTAACGTGACGGCAACGAATATAGTTGCGGATTCACCACTGTTAATTACCGGTTCGATAAATGCAAGTGG  >  CP009273/1469323‑1469810                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                                    tATTTCGCGAGAATAACGAATATACAAAAGGGAAAGATGCATTTCCCTTTTTTTCTTTTTTAATGGCATGGAGTGCATATGTTGAAGGCCAGGAATTGCGGCTGGATACGTTTACTGCCCCTGTTTATGCTGAGTCTACCAGTACAGGCGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTTAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTacc                                                                                                                                                                                                                       >  1:193526/1‑273 (MQ=255)      cgcgAGAATAACGAATATACAAAAGGGAAAGATGCATTTCCCTTTTTTTCTTTTTTAATGGCATGGAGTGCATATGTTGAAGGCCAGGAATTGCGGCTGGATACGTTTACTGCCCCTGTTTATGCTGAGTCTACCAGTACAGGCGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATc                                                                                                                                                                                                                                                          >  1:31394/1‑235 (MQ=255)          agaATAACGAATATACAAAAGGGAAAGATGCATTTCCCTTTTTTTCTTTTTTAATGGCATGGAGTGCATATGTTGAAGGCCAGGAATTGCGGCTGGATACGTTTACTGCCCCTGTTTATGCTGAGTCTACCAGTACAGGCGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACa                                                                                                                                                                                                                                                      <  2:31394/235‑1 (MQ=255)                                                                                    gAAGGCCAGGAATTGCGGCTGGATACGTTTACTGCCCCTGTTTATGCTGAGTCTACCAGTACAGGCGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCGAACTGGAAAGTGCATCGTGGCGATTTAGTGGTAGAAGGTAATATAGAGAGTAATCaaaaa                                                                                                                                                    >  1:306534/1‑259 (MQ=255)                                                                                        gCCAGGAATTGCGGCTGGATACGTTTACTGCCCCTGTTTATGCTGAGTCTACCAGTACAGGCGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCGAACTGGAAAGTGCATCGTGGCGATTTAGTGGTAGAAGGTAATATAGAGAGTAATCAAAAattga                                                                                                                                                <  2:306529/259‑1 (MQ=255)                                                                                                        ggATACGTTTACTGCCCCTGTTTATGCTGAGTCTACCAGTACAGGCGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCg                                                                                                                                                                                                                >  2:174343/1‑179 (MQ=255)                                                                                                            aCGTTTACTGCCCCTGTTTATGCTGAGTCTACCAGTACAGGCGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCGAACt                                                                                                                                                                                                            <  1:174347/179‑1 (MQ=255)                                                                                                             cGTTTACTGCCCCTGTTTATGCTGAGTCTACCAGTACAGGCGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGACCCCTTCGGTTTATCTGCa                                                                                                                                                                                                                   <  1:553073/171‑1 (MQ=255)                                                                                                                             ntATGCTGANTCTACCAGTACATGCGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCGCACTGGAACGTGCATCGTGGCGATTTAGTGGTAGa                                                                                                                                                                             <  1:443804/192‑1 (MQ=255)                                                                                                                                  gggggtgtaacAGTACAGGCGGAAGTTCGTTGTGTTGATAATGCAGTTGATTTTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCGAACTGGAAAGTGCATCGTGGCGATTTAGTGGTAGAAGGTAATATAGAGAGTAATCAAAAATTGATTGTTCTTGGGAATTTGACAGTCAAAGGTAATATTTCCACTTTCTCTCTTTCTAATcc                                                                                      <  2:193522/265‑1 (MQ=255)                                                                                                                                           ccAGTACAGGCGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCGAACTGGAAAGTGCATCGTGGCGATTTAGTgg                                                                                                                                                                                 >  1:301737/1‑175 (MQ=255)                                                                                                                                            cAGTACAGGCGGAACTTCGATGTGTTGCAAATGCAGTTTATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTTAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCGAACTGGAAAGTGCATCGTGGCGATTTAGTGGTAGAAGGTAATATAGAGAGTAATCAAAAATTGATTGTTCTTGGGAATTTGACAGTCAAAGGTAATATTTCCACTTTCTCTCTTTCTAATCCATGGGTTAtt                                                                            <  1:553593/275‑1 (MQ=255)                                                                                                                                               tACAGGCGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCGAACTGGAAAGTGCATCGTGGCGATTTAGTGGTAGa                                                                                                                                                                             <  2:301732/175‑1 (MQ=255)                                                                                                                                                 cAGGCGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTa                                                                                                                                                                                                                                                            >  1:428679/1‑94 (MQ=255)                                                                                                                                                 cAGGCGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTg                                                                                                                                                                                                                                              >  1:97831/1‑108 (MQ=255)                                                                                                                                                     cGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAAc                                                                                                                                                                                                                                                                  <  2:590048/84‑1 (MQ=255)                                                                                                                                                     cGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCaa                                                                                                                                                                                                                                                        <  2:428673/94‑1 (MQ=255)                                                                                                                                                     cGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATc                                                                                                                                                                                                                                          <  2:97831/108‑1 (MQ=255)                                                                                                                                                         aCTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTTAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCGAACTGGAAAGTGCATCGTGGCGATTTAGTGGTAGa                                                                                                                                                                             >  1:113471/1‑165 (MQ=255)                                                                                                                                                             cGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTTAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCGAACTGGAAAGTGCATCGTGGCGATTTAGTGGTAGAAGGt                                                                                                                                                                         <  2:113470/165‑1 (MQ=255)                                                                                                                                                                            gCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTTAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATc                                                                                                                                                                                                                       >  2:74433/1‑104 (MQ=255)                                                                                                                                                                              aGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATc                                                                                                                                                                                                                       >  1:491163/1‑102 (MQ=255)                                                                                                                                                                                ttGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTTAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCa                                                                                                                                                                                                                   <  1:74433/104‑1 (MQ=255)                                                                                                                                                                                  gATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCa                                                                                                                                                                                                                   <  2:491155/102‑1 (MQ=255)                                                                                                                                                                                     atTGAATCATTTTTTTCTGCGGCTACCGCTTAAGATAAACAACAAGTTGAACAAGCTATCa                                                                                                                                                                                                                                                         >  1:98574/1‑61 (MQ=255)                                                                                                                                                                                         aaTCATTTTTTTCTGCGGCTACCGCTTAAGATAAACAACAAGTTGAACAAGCTATCAACAg                                                                                                                                                                                                                                                     <  2:98574/61‑1 (MQ=255)                                                                                                                                                                                            cATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCGAACTGGAAAGTGCATCGTGGCGATCTAGTGGTAGAAGGTAATATAGAGAGTAATCAAAAATTGATTGTTCTTGGGAATTTGACAGTCAAAGGTAATATTTCCACTTTCTCTCTTTCTAATCCATGGGTTATTCTCGGTAACGTGACGGCAAAGAATATAGTTGCGGATTCACCACTGtt                             <  1:393739/274‑1 (MQ=255)                                                                                                                                                                                              tttttttCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCGAACTGGAAAGTGCATCGTGGc                                                                                                                                                                                           >  2:181354/1‑114 (MQ=255)                                                                                                                                                                                                  tttCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCGAACTGGAAAGTGCATCGTGGCGAtt                                                                                                                                                                                       <  1:181358/114‑1 (MQ=255)                                                                                                                                                                                                                         aaaCAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCGAACTGGAAAGTGCATCGTGGCGATTTAGTGGTAGAAGGTACTATCGAGAGTAATCAAAAATTGATTGTTCTTGGGAATTTGACAGTCAAAGGTAATATTTCCACTTTCTCTCTTTCTAATCCCTGGGTTATTCCCGGTAACGTGTCGGCAAAGCATATCGTTGCGGATTTACCACTGTTCATTCCCTGTTCCATAAATGAAAGttg  >  2:311610/1‑270 (MQ=255)                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                                    TATTTCGCGAGAATAACGAATATACAAAAGGGAAAGATGCATTTCCCTTTTTTTCTTTTTTAATGGCATGGAGTGCATATGTTGAAGGCCAGGAATTGCGGCTGGATACGTTTACTGCCCCTGTTTATGCTGAGTCTACCAGTACAGGCGGAACTTCGATGTGTTGCAAATGCAGTTGATATTGAATCATTTTTTTCTGCGGCTACCGCTGAAGATAAACAACAAGTTGAACAAGCTATCAACAGTAGCGTGAATCTTGTCCCCTTCGGTTTATCTGCATCGAACTGGAAAGTGCATCGTGGCGATTTAGTGGTAGAAGGTAATATAGAGAGTAATCAAAAATTGATTGTTCTTGGGAATTTGACAGTCAAAGGTAATATTTCCACTTTCTCTCTTTCTAATCCATGGGTTATTCTCGGTAACGTGACGGCAACGAATATAGTTGCGGATTCACCACTGTTAATTACCGGTTCGATAAATGCAAGTGG  >  CP009273/1469323‑1469810

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑