Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	36,413	C→T	8.1%	V47I (GTC→ATC)	tpn ←	IS431mec transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	36,413	0	C	T	8.1%	153.1 / 4.6	63	V47I (GTC→ATC)	tpn	IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base C (31/25);  new base T (3/2);  total (35/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.00e-01

GCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCA  >  CP000730/36277‑36550                                                                                                                                         |                                                                                                                                          gCACGTTATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTCTACCGtt                                                                                                                                       <  1:216200/141‑1 (MQ=255)    cGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTTaa                                                                                                                                    >  1:68961/1‑141 (MQ=255)    cGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGaa                                                                                                                                    >  1:96042/1‑141 (MQ=40)      atatAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAatg                                                                                                                                  <  2:379554/141‑1 (MQ=40)          aattAGCTCCATTTTCCTCTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAAtgatga                                                                                                                              <  1:483970/138‑1 (MQ=255)           aaTAGCTCCATTTTCCTTTTATTTTGATATACGTCTCATCAATACGCCATTTGATATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGaa                                                                                                                             >  1:541872/1‑141 (MQ=11)           aaTACCGCCATTTTCCTTTTATTTTGATGTACGTCGCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATCAGAAAAAACACTGGGGCATATTCTTGAACCCAACGGTAGACCGTTCAATGATGaa                                                                                                                             <  2:585779/141‑1 (MQ=11)              aGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCACCGGTAGACCGTTGGATGATGAACGt                                                                                                                          >  1:544553/1‑141 (MQ=255)              aGCTCCATTTTCCTGTGATTTTGATGTACGCCTCATCAATACGCCATTTGTAATAAGCGTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATGGAGGAACATTCTTCAACCCAACCGACAACCCTGGGATGATGAACGt                                                                                                                          >  2:559397/1‑141 (MQ=11)                cTCCATTTTCCTTTTATTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGttt                                                                                                                        >  1:392754/1‑141 (MQ=255)                   cATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTaca                                                                                                                     >  1:481481/1‑141 (MQ=40)                    aTTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTTATACAACATTGGGGCATATTCTTGAACCCAACGGTAGACCGCTGCATGGTCACCGtttttac                                                                                                                    >  2:247622/1‑137 (MQ=14)                    aTTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTacac                                                                                                                    >  1:525587/1‑141 (MQ=40)                     ttttCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTAcacc                                                                                                                   <  1:38464/141‑1 (MQ=40)                         ccTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGt                                                                                                               <  2:96042/141‑1 (MQ=40)                         ccTTTTATTTTGACAAACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGTACGTTTACACCACGt                                                                                                               <  2:467641/141‑1 (MQ=11)                           ttttATTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTc                                                                                                             <  1:455602/141‑1 (MQ=255)                            tttATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTcc                                                                                                            >  1:32683/1‑141 (MQ=40)                             ttATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTccc                                                                                                           <  1:174817/141‑1 (MQ=40)                             ttATTGTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTccc                                                                                                           <  1:300952/141‑1 (MQ=255)                               tttttGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTTTGGTGTGTCTGCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCtt                                                                                                         <  1:17232/140‑1 (MQ=14)                               aTTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCtt                                                                                                         <  2:461496/141‑1 (MQ=39)                                    gATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGATTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGGAGACCGTTGAATGATGAACGTTTAAACAACGTGCCCTTGatat                                                                                                    >  1:507434/1‑141 (MQ=14)                                    gATGTACGTCTCATCAATACGCAATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAAATGGGAAATATAATTACACCCAACGGTAACACGTTGAATGATGAACGTTTACACCACGTTCCCTTAatat                                                                                                    >  1:580722/1‑141 (MQ=14)                                       gTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAGATTTGATACAAAATTGGGGAATATTCGTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTACCTTAATATTTc                                                                                                 >  2:336583/1‑141 (MQ=255)                                           ttctcATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGat                                                                                             <  2:312879/140‑1 (MQ=40)                                            tctcATCAATACGCCATTTGTAATAAGTTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGata                                                                                            <  2:515355/141‑1 (MQ=255)                                             ctcATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGatat                                                                                           >  1:251282/1‑141 (MQ=40)                                                 tcaATACGCCATTTGTAATCAAAGATTTGATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAATGGTAGACCGTTGAATGATGAACGTTTACACAACGTTCCCTTAATATTTCAGATATATCa                                                                                       >  2:281828/1‑141 (MQ=11)                                                 tcaATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCa                                                                                       <  1:572591/141‑1 (MQ=40)                                                    aTACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGa                                                                                    <  1:486745/141‑1 (MQ=39)                                                    aTACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGa                                                                                    <  1:447603/141‑1 (MQ=39)                                                    aTACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAAGTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGa                                                                                    <  2:366754/141‑1 (MQ=255)                                                       cGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGTCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATag                                                                                 >  2:177700/1‑140 (MQ=255)                                                         ccATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAAGGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACt                                                                               >  2:84331/1‑141 (MQ=255)                                                                  ataaGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGtata                                                                      <  1:191739/141‑1 (MQ=40)                                                                     aGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCt                                                                   <  2:408153/141‑1 (MQ=38)                                                                     aGCTTGTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTCCCCTTAATATTTCAGATATATCACGATAACTCAATGTATctct                                                                   >  2:86107/1‑141 (MQ=255)                                                                       cTTTTTTAGGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTa                                                                 <  1:426853/141‑1 (MQ=37)                                                                        ttttttATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAg                                                                >  1:356141/1‑141 (MQ=35)                                                                         tttttATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGa                                                               >  2:553933/1‑141 (MQ=35)                                                                          ttttATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACAATAACTCAATGTATATCTTAGaa                                                              >  2:116333/1‑140 (MQ=25)                                                                                 atttttCTTCCACAGTTGAAACCAAACCGGGGCATATTCTTGAACCCAACGGTAGGCCGTTGAATGATGAACGTGTACACCACGTTCCCTTAATGTTTCAGATATATCACCATACCTCAATGTATATCTAAGATAATGGcc                                                       >  2:37945/2‑141 (MQ=11)                                                                                    tttCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCACTGTATATCTTAGATAGTAGCCAAc                                                    >  1:241858/1‑141 (MQ=25)                                                                                      tcttcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGAAGACCGTTGGATGATGAACGTGTACACCACGTTCCCTTACTATTTCAGATATACCACGCTAACCCCGTGTCTATCTTAGAtagtcaacgtagc                                                  >  1:283545/1‑132 (MQ=11)                                                                                       cttcCAAATTGGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGc                                                 <  1:576262/141‑1 (MQ=25)                                                                                        ttcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGGTACCTCAATGTATATCTTAGCTAGTAGACAACggat                                                >  2:499882/1‑139 (MQ=255)                                                                                                          aTTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTg                              <  2:496123/141‑1 (MQ=32)                                                                                                           ttGGGGCATATTCCTGATCCCAACGGTAGACCGGTGAATGATGAACGTTTAAACCACTTTCTCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGt                             <  2:523551/141‑1 (MQ=11)                                                                                                             ggggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTa                           >  2:37356/1‑141 (MQ=32)                                                                                                             ggggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTa                           >  1:562150/1‑141 (MQ=32)                                                                                                              gggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTaa                          >  1:572755/1‑141 (MQ=32)                                                                                                                     ttCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGttt                   <  1:332576/141‑1 (MQ=32)                                                                                                                        ttGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATATTAGATAGTAACCAACGGCTACAGTGCTACAATCCTTGTTAAATTGTTttta                >  2:323642/1‑141 (MQ=11)                                                                                                                         tGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCGGATATATCACGATAACTCTATGTATATCTTGGTTACGAGCCAACGGCTACAGTGATAACCACGTGGTTCAATCGTTTatat               >  1:536746/1‑141 (MQ=11)                                                                                                                              ccAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGaa          >  2:15157/1‑141 (MQ=32)                                                                                                                               cAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGaaa         >  1:392396/1‑141 (MQ=32)                                                                                                                                aaCGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACCTCCTTGTTAAATTGTTTATATCTGAAAt        >  2:121024/1‑141 (MQ=17)                                                                                                                                aaCGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAAt        >  2:120974/1‑141 (MQ=32)                                                                                                                                    gTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGtt    <  2:32683/141‑1 (MQ=32)                                                                                                                                    gTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGtt    <  2:142263/141‑1 (MQ=32)                                                                                                                                    gTAGAACGTTGAATGATGAACGTTTACCCCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGtt    <  2:380277/141‑1 (MQ=17)                                                                                                                                      ctaCCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCa  >  1:172451/3‑141 (MQ=17)                                                                                                                                         |                                                                                                                                          GCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCA  >  CP000730/36277‑36550

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑