Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,889,135	T→A	9.5%	N2Y (AAT→TAT)  *260C (TGA→TGT)	ygcQ ← ygcR ←	putative flavoprotein putative flavoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,889,135	0	T	A	9.5%	104.5 / 2.6	38	N2Y (AAT→TAT)  *260C (TGA→TGT)	ygcQ ygcR	putative flavoprotein putative flavoprotein
Reads supporting (aligned to +/- strand):  ref base T (18/16);  new base A (2/2);  total (20/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

CGAAGTCACCTGGCAGATGCTTGCACCATGTAAACGCCAGGCCAGCCGGGTCGACAGTTCATCGCCAAACGTTCCCGGCGGAAAGAGAACAACGTCCGCAGGCGTTCGCTGCCACTGTTCCACCAACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGACACTGCATCGCTGGCATTTCGGCAGCAACAGTTTTACGGATAATTTCTGCTTTCCCCGCAGCCATTCGCTGGCGCATTCCCGGTACTGGCAAGGCCACTTCACCGCACTGACGCACGGCAATCACCGCAGGCAAGCGAACCCGGCAACAACGC  >  CP009273/2888872‑2889405                                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                                               cGAAGTCACCTGGCAGATGCTTGCACCGTGTAAACGCCAGGCCAGCCGGGTCGACAGTTCATCGCCAAACGTTCCCGGCGGAAAGAGAACAACGTCCGCAGGCGTTCGCTGCCACTGTTCCACCAACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTAAAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCGATTGCGGCATTCACCTGATTTATTGCCACCATCTCGATCTTccgtgtctcca                                                                                                                                                                                                                                                                     >  2:178909/1‑265 (MQ=255)                             tGTAAACGCCAGGCCAGCCGGGTCGACAGTTCATCGCCAAACGTTCCCGGCGGAAAGAGAACAACGTCCGCAGGCGTTCGCTGCCACTGTTCCACCAACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAAGCTGCCAGTGCGCNAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGc                                                                                                                                                                                                                                         >  1:688790/1‑275 (MQ=255)                             tGTAAACGCCAGGCCAGCCGGGTCGACAGTTCATCGCCAAACGTTCCCGGCGGAAAGAGAACAACGTCCGCAGGAGTTCGCTGCCACTGTTCCACCAACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGGACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGAGATACATGGCTGCATCCTTTGGTTTACATAGTCCTGccc                                                                                                                                                                                                                                             >  2:279456/1‑270 (MQ=255)                                        ggccagCCGGGTCGACAGTTCATCGCCAAACGTTCCCGGCGGAAAGAGAACAACGTCCGCAGGCGTTCGCTGCCACTGTTCCACCAACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGGTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCAAAGCTTTTGAGCttt                                                                                                                                                                                                                              >  1:45306/1‑275 (MQ=255)                                                                 ccAAACGTTCCCGGCGGAAAGAGAACAACGTCCGCAGGCGTTCGCTGCCACTGTTCCACCAACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATACATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCatcaat                                                                                                                                                                                                      <  1:279460/274‑1 (MQ=255)                                                                                                                                             gTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGACACTGCATCGCTGGCATTTAGGCAGCAACAg                                                                                                                            >  1:482457/1‑272 (MQ=255)                                                                                                                                              ttCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCGGACACTGAATCGCTGGCATTTCGGCAGCAACAGttt                                                                                                                         >  1:43232/1‑274 (MQ=255)                                                                                                                                                                aGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGtt                                                                                                                                                                                                                 >  2:668245/1‑168 (MQ=255)                                                                                                                                                                 ggTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCta                                                                                                                                                                                                                                                                 >  1:471759/1‑118 (MQ=255)                                                                                                                                                                    tCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGcc                                                                                                                                                                                                             <  1:668252/168‑1 (MQ=255)                                                                                                                                                                     cAATCTGCCAGTGCGCAAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTATGGc                                                                                                                                                                                                                                                             <  2:471754/119‑1 (MQ=255)                                                                                                                                                                            ccAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGACACTGCATCGCTGGCATTTCgg                                                                                                                                     >  1:374510/1‑232 (MQ=255)                                                                                                                                                                                tGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGACACTGCATCGCTGGCATTTCGgcagc                                                                                                                                 <  2:374505/232‑1 (MQ=255)                                                                                                                                                                                           aCAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGACACTGCATCGCTGGCATTTCGGCAGCAACAGTTTTACGGATAATTTCTGCTTTCCCCGCAGCCATTCGCTGGCGCATTcc                                                                           <  1:178911/275‑1 (MQ=255)                                                                                                                                                                                            cAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCCTTTTCCTGATTTATTGTCACAATTGCGATCTTCATGGc                                                                                                                                                                                                                                                                          >  1:786016/1‑83 (MQ=255)                                                                                                                                                                                                cGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTAGTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGCGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGcgtcg                                                                                                                                                                                    <  1:792671/165‑1 (MQ=255)                                                                                                                                                                                                cGCTGAAAGCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCGGAGTTATTGTCACAATTGCGATATTCATGGCGGCa                                                                                                                                                                                                                                                                      <  2:786007/83‑1 (MQ=255)                                                                                                                                                                                                  cTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTaaa                                                                                                                                                                                                                                                        >  2:371373/1‑95 (MQ=255)                                                                                                                                                                                                  cTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATGGTGCTGCCATAGCTGTTGAGCTTTTTCTGCTACCGTTTGCCCATAAATCAGCGTCGGTCCGCGTCGGTGCTCTGCTCTGGCCAGTTGCAGAACCAGCATCGATGGCAGTTCGGCCGCACCAGTTTTAAGGATAATTGTTGATTTCACCGCAGCCCTTCTCGGgcgactgcccgttgct                                                                    >  2:380786/1‑262 (MQ=255)                                                                                                                                                                                                  cTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGa                                                                                                                                                           >  1:265216/1‑188 (MQ=255)                                                                                                                                                                                                  cTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGACACTGCATCGCTGGCATTTCGGCAGCACCAGTTTTACGGATAATTTCTGCTTTCCCCGCAGCCATTCGCTGGCGCATTCCTGTTACt                                                                    >  1:380764/1‑275 (MQ=255)                                                                                                                                                                                                  cTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGACACTGCATCGCTGGCATTTCGGCAGCAACAGTTTTACGGATAATTTCTGCTTTCCCCGCAGCCATTCGCTGGCGCATTCCCGGTACt                                                                    >  1:713704/1‑275 (MQ=255)                                                                                                                                                                                                      aaTCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATCGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGACACt                                                                                                                                                       <  2:265212/188‑1 (MQ=255)                                                                                                                                                                                                      aaTCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGt                                                                                                                                                                                                                                                    <  1:371378/95‑1 (MQ=255)                                                                                                                                                                                                             cgccgcCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCa                                                                                                                                                                                                                                                                      >  1:373030/1‑70 (MQ=255)                                                                                                                                                                                                                 gcccgccaGCTTGCTATGGCGTCATGCTCCGGATTTATTTTCCCAATTTCGATTTTCTGGGTCTCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGACACTGCATCGCTGGCATTTCGGCAGCAACAGTTTTACGGATAATTTCTGCTTTCCCCGCAGCCATTCGCTGGCGCATTCCCGGTACTGGCAAGGCCACtt                                                       <  2:380759/273‑1 (MQ=255)                                                                                                                                                                                                                 gccagccaGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCt                                                                                                                                                                                                                                                                  <  2:373025/70‑1 (MQ=255)                                                                                                                                                                                                                 gaaagccagcTTGTTATTCCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGACACTGCATCGCTGGCATTTCGGCAGCAACAGTTTTACGGATAATTTCTGCTTTCCCCGCAGCCATTCGCTGGCGCATTCCCGGTACTGGCAAGGCCACTTCa                                                     <  2:688783/272‑1 (MQ=255)                                                                                                                                                                                                                       cagcTTGCTATCGCTGCATTTTCCTGCTTTATTGTCACGATTGCGTTATTCATGGCTGCATCCTTTGCCGTACATAGTCCTGCCGTCGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATGCATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGACACTGCAGCGCTGGCATGTCGGCAGCAACAGTTTTACGGATAATTTCTGCTTTCCCCGCAGCCATTCGCTGGCGCATTCCCGGTACTGGCAAGGCCACTTCACCGCAc                                               <  2:43232/275‑1 (MQ=255)                                                                                                                                                                                                                                    cGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTc                                                                                                                                                                                               >  1:193923/1‑118 (MQ=255)                                                                                                                                                                                                                                       cATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTGGGCGTAAATAGTCCTGCCATAGCTTTTGATCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGGCGCTCCGCGTCGTTGCTCTGCTCTCGCCAGTTGCAGACACTGCATCGCTGTCATCTCGGCCGCAACAGTTTTACGGATACTTTCTGCTTTTCCCGCAGCCATTCGCTGGCGCATTCCCGGTACTGGCAAAGCCACTTCACTGCACTGACGCAAGGCCATCa                               >  1:148667/1‑275 (MQ=255)                                                                                                                                                                                                                                        aTTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTc                                                                                                                                                                                           <  2:193920/118‑1 (MQ=255)                                                                                                                                                                                                                                                 aTTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAg                                                                                                                                                                                                                                  >  1:512700/1‑70 (MQ=255)                                                                                                                                                                                                                                                     aTTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCttt                                                                                                                                                                                                                              <  2:512695/70‑1 (MQ=255)                                                                                                                                                                                                                                                             aaTTGCGATATACATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGACACTGCATCg                                                                                                                                                 >  1:266904/1‑139 (MQ=255)                                                                                                                                                                                                                                                                 gCGATATACATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGACACTGCATCGCTgg                                                                                                                                             <  2:266900/139‑1 (MQ=255)                                                                                                                                                                                                                                                                    ttatTCATGGCTTCATCCTTTTGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATTAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGACACTGCATCGCTGGCATTTCGGCAGCAACAGTTTTACGGATAATTTCTGCTTTCCCCGCAGCCATTCGCTGGCGCATTCCCGGTACTGGCAAGGCCACTTCACCGCACTGACGCACGGCAATCACCGCAGGCAAGCGAACCCGGCAACAACGc  <  1:794940/274‑1 (MQ=255)                                                                                                                                                                                                                                                                      atTCATTGCTTTATCCTTTGGCGTAAATACTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGACACTGCATCGCTGGCATTTCGGCAGCAACAGTTTTACGGATAATTTCTGCTTTCCCCGCAGCCATTCGCTGGCGCATTCCCGGTACTGGCAAGGCCACTTCACCGCACTGACGCACGGCAATCACCGCAGGCAAGCGAACCCGGCAACAACGc  <  2:713696/273‑1 (MQ=255)                                                                                                                                                                                                                                                                       ttCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAg                                                                                                                                                                  >  1:771926/1‑112 (MQ=255)                                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                                               CGAAGTCACCTGGCAGATGCTTGCACCATGTAAACGCCAGGCCAGCCGGGTCGACAGTTCATCGCCAAACGTTCCCGGCGGAAAGAGAACAACGTCCGCAGGCGTTCGCTGCCACTGTTCCACCAACGCATCCAGCACCTGTTCCGCCACTACAGGCTGAGGTTCAATCTGCCAGTGCGCCAGGGTACAACCGCTGAAATCCTGCGCCGCCAGCCAGCTTGCTATTGCGGCATTCTCCTGATTTATTGTCACAATTGCGATATTCATGGCTGCATCCTTTGGCGTAAATAGTCCTGCCATAGCTTTTGAGCTTTTTCTGCTACCGTTTGCCCATCAATCAGCGTCGCTCCGCGTCGTTGCTCTGCTCTTGCCAGTTGCAGACACTGCATCGCTGGCATTTCGGCAGCAACAGTTTTACGGATAATTTCTGCTTTCCCCGCAGCCATTCGCTGGCGCATTCCCGGTACTGGCAAGGCCACTTCACCGCACTGACGCACGGCAATCACCGCAGGCAAGCGAACCCGGCAACAACGC  >  CP009273/2888872‑2889405

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑