Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	36,479	T→C	15.2%	T25A (ACA→GCA)	tpn ←	IS431mec transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	36,479	0	T	C	15.2%	86.5 / 9.8	45	T25A (ACA→GCA)	tpn	IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base T (20/18);  new base C (4/3);  total (24/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

TAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAA  >  CP000730/36340‑36618                                                                                                                                            |                                                                                                                                            taataaGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGta                                                                                                                                            <  2:18623/141‑1 (MQ=40)  aataaGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGtat                                                                                                                                           >  1:198179/1‑141 (MQ=255)        cTTTTGTGTTCTTTTTCTTACAAATTTGATACAAAATTGGGGTATATTCTTGAACCCAACGGTAGAACGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTa                                                                                                                                     <  2:157256/141‑1 (MQ=11)           ttgtATGCTTGTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGAt                                                                                                                                  <  1:165218/138‑1 (MQ=25)              tATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATCTTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGAtagt                                                                                                                               >  1:161027/1‑141 (MQ=25)              tATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGAtagt                                                                                                                               >  1:238464/1‑141 (MQ=35)                tGCTTTTTCTTCCAAATTTGATACAAAATTGGGGTATATTCTTGAACCCAACGGTAGACCGTTAAATGATGAACGTTTACACCACGTTCCCTTAATATTTAAGATATCTCACGATAACTCCATGTATTTCTTACAtagtag                                                                                                                             >  2:63843/1‑141 (MQ=11)                 gCTTTTTCTTCCAAATTTTATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGc                                                                                                                            <  1:13687/141‑1 (MQ=21)                        cttcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGc                                                                                                                     <  2:63515/141‑1 (MQ=35)                          tcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTa                                                                                                                   <  1:102523/141‑1 (MQ=35)                          aacAAAGTTTATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTCTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTa                                                                                                                   <  2:266484/139‑1 (MQ=255)                                 ttGTTACAAAATTTGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGCTGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGAt                                                                                                            <  1:160250/141‑1 (MQ=255)                                 ttGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGAt                                                                                                            <  2:7160/141‑1 (MQ=35)                                  tGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCAAACGGCTACAGTGATa                                                                                                           >  2:267110/1‑141 (MQ=25)                                             tGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGtt                                                                                                <  2:105824/141‑1 (MQ=32)                                             tGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGtt                                                                                                >  2:285829/1‑141 (MQ=32)                                             tGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGtt                                                                                                <  2:65203/141‑1 (MQ=32)                                              ggggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTa                                                                                               >  1:320257/1‑141 (MQ=32)                                              ggggCATATTCTTGAACCCAACGGTAGACCGGTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAAAATCCTTGTTa                                                                                               >  1:183682/1‑141 (MQ=17)                                                       tCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTta                                                                                      <  1:359210/141‑1 (MQ=32)                                                       tCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTta                                                                                      <  1:256047/141‑1 (MQ=32)                                                            aaCCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCt                                                                                 <  2:156032/141‑1 (MQ=32)                                                                       aGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCa                                                                      >  1:205800/1‑141 (MQ=32)                                                                           cGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACa                                                                  <  1:208113/141‑1 (MQ=32)                                                                                  tgatgaACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGAcc                                                           >  1:341572/1‑140 (MQ=17)                                                                                          gTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGACACAACAGTTTACAGCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTg                                                   >  1:170544/1‑141 (MQ=11)                                                                                            ttACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACCTCCTTGTTAAATTGTTTCTATCTGAAATAGTTCATACAGAAGACTCCTTTTAGtt                                                 >  2:207319/1‑141 (MQ=12)                                                                                                    cGTTTCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATtat                                         <  2:302329/141‑1 (MQ=17)                                                                                                    cGTTCCCTGAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATtat                                         <  2:302431/141‑1 (MQ=17)                                                                                                          cTTAATATTCCAGATATATCACGATAACTCAATGTATATCTTAGATAGCAGCCAACGGCTACAGTGATAACATCCTTGTCAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACtata                                   <  1:261740/141‑1 (MQ=12)                                                                                                               tttgtCAGATATATCACGATAGCTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTc                              <  2:256962/137‑1 (MQ=255)                                                                                                                   tCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCaaat                          >  1:311228/1‑139 (MQ=21)                                                                                                                   tCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACt                          >  1:143815/1‑141 (MQ=35)                                                                                                                   tCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTCCATACAGAAGACTCCTTTTTGTTAAAATTATACTCTAAATTCAACt                          >  1:164453/1‑141 (MQ=21)                                                                                                                       atatatCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAATGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTGAAAATTATACTATAAATTCAACTTTGc                      >  1:49910/1‑141 (MQ=25)                                                                                                                          tatCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGCATACAGTGATAACATCCTTGTTAAATTGCTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTCCaaa                   >  2:172205/1‑140 (MQ=255)                                                                                                                             cACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGa                >  1:92812/1‑141 (MQ=35)                                                                                                                                 aTAACTCAATGTATTTCTTAGATAGTAGCCAACGGCGACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCg            <  2:98122/141‑1 (MQ=25)                                                                                                                                   agcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGCTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGta          <  2:1101/139‑1 (MQ=255)                                                                                                                                     cTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGtatt        >  1:324118/1‑141 (MQ=40)                                                                                                                                      tCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattt       >  1:83529/1‑140 (MQ=16)                                                                                                                                      tCAATGCATATCTTAGATAGTAGCCAAAGGCTAAAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGAATCCTTTTTGTTAAAATTATATTATAAATTCAACTTTTCAGCGGCACCGtattt       >  1:85105/1‑140 (MQ=11)                                                                                                                                       cAATGCATATTTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatttt      <  2:85732/141‑3 (MQ=255)                                                                                                                                       cAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatttt      >  1:348638/1‑139 (MQ=16)                                                                                                                                       cAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtatttt      >  1:348519/1‑139 (MQ=255)                                                                                                                                        aaTGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGCTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATg     >  1:318484/1‑141 (MQ=255)                                                                                                                                           gTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGaa  >  1:236359/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                            TAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAA  >  CP000730/36340‑36618

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑