Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,511,819	G→T	20.9%	intergenic (‑109/‑127)	alaW ← / → yfeC	tRNA‑Ala/DUF1323 family putative DNA‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,511,819	0	G	T	20.9%	78.7 / 5.1	32	intergenic (‑109/‑127)	alaW/yfeC	tRNA‑Ala/DUF1323 family putative DNA‑binding protein
Reads supporting (aligned to +/- strand):  ref base G (13/12);  new base T (3/4);  total (16/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

TGCAAGCGCTCTCCCAGCTGAGCTATAGCCCCGTCACGTAAAGCTTGTCGAGTTGACGGGCGGCATCATATGAATTCCGCCCGAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTATTCATGTCACGGTTTCCTGTAAAGTGGTGTTATAAAATGAACTACTAATAGACCCACATACATTCAGGGAATTGTTATGTTCAAGGAGAGGATGACACCAGATGAACTTGCCAGACTGACCGGCTATAGCCGCCAGACCATTAATAAATGGGTACGCAAGGAAGGCTGGACAACGTCACCAAAACCTGGCGTCCAGGGTGGCAAAGCCCGACTGGT  >  CP009273/2511679‑2512070                                                                                                                                             |                                                                                                                                                                                                                                                            tgcAAGCGCTCTCCCAGCTGAGCTATAGCCCCGTCACGTAAAGCTTGTCGAGTTGACGGGCGGCATCATATGAATTCCGCCCGAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTATTCATGTCACgg                                                                                                                                                                                                              >  2:244298/1‑188 (MQ=255)     aGCGCTCTCCCAGCTGAGCTATAGCCCCGTCACGTAAAGCTTGTCGAGTTGACGGGCGGCATCATATGAATTCCGCCCGAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTATTCATGTCACGGTTTc                                                                                                                                                                                                          <  1:244302/188‑1 (MQ=255)                                 gTCACGTAAAGCTTGTCGAGTTGACGGGCGGCATCATATGAATTCCGCCCGAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCg                                                                                                                                                                                                                                       >  1:182299/1‑131 (MQ=255)                                 gTCACGGAAAGCTTGTCGAGTTGACGGGCGGCATCATATGAATTCCGCCCGAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTAtt                                                                                                                                                                                                                        >  2:388782/1‑146 (MQ=255)                                     cGTAAAGCTTGTCGAGTTGACGGGCGGCATCATATGAATTCCGCCCGAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCAtt                                                                                                                                                                                                                                   <  2:182295/131‑1 (MQ=255)                                     cGTAAAGCTTGTCGAGTTGACGGGCGGCATCATATGAATTCCGCCCGAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTATTCATg                                                                                                                                                                                                                    <  1:388787/146‑1 (MQ=255)                                               gTCGAGTTGACGGGCGGCATCATATGAATTCCGCCCGAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTTAAAAATCAGGCAAATTAACAATTTTGGaaaa                                                                                                                                                                                                                                              >  2:877/1‑110 (MQ=255)                                                   aGTTGACGGGCGGCATCATATGAATTCCGCCCGAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTTAAAAATCAGGCAAATTAACAATTTTGGAAAACCGc                                                                                                                                                                                                                                          <  1:877/110‑1 (MQ=255)                                                              ggcATCATATGAATTCCGCCCGAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTATTCATGTCACGGTTTCCTGTAAAGTGGTGTTATAAAATGAACTAATAATAGACCCACATAAATTCAGGGAATTGTTATGTTCAAGGAGAGGATGAAAACAGAAGAACTTGCCAGAATGAACGGATAAAGCAGCCAGAACATTAATAAAATGGGACGCaaa                                                          >  2:568005/1‑274 (MQ=255)                                                               gcATCATATTAATTCCGCCCGAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGa                                                                                                                                                                                                                                                            >  1:215454/1‑80 (MQ=255)                                                                  tcatATGAATTCCGCCCGAATGTGTCAACGGCAAATGGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATTAACAATTTTGGAAAACCGCTCGCATTCAGTAGNTATTCATGTCACAGTTTCCTGTAAAGTGGTGTTATAAAATGAACTACTAATAGACCCACATACATTCAGGGAATTGTTATGTTCAAGGAGAGGATGACACCAGATGAACTTGCCAGACTGACCGGCTATAGCCGCCAGACCATTAATAAATg                                                                    <  1:568016/261‑1 (MQ=255)                                                                   catATTAATTCCGCCCGAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACaa                                                                                                                                                                                                                                                        <  2:215450/80‑1 (MQ=255)                                                                               gCCCGAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTCagtag                                                                                                                                                                                                                             >  1:57470/1‑95 (MQ=255)                                                                                cccGAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCg                                                                                                                                                                                                                                       >  1:118515/1‑84 (MQ=255)                                                                                cccGAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGc                                                                                                                                                                                                                                      >  1:110805/1‑85 (MQ=255)                                                                                   gAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTAt                                                                                                                                                                                                                         <  2:57470/95‑1 (MQ=255)                                                                                    aaTGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCAtt                                                                                                                                                                                                                                   <  2:118514/84‑1 (MQ=255)                                                                                    aaTGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTc                                                                                                                                                                                                                                  <  2:110804/85‑1 (MQ=255)                                                                                               ggCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATTAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTATTCa                                                                                                                                                                                                                      >  1:420369/1‑86 (MQ=255)                                                                                                   aaTTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATTAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTATTCATGTc                                                                                                                                                                                                                  <  2:420364/86‑1 (MQ=255)                                                                                                    aTTGCAACGTGTAGTTTCAGTCGCTGAAAAATCAGGCAAATTAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTATTCATGTCACGGTTTCCTGTAAAGTGGTGTTATAAAATGAACTACTAATAGACCCACATACAtt                                                                                                                                                          >  1:548420/1‑141 (MQ=255)                                                                                                        cAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATTAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTATTCATGTCACGGTTTCCTGTAAAGTGGTGTTATAAAATGAACTACTAATAGACCCACATACATTCAgg                                                                                                                                                      <  2:548409/141‑1 (MQ=255)                                                                                                         aaCGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTATTCATGTCACGGTTTCCTGTAAAGTGGTGTTATAAAATGAACTACTAATAGACCCACATACATTCAGGGaa                                                                                                                                                   >  2:270468/1‑143 (MQ=255)                                                                                                             tgtAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTATTCATGTCACGGTTTCCTGTAAAGTGGTGTTATAAAATGAACTACTAATAGACCCACATACATTCAGGGAATTGt                                                                                                                                               <  1:270473/143‑1 (MQ=255)                                                                                                                       aTCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCt                                                                                                                                                                                                                                         >  2:4895/1‑43 (MQ=255)                                                                                                                       aTCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGc                                                                                                                                                                                                                                      >  2:121455/1‑46 (MQ=255)                                                                                                                       aTCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTATTCATGTCACGGTTTCCTGTAAAGTGGTGTTATAAAATGAACTACTAATAGACCCACATACATTCAGGGAATTGTTATGTTCAAGGAGAGGATGACACCAGATGAACTTGCCAGACTGACCGGCTATAGCCGCCAGACCATTAATAAATGGGTACGCAAGGAAGGCTGGACAACGTCACCAAAACCTGGCTTCCAGGGGGGCAAATACCGACTGGt  >  2:582159/1‑274 (MQ=255)                                                                                                                           cTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCa                                                                                                                                                                                                                                     <  1:4895/43‑1 (MQ=255)                                                                                                                           cTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTc                                                                                                                                                                                                                                  <  1:121456/46‑1 (MQ=255)                                                                                                                           cTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTATTCATGTCACGGTTTCCTGTAAAGTGGTGTTATAAAATGAACTACTAATAGACCCACAGACATTCAGGGAATTGTTATGTTCAAGGAGAGGATGACACCAGATGAACTTGCCAGACTGACCGGCTATAGCCGCCAGACCATTAATAAATGGGTACGCAAGGAAGGCTGGACAACGTCACCAAAACCTGGCGTCCAGGGTGGCAAAGCCCGa       <  1:582170/265‑1 (MQ=255)                                                                                                                            tGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTATTCATGTCACGGTTTCCTGTAAAGTGGTGTTATAAAATGAACTACTAATAGACCCACATACATTc                                                                                                                                                         >  1:425281/1‑118 (MQ=255)                                                                                                                                aaaTCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTATTCATGTCACGGTTTCCTGTAAAGTGGTGTTATAAAATGAACTACTAATAGACCCACATACATTCAggg                                                                                                                                                     <  2:425275/118‑1 (MQ=255)                                                                                                                                             |                                                                                                                                                                                                                                                            TGCAAGCGCTCTCCCAGCTGAGCTATAGCCCCGTCACGTAAAGCTTGTCGAGTTGACGGGCGGCATCATATGAATTCCGCCCGAATGTGTCAACGGCAAATTGCAACGTGTAGTTTCAATCGCTGAAAAATCAGGCAAATGAACAATTTTGGAAAACCGCTCGCATTCAGTAGTTATTCATGTCACGGTTTCCTGTAAAGTGGTGTTATAAAATGAACTACTAATAGACCCACATACATTCAGGGAATTGTTATGTTCAAGGAGAGGATGACACCAGATGAACTTGCCAGACTGACCGGCTATAGCCGCCAGACCATTAATAAATGGGTACGCAAGGAAGGCTGGACAACGTCACCAAAACCTGGCGTCCAGGGTGGCAAAGCCCGACTGGT  >  CP009273/2511679‑2512070

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: ‑