Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	36,315	G→A	10.5%	Y79Y (TAC→TAT)	tpn ←	IS431mec transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	36,315	0	G	A	10.5%	132.8 / 5.8	56	Y79Y (TAC→TAT)	tpn	IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base G (24/25);  new base A (3/3);  total (27/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.01e-01

TTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATAT  >  CP000730/36175‑36452                                                                                                                                             |                                                                                                                                          ttACTAAATTGTTTAACGGTACGTTTGATAATCGCATATGCTTAATGTGTATCTCGTTTCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATg                                                                                                                                           <  2:173622/141‑1 (MQ=11)        aTTGTTTAATGAGACGATTGATAAACGCATATGCTGAATGATTGTCTCGATGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGGTATAAATAGCTCCATATTCCTTTTATTTTTATGTACGtct                                                                                                                                    >  1:63434/1‑141 (MQ=11)              tAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCaa                                                                                                                              <  1:391695/141‑1 (MQ=32)                 tGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATAc                                                                                                                           <  1:434330/141‑1 (MQ=32)                    gagtgttgtgcaaCGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATCTCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATTTACGTCTCATCAATACGcc                                                                                                                        <  1:12044/130‑1 (MQ=11)                     aCGTTTGATAAACGAATATACTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCTCTTTCCTTTTATTTTGATGTACGTCTCATCAATACACCa                                                                                                                       >  1:301031/1‑141 (MQ=11)                      cGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGTATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATATACGTCTCATCAATACGCCAt                                                                                                                      >  2:54250/1‑141 (MQ=17)                         ttGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCCTTTg                                                                                                                   >  1:163164/1‑141 (MQ=17)                            aTAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCATTTTATTTTGATGTACGTCTCATCAATACGCCATTTTtaa                                                                                                                >  2:372056/1‑141 (MQ=17)                               aaCGGATATGCTGAATGATTATCTCGTGGGTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCGTTTTCCTTTTATTTTTATGTACGTCTCATCAATACGCCATTTGtaataa                                                                                                             <  1:54767/141‑1 (MQ=11)                                 cGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGc                                                                                                           >  1:330927/1‑141 (MQ=35)                                             aTGATTATCTCGTTGCTTACGCAACCAAATCTCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATGAATACGCCATTTGTAATAAGCTTTTTTATGCtt                                                                                               <  2:304469/141‑1 (MQ=255)                                                   aTCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTttctt                                                                                         >  2:155169/1‑141 (MQ=40)                                                    tctcGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTTTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTttcttc                                                                                        <  2:438116/141‑1 (MQ=255)                                                    tctcGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCTATTTTCCTTTTATTTTGATGTACGTCTCATCAATCCGCCATTTGTACTAAGTTTTTTTATGCTTTttcttc                                                                                        >  1:182092/1‑141 (MQ=255)                                                    tctcGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTttcttc                                                                                        <  2:438068/141‑1 (MQ=40)                                                    tctaGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTttcttc                                                                                        <  1:423537/141‑1 (MQ=255)                                                     ctcGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTGTTTATGCTTTTTCTTcc                                                                                       <  1:223389/141‑1 (MQ=25)                                                     ctagTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTcc                                                                                       <  1:451024/138‑1 (MQ=255)                                                           gCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCAACAttt                                                                                 >  2:433556/1‑141 (MQ=255)                                                            cTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAAtttt                                                                                >  2:453092/1‑140 (MQ=255)                                                             gtaagCAACCAAATATCTAATGTATGTCCCTCTGTATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGa                                                                               >  2:181296/5‑141 (MQ=255)                                                              tACGCAACCAAATCTCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACTTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGAt                                                                              <  1:432081/141‑1 (MQ=255)                                                              tACGCAACCAAATATCTAATGTATGTCCCTCTTCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGGACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGAt                                                                              <  1:432182/141‑1 (MQ=255)                                                              tACGCAACCAAATATCCAATGTATGTCCCTCTGTATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGAt                                                                              <  1:54250/141‑1 (MQ=255)                                                               aCGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATa                                                                             >  2:168671/1‑141 (MQ=40)                                                               aCGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGCCACGATATAAATCGATCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATCTGTAATAAGCTCTTTTATGCTTTTTCTTCCAAATTTgcca                                                                             <  2:406855/141‑4 (MQ=11)                                                                cGCAAACAAACATGCTATGTATGTCCCTCTGCATCCATGGCACGATATAAATCGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTACGCTTTTTCTTCCAAATTTGATAc                                                                            <  2:66623/141‑1 (MQ=14)                                                                  cAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAATTTGGATACaa                                                                          >  2:359524/1‑141 (MQ=255)                                                                    aCCAAATATCTAATGGATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATaaaa                                                                        <  2:460494/141‑1 (MQ=255)                                                                         atatCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCGCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGATTTTTCTTCCAAATTTGATACAAAATTggg                                                                   >  2:152274/1‑141 (MQ=255)                                                                          tatCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTgggg                                                                  <  2:348516/141‑1 (MQ=255)                                                                          tatCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTgggg                                                                  <  2:413688/141‑1 (MQ=255)                                                                          tatCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTATTCTTCCAAATTTGATACAACATTgggg                                                                  >  2:33162/1‑141 (MQ=255)                                                                                    atgtCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAACATTggggacgatccgtc                                                        >  1:419953/1‑131 (MQ=255)                                                                                     tgtCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGa                                                       <  2:387828/141‑1 (MQ=255)                                                                                     tgtCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGa                                                       <  2:387833/141‑1 (MQ=255)                                                                                       tCCCTCTTCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACTTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACACAATTTGGGCGTATTTTTGGAc                                                     >  1:45360/1‑141 (MQ=14)                                                                                       tCCCTCTGTATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCACATTTGGTATCAAATTGTGGAGTATGCTTTAAc                                                     >  1:379607/1‑141 (MQ=11)                                                                                        cccTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGACTATTCTTTAAcc                                                    >  2:85203/1‑141 (MQ=255)                                                                                         ccTCTGCATCAATGGCACGATATACATAACTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAAccc                                                   <  2:301031/141‑1 (MQ=255)                                                                                         ccTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAAccc                                                   >  2:178699/1‑141 (MQ=40)                                                                                            ctGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCTAAc                                                >  2:251818/1‑141 (MQ=255)                                                                                                aTCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTa                                            <  2:394022/141‑1 (MQ=18)                                                                                                 tCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGATTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAg                                           >  1:183236/1‑141 (MQ=255)                                                                                                        cACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTg                                    >  1:181086/1‑141 (MQ=39)                                                                                                                 aaTAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAatgaaaac                           >  2:461892/1‑137 (MQ=255)                                                                                                                           ttttCCTTTTATTTTGATGTACGTCTGATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGACAAAAAATTGGGGAATATATTTTAACCCAACGGTAAACCGTTGAATGATGAACCATAAcacc                 >  2:287151/1‑141 (MQ=11)                                                                                                                            tttCCTTTTATTTTGTTGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTAcacca                <  2:361280/141‑1 (MQ=255)                                                                                                                             ttCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTAcaccac               <  1:2304/141‑1 (MQ=39)                                                                                                                              tCCTCTTACTTTGATGTACGTCCCATCAATACGCTATTTGTAACAAGCTTTATTCTGCTTTTTCTTGCAAATTTGACACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACg              <  1:324436/141‑1 (MQ=11)                                                                                                                                cTTTTATTTTGATATACGTTTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGtt            <  1:52349/141‑1 (MQ=255)                                                                                                                                 ttttATTTTGATGGACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTCGTCCGTTGAATGATGAACGTTTACACCACGTTc           <  2:14616/141‑1 (MQ=255)                                                                                                                                   ttATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTccc         <  1:214765/141‑1 (MQ=39)                                                                                                                                       tttGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTaa     <  2:348159/141‑1 (MQ=40)                                                                                                                                          gATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAatct  >  2:12353/1‑139 (MQ=255)                                                                                                                                          gATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAatat  >  2:55760/1‑141 (MQ=40)                                                                                                                                             |                                                                                                                                          TTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATAT  >  CP000730/36175‑36452

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑