Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,412,011	G→T	7.6%	R409R (CGG→AGG)	intR ←	Rac prophage; integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,412,011	0	G	T	7.6%	154.8 / 3.4	53	R409R (CGG→AGG)	intR	Rac prophage; integrase
Reads supporting (aligned to +/- strand):  ref base G (25/24);  new base T (2/2);  total (27/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.89e-01

GCTTCGCCCACGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTA  >  NC_000913/1411863‑1412159                                                                                                                                                     |                                                                                                                                                     gCTTCGCCCACGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACcg                                                                                                                                                      <  1:237720/149‑1 (MQ=255)     atgagtcagagagttgtgatttttgcccttacTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCa                                                                                                                                                  <  5:81824‑M1/117‑1 (MQ=255)          tcagagagttgtgatttttgcccttacTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCaa                                                                                                                                             >  6:81824‑M1/28‑149 (MQ=255)           cGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCaa                                                                                                                                             >  6:374553/1‑148 (MQ=255)                cgacgCAGACGTTTTTGTAATTTGTTCAGGTTGTTTTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGAATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATgg                                                                                                                                        <  1:252987/148‑1 (MQ=255)                 gacgCAGACCTTTTTCTAATTTGTTCAGGTTGTATTGTTCTTTATTTCTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGAAAAGTGCGGGCAAACTTTGCAACTACGATAACAGCGCATACAACATGGc                                                                                                                                       >  4:178614/1‑148 (MQ=255)                    gccgACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTAGTTGATTTTCTTGCATTATGTCAGTTCTCTGGAACTAAATGGGGCAAATTGGGGGCACACTTTGCAGCTACGATAACCGCGCAGTCAACAGGGcgctc                                                                                                                                   >  2:38677/4‑145 (MQ=255)                                    tttGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGt                                                                                                                   <  3:135036/149‑1 (MQ=255)                                        TTCAGGTTGTATTGTTCTTTCTTTTTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcat                                                                                                                >  7:27930‑M1/1‑148 (MQ=255)                                        TTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGtcat                                                                                                                >  5:374553‑M1/1‑148 (MQ=255)                                           AGGTTGTATTGTTCTTTCTTTGTAATTTGTTGTTTTTCTTGCATTATTTCAGTTCTCTGGTACTATATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCTACATGGCTATCTGTTCGTCGTTCATGTCATCAAt                                                                                                            >  3:178614‑M1/1‑149 (MQ=255)                                             GTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGTCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATc                                                                                                           <  7:210540‑M1/148‑1 (MQ=255)                                                GTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCcac                                                                                                        >  4:99923‑M1/1‑148 (MQ=255)                                                   TTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACAGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATAc                                                                                                    <  3:348794‑M1/149‑1 (MQ=255)                                                      TTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATAGCGt                                                                                                 >  8:210540‑M1/1‑149 (MQ=255)                                                      TTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCg                                                                                                  <  8:261690‑M1/148‑1 (MQ=255)                                                      TTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCg                                                                                                  <  3:249504‑M1/148‑1 (MQ=255)                                                        CTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTa                                                                                                <  2:150973‑M1/148‑1 (MQ=255)                                                               tGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCa                                                                                         <  8:39148/148‑1 (MQ=255)                                                               tGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCa                                                                                         >  2:384528/1‑148 (MQ=255)                                                                 tAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATa                                                                                       <  7:261690/148‑1 (MQ=255)                                                                   aTTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATaca                                                                                     <  4:249504/148‑1 (MQ=255)                                                                        ttgATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGTGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGATATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCt                                                                               >  5:92320/1‑149 (MQ=255)                                                                          gATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTg                                                                              <  7:184771/148‑1 (MQ=255)                                                                           aTTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTgc                                                                             <  8:20525/148‑1 (MQ=255)                                                                                    cATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCAt                                                                   >  3:78600/1‑149 (MQ=255)                                                                                    cATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCAt                                                                   <  4:285786/149‑1 (MQ=255)                                                                                      ttattTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGc                                                                 >  7:345646/1‑149 (MQ=255)                                                                                        attTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCt                                                                               <  1:307998/133‑1 (MQ=255)                                                                                        attTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCt                                                                               >  2:307998/1‑133 (MQ=255)                                                                                         tttCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGccc                                                               >  5:25920/1‑148 (MQ=255)                                                                                          ttCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCACCATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAAATACATACACCATCTGCGCACTTTCATggtgga                                                             >  1:332578/1‑144 (MQ=255)                                                                                            cAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCAtt                                                           >  8:284781/1‑149 (MQ=255)                                                                                                     ggTACTAAATGGGGCAAATTGGGGGCAAACTTTGAAACTACGATAACCGAGAATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCAACATACCGTAAATTTCATACACCATATGCGCAGTTTCATTCCCCATTtggatggc                                                   >  8:153695/1‑148 (MQ=255)                                                                                                       tACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCtat                                                <  6:25920/149‑1 (MQ=255)                                                                                                           aaaTGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAAt                                            >  1:251849/1‑149 (MQ=255)                                                                                                                   cAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGtt                                    <  5:239341/149‑1 (MQ=255)                                                                                                                       ttGGGGGCAATCTTTGCAACTTCGATAACCGCGCATTCATCATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAATTTTCATACACCATCTGCGCAGTTTCATGCCCCAt                                                            <  2:236324/121‑1 (MQ=255)                                                                                                                       ttGGGGGCAAACTTTGCAACTACGATAACCGCGCAATCAACATGGCTATCTGTTGGTCGTTCATGTCATCAATCGACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATTCCCCAt                                                            >  1:236324/1‑121 (MQ=255)                                                                                                                           gggCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTg                            <  4:78600/149‑1 (MQ=255)                                                                                                                             gCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCAttt                                                          <  5:7823/117‑1 (MQ=255)                                                                                                                             gCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCAttt                                                          >  6:7823/1‑117 (MQ=255)                                                                                                                             gCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGcc                          >  7:308030/1‑149 (MQ=255)                                                                                                                              cAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGACATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCg                         >  6:10423/1‑149 (MQ=255)                                                                                                                               aaaCTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGt                        >  1:104594/1‑149 (MQ=255)                                                                                                                                       cAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAAcagc                 <  6:92320/148‑1 (MQ=255)                                                                                                                                        aaCTACGATAACCTCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAAcagc                 >  4:41370/1‑147 (MQ=255)                                                                                                                                        aaCTACGATAACCTCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAAcagc                 >  4:36431/1‑147 (MQ=255)                                                                                                                                              gATAACCTCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGc         <  3:36431/149‑1 (MQ=255)                                                                                                                                              gATAACCTCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGc         <  3:41370/149‑1 (MQ=255)                                                                                                                                              gATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTg                            <  3:151787/130‑1 (MQ=255)                                                                                                                                              gATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTg                            >  4:151787/1‑130 (MQ=255)                                                                                                                                                  aCCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCaaaa     <  5:10423/149‑1 (MQ=255)                                                                                                                                                  aCCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCaaaa     <  8:345646/149‑1 (MQ=255)                                                                                                                                                     gcgcATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTa  >  8:316844/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                     GCTTCGCCCACGTTACGACGCAGACGTTTTTGTAATTTGTTCAGGTTGTATTGTTCTTTCTTTGTAATTTGTTGATTTTCTTGCATTATTTCAGTTCTCTGGTACTAAATGGGGCAAATTGGGGGCAAACTTTGCAACTACGATAACCGCGCATTCAACATGGCTATCTGTTCGTCGTTCATGTCATCAATCCACATACCGTAAATTTCATACACCATCTGCGCAGTTTCATGCCCCATTTGGCTGGCTATAAATGCCGGGTTCGCTCCTGCCGTCAACAGCCAGCAGGCAAAAGTA  >  NC_000913/1411863‑1412159

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑