Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,634,019	T→C	I125V (ATT→GTA)	nohA ←	NohA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,634,019	0	T	C	84.2%	27.3 / 26.7	76	I125V (ATT→GTA)	nohA	NohA
Reads supporting (aligned to +/- strand):  ref base T (7/5);  new base C (26/38);  total (33/43)
Fisher's exact test for biased strand distribution p-value = 3.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.79e-01

AACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGG  >  NC_000913/1633948‑1634111                                                                        |                                                                                             aataTGTCGGTTTTCCAGCTCCGGGAAGTGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAg                                                                         <  1:2544476/90‑1 (MQ=0) aataTGTCGGTTTTCCAGCTCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAg                                                                         >  1:1013622/4‑93 (MQ=0) aataTGTCGGTTTTCCAGCTCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAg                                                                         >  1:5892741/4‑93 (MQ=0) aataTGTCGGTTTTCCAGCTCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAg                                                                         >  2:758939/4‑93 (MQ=0) aataTGTCGGTTTTCCAGCTCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAg                                                                         >  1:4896044/4‑93 (MQ=0) aataTGTCGGTTTTCCAGCTCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAg                                                                         >  2:467867/4‑93 (MQ=0) aataTGTCGGTTTTCCAGCTCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAg                                                                         >  2:5549751/4‑93 (MQ=0) aataTGTCGGTTTTCCAGCTCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAg                                                                         >  1:3062528/4‑93 (MQ=0) aataTGTCGGTTTTCCAGCTCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAg                                                                         <  1:302118/90‑1 (MQ=0) aataTGTCGGTTTTCCAGCTCCGGGAAGCGCCGCTGAAACGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTACGGCCATCCGCGACAg                                                                         >  2:467868/4‑93 (MQ=0)     tgccGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACg                                                                     >  2:4331045/4‑93 (MQ=1)                 agctCCGGGAAGCGCCGCTGAACCGACAGAGGGACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAAt                                                         >  2:957916/4‑93 (MQ=0)                 agctCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAAt                                                         <  2:1820950/90‑1 (MQ=0)                 agctCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAAt                                                         <  1:4470519/90‑1 (MQ=0)                 agctCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAAt                                                         >  1:3850898/4‑93 (MQ=0)                 agctCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAAt                                                         <  1:223105/90‑1 (MQ=0)                 agctCCGGGAAGCGCCGCTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAAt                                                         >  1:1043282/4‑93 (MQ=0)                         gaagcgccgcTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTc                                                 >  1:2627185/5‑93 (MQ=0)                         gaagcgccgcTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTc                                                 >  2:538923/5‑93 (MQ=0)                         gaagcgccgcTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTc                                                 <  2:1980592/89‑1 (MQ=0)                         gaagcgccgcTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTc                                                 >  2:1164780/5‑93 (MQ=0)                         gaagcgccgcTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTc                                                 <  2:5821295/89‑1 (MQ=0)                         gaagcgccgcTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTc                                                 >  1:1847530/5‑93 (MQ=0)                         gaagcgccgcTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTc                                                 <  2:2125120/89‑1 (MQ=0)                         gaagcgccgcTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTc                                                 <  2:918029/89‑1 (MQ=0)                         gaagcgccgcTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTc                                                 <  2:25663/89‑1 (MQ=0)                         gaagcgccgcTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTc                                                 <  2:3222457/89‑1 (MQ=0)                         gaagcgccgcTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTc                                                 >  1:5566779/5‑93 (MQ=0)                         gaagcgccgcTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTc                                                 >  2:3656943/5‑93 (MQ=0)                          aagcgccgcTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTcc                                                <  2:546851/90‑1 (MQ=0)                          aagcgccgcTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTcc                                                <  2:3646654/90‑1 (MQ=0)                          aagcgccgcTGAACCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTACGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTcc                                                <  2:4379135/90‑1 (MQ=0)                                   tgaaCCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCa                                       >  1:1463636/4‑93 (MQ=0)                                   tgaaCCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCa                                       <  2:6117300/90‑1 (MQ=0)                                   tgaaCCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCa                                       <  1:6090364/90‑1 (MQ=0)                                   tgaaCCGACAGAGGAACTCCATCAAGAATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCa                                       <  1:3893079/90‑1 (MQ=0)                                             ggaggATCCCGTCGAGAATACTGGCAATTTCACATGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGtctc                             <  2:4239219/90‑1 (MQ=0)                                                       atcaagaATGCTGGCTACTTCTCCNGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCAttttt                   <  1:5840806/89‑1 (MQ=0)                                                       atcaagaATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCAttttt                   <  2:4289596/89‑1 (MQ=0)                                                       atcaagaATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCAttttt                   >  1:2349360/5‑93 (MQ=0)                                                        tcaagaATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCAtttttt                  >  2:3381734/4‑92 (MQ=0)                                                        tcaagaATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCAtttttt                  >  2:4995913/4‑92 (MQ=0)                                                        tcaagaATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCAtttttt                  >  2:1111677/4‑92 (MQ=0)                                                        tcaagaATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCAtttttt                  >  1:1028200/4‑92 (MQ=0)                                                        tcaagaATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCAtttttt                  >  1:143654/4‑92 (MQ=0)                                                        tcaagaATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCAtttttt                  <  1:6120974/90‑2 (MQ=0)                                                        tcaagaATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCAtttttt                  <  1:5322687/90‑2 (MQ=0)                                                        tcaagaATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCAtttttt                  <  1:5832811/90‑2 (MQ=0)                                                        tcaagaATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCAtttttt                  >  1:5626031/4‑92 (MQ=0)                                                        tcaagaATGCTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCAtttttt                  >  1:3221108/4‑92 (MQ=0)                                                        tcaagaATGCTGGCTACTCCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCGCCTCAGCGGAATCTTTTGCAtttttt                  <  1:5853229/90‑2 (MQ=0)                                                              atgcTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCATTTTTTAGTTcc            <  2:1676432/90‑1 (MQ=0)                                                              atgcTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCATTTTTTAGTTcc            <  1:4660852/90‑1 (MQ=0)                                                              atgcTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCATTTTTTAGTTcc            <  2:451229/90‑1 (MQ=0)                                                              atgcTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCATTTTTTAGTTcc            <  1:3629720/90‑1 (MQ=0)                                                              atgcTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCATTTTTTAGTTcc            <  2:5056144/90‑1 (MQ=0)                                                              atgcTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCATTTTTTAGTTcc            <  1:306722/90‑1 (MQ=0)                                                              atgcTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCATTTTTTAGTTcc            <  1:2471618/90‑1 (MQ=0)                                                              atgcTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCATTTTTTAGTTcc            <  1:1948096/90‑1 (MQ=0)                                                              atgcTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCATTTTTTAGTTcc            <  1:1807220/90‑1 (MQ=0)                                                              atgcTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCATTTTTTAGTTcc            <  2:74279/90‑1 (MQ=0)                                                              atgcTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCATTTTTTAGTTcc            <  1:4796918/90‑1 (MQ=0)                                                              atgcTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCATTTTTTAGTTcc            <  2:1663394/90‑1 (MQ=0)                                                              atgcTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCATTTTTTAGTTcc            <  2:2272909/90‑1 (MQ=0)                                                              atgcTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCATTTTTTAGTTcc            <  2:3808593/90‑1 (MQ=0)                                                              atgcTGGCTACTTCTCCGGCCATCCGCGACAGCACGAACGTGCAGAATGCGGTTTCCACCACCTCAGCGGAATCTTTTGCATTTTTTAGTTcc            <  2:3808592/90‑1 (MQ=0)                                                                    gCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCg      >  2:4066815/1‑93 (MQ=31)                                                                    gCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCg      >  2:4835661/1‑93 (MQ=31)                                                                    gCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCg      >  2:5313342/1‑93 (MQ=31)                                                                    gCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGACTCTGGCATTTTTCAGCTCCTGTGCg      >  1:1209582/1‑93 (MQ=14)                                                                     cAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGt     <  1:5276352/93‑1 (MQ=32)                                                                     cAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGt     <  1:5890668/93‑1 (MQ=32)                                                                     cAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGt     <  1:5679811/93‑1 (MQ=32)                                                                      aaTTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTc    >  2:4810619/1‑93 (MQ=33)                                                                      aaTTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTc    <  1:4099855/93‑1 (MQ=33)                                                                       aTTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCg   >  2:1933835/1‑93 (MQ=33)                                                                        tttCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCgg  >  2:3594405/1‑93 (MQ=33)                                                                        tttCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCgg  >  2:291050/1‑93 (MQ=33)                                                                        tttCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCgg  >  1:3454148/1‑93 (MQ=33)                                                                        |                                                                                             AACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGG  >  NC_000913/1633948‑1634111

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑