Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,412,294	C→T	L314L (CTG→CTA)	intR ←	putative integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,412,294	0	C	T	97.1%	119.6 / NA	35	L314L (CTG→CTA)	intR	putative integrase
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (15/18);  total (16/19)
Fisher's exact test for biased strand distribution p-value = 4.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

CATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGCAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGACCGAACATATCAAGTATCGTCAGGTTTCTTCTGACATTCACTATTCCCTTTTCGAGATCCACATCCTCCCACGCCAGAGCTGCCAGTTCC  >  NC_000913/1412047‑1412537                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                    catcaATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTGCCGTTACACACCCTGGGCATGAAAACAAAATGTAGt                                                                                                                                                                                                                                                  <  2:94332/251‑1 (MQ=255)  atcaATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGtt                                                                                                                                                                                                                                                 <  1:249499/251‑1 (MQ=255)                    aaTTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGc                                                                                                                                                                                                                               <  2:332341/251‑1 (MQ=255)                        tCATACACCATCTGCGCATTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGt                                                                                                                                                                                                                            <  1:354203/250‑1 (MQ=255)                        tCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGt                                                                                                                                                                                                                            <  1:90913/250‑1 (MQ=255)                            acacCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTcc                                                                                                                                                                                                                       >  2:373637/1‑251 (MQ=255)                                     gcgcAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTGTTGGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGGTCTGCCGTACTCCCGATGATa                                                                                                                                                                                                               <  2:200797/250‑1 (MQ=255)                                          gTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGt                                                                                                                                                                                                         <  1:195592/251‑1 (MQ=255)                                                               gctATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGatgatg                                                                                                                                                                                    <  1:23184/251‑1 (MQ=255)                                                               gctATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGatgatg                                                                                                                                                                                    >  1:325848/1‑251 (MQ=255)                                                                           gggTTCTCGCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCTCCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGAGAAAAGGTGATTTCGCTTTTGCGATGATGCCCTGTCAGttt                                                                                                                                                                        <  2:253751/251‑1 (MQ=255)                                                                               tCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTAt                                                                                                                                                                    >  1:155806/1‑251 (MQ=255)                                                                                              aCAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGAt                                                                                                                                                                                                      >  2:253016/1‑202 (MQ=255)                                                                                              aCAGCCAGCAGGCAAAAGTATGCTGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGAt                                                                                                                                                                                                      <  1:253016/202‑1 (MQ=255)                                                                                                                                cGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTc                                                                                                                                                                                                                        <  1:395311/150‑1 (MQ=255)                                                                                                                                cGGATTACGGCGGCGAATACCAGCAAGTTTTACTGCTGCATTCCACCTTGACCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTc                                                                                                                                                                                                                        >  2:395311/1‑150 (MQ=255)                                                                                                                                                        aCGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGAc                                                                                           >  1:188047/1‑251 (MQ=255)                                                                                                                                                                 tgctgcATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCa                                                                                                                                                                            >  2:287105/1‑161 (MQ=255)                                                                                                                                                                 tgctgcATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCa                                                                                                                                                                            <  1:287105/161‑1 (MQ=255)                                                                                                                                                                   ctgcATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACACAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGACCGAACATATc                                                                                 >  1:38417/1‑250 (MQ=255)                                                                                                                                                                     gcATTCCACCTTGCCCCCAAACTGCTTACCGATTAATAAGGTGTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGACCGAACATATCa                                                                                <  1:226614/249‑1 (MQ=255)                                                                                                                                                                     gcATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGACCGAACATATCa                                                                                <  2:155806/249‑1 (MQ=255)                                                                                                                                                                          ccaccaTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACCCCCTGGGCATGAAAACAAAATGGAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGACCGAACATATCAAGTATCg                                                                         <  2:235930/251‑1 (MQ=255)                                                                                                                                                                             ccTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTCCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGACCGAACATATCAAGTATCGTc                                                                       >  2:277997/1‑250 (MQ=255)                                                                                                                                                                                                  cGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGACCGAACATATCAAGTATCGTCAGGTTTCTTCTGACATTCACTa                                                 <  1:399770/251‑1 (MQ=255)                                                                                                                                                                                                        ataaGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGACCGAACATATCAAGTATCGTCAGGTTTCTTCTGACATTCACTATTCCCt                                           >  1:222367/1‑251 (MQ=255)                                                                                                                                                                                                         taaGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGACCGAACATATCAAGTATCGTCAGGTTTCTTCTGACATTCACTATTCCCtt                                          >  1:14042/1‑251 (MQ=255)                                                                                                                                                                                                              tttttGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGACCGAACATATCAAGTATCGTCAGGTttcttc                                                             >  2:294927/1‑227 (MQ=255)                                                                                                                                                                                                              tttttGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGACCGAACATATCAAGTATCGTCAGGTttcttc                                                             <  1:294927/227‑1 (MQ=255)                                                                                                                                                                                                                     tttCCGTTACACACCCTGGGCATGAAAACACAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGACCGAACATATCAAGTATCGTCAGGTTTCTTCTGACATTCACTATTCCCTTTTCGAGATCcac                              >  1:178539/1‑251 (MQ=255)                                                                                                                                                                                                                                 acCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTg                                                                                                                         >  2:324917/1‑148 (MQ=255)                                                                                                                                                                                                                                 acCCTGGGCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTg                                                                                                                         <  1:324917/148‑1 (MQ=255)                                                                                                                                                                                                                                       ggCATGAAAACAAAATGTAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGACCGAACATATCAAGTATCGTCAGGTTTCTTCTGACATTCACTATTCCCTTTTCGAGATCCACATCCTCCCACGCCAGAGc            >  2:114602/1‑251 (MQ=255)                                                                                                                                                                                                                                            gAAAACAAAATGCAGTTTTTGCTTTTCGGATATGCCGAACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGACCGAACATATCAAGTATCGTCAGGTTTCTTCTGACATTCACTATTCCCTTTTCGAGATCCACATCCTCCCACGCCAGAGCTGcc        >  2:201458/1‑250 (MQ=255)                                                                                                                                                                                                                                                 cAAAATGTAGTTTTTGCTGTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGACCGAACATATCAAGTATCGTCAGGTTTCTTCTGACATTCACTATTCCCTTTTCGAGATCCACATCCTCCCACGCCAGAGCTGCCAGTTcc  <  2:14042/251‑1 (MQ=255)                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                    CATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTATGCCGCGTATGGTACGGATTACGGCGGCGAATACCAGCACGTTTTACTGCTGCATTCCACCTTGCCCCCAAACTGCTTACCGAGTAATAAGGTTTTTGTTTTCCGTTACACACCCTGGGCATGAAAACAAAATGCAGTTTTTGCTTTTCGGTTCTGCCGTACTCCCGATGATAAAAGGTGATTTCGCTTTTGCGATGATGCCCGGTCAGTTTGTATTGCTCCTTCAGTGCTTCAAGAGCAGGCTGCAGTAGTGTTACTGTTCGGATCCCGGCATTTGTTTTTGGGGGACCGAACATATCAAGTATCGTCAGGTTTCTTCTGACATTCACTATTCCCTTTTCGAGATCCACATCCTCCCACGCCAGAGCTGCCAGTTCC  >  NC_000913/1412047‑1412537

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑