Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	36,501	G→A	14.3%	A17A (GCC→GCT)	tpn ←	IS431mec transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	36,501	0	G	A	14.3%	101.1 / 8.6	54	A17A (GCC→GCT)	tpn	IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base G (21/25);  new base A (4/4);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-01

TCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACA  >  CP000730/36362‑36635                                                                                                                                            |                                                                                                                                       tcttcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACgg                                                                                                                                       <  2:207615/141‑1 (MQ=35)  cttcCATATTTGATACAAAATTGGGGCATATTCTTGAACCCACCGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTCATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGc                                                                                                                                      <  2:108500/141‑1 (MQ=255)   ttcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAATGGCt                                                                                                                                     >  1:291155/1‑141 (MQ=25)    tcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTa                                                                                                                                    <  2:113635/141‑1 (MQ=35)        aaTTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGt                                                                                                                                >  1:118378/1‑141 (MQ=35)            tGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATa                                                                                                                            >  1:323081/1‑141 (MQ=35)                        ggggCATATTCTTGAACCCAACGGTAGACCGTTGACTGATGAACGATTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGAAGGAAGCCAACGGCTACAGTGATAACATCCTCGTTa                                                                                                                >  1:172309/1‑141 (MQ=11)                        ggggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACCGATCATTTATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTa                                                                                                                >  1:108224/1‑141 (MQ=11)                              tatTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGt                                                                                                          <  1:125598/141‑1 (MQ=32)                               atTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTCCCCTTAATATGTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGtt                                                                                                         <  2:217931/141‑1 (MQ=17)                                 tCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTta                                                                                                       <  1:13723/141‑1 (MQ=32)                                    tGAACCCAACGGTAGACCGTTGTATTATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTatat                                                                                                    <  1:116132/141‑1 (MQ=17)                                      aaCCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCt                                                                                                  <  2:102456/141‑1 (MQ=32)                                      aaCCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCt                                                                                                  <  2:237456/141‑1 (MQ=32)                                       aCCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTg                                                                                                 <  2:4894/141‑1 (MQ=32)                                           aaCGGTAGACCGTTGAATGATGAACGTTTACACCCCGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAAt                                                                                             <  2:172309/141‑1 (MQ=17)                                                       ttGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTAATAAaga                                                                                 >  2:5408/1‑141 (MQ=17)                                                         gAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACagaag                                                                               >  1:7897/1‑141 (MQ=32)                                                           atgatgAACGTTTACACCTCGTTCCATTAATATTTCACTTATATCACGATAACTCAATGTATAGCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTCAGATCATAAATAGTTCATACAGAAGAc                                                                             <  1:161215/141‑1 (MQ=11)                                                                    gTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTg                                                                    <  2:57195/141‑1 (MQ=32)                                                                       tACGCCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTa                                                                 <  2:282617/141‑1 (MQ=17)                                                                            cacGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAAtt                                                            >  1:162333/1‑141 (MQ=32)                                                                                  cccTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACta                                                      <  2:7897/141‑1 (MQ=32)                                                                                         tacttCAGATATATCACGATAACTCAATGCATATCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTc                                               >  1:304285/4‑141 (MQ=2)                                                                                             tctgATAGATCACGATAGAACAACGCATATCTTAGATAGGATCCAACGGCTACAGTTATAACAACCTTTTTAAATTGTGTATATCTGAAATAGTTCATACAGACGACTCCTTTTTGTTAAAAATATATTATAAATTCAACt                                           <  2:271922/138‑1 (MQ=1)                                                                                               aGATATATCACGATAGCTCAATGGATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAACTTCAACttt                                         <  2:214127/141‑1 (MQ=255)                                                                                                   atatCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGGTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCaa                                     >  1:210175/1‑141 (MQ=25)                                                                                                    tatCACGATAGCTCAATGAATATATTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTAATACAGAAGCCTCCTTTTTATTCAAATTATGTTATAAATTCAACTTTGCaag                                    >  1:130499/1‑140 (MQ=11)                                                                                                     atCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACa                                   >  1:97397/1‑141 (MQ=35)                                                                                                     atCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACa                                   >  2:272158/1‑141 (MQ=35)                                                                                                      acacggcaaCTCAATGCATATCTTAGATAGTAGCCAACAGCTACAGTGACAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAg                                  <  1:183352/134‑1 (MQ=1)                                                                                                          ggtagcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTGAAAATTATATTATAAATTCAACTTTGCAACAGAAcc                              <  1:47459/136‑1 (MQ=11)                                                                                                            tagcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGt                            >  2:154003/4‑141 (MQ=2)                                                                                                            acgcttaaTGCATATCTTAGATAGTAGCCAACGGCTACAGTGAAAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGt                            <  2:186749/135‑1 (MQ=11)                                                                                                              gcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtat                          >  1:320322/2‑141 (MQ=12)                                                                                                              gcTCAATGCATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtat                          >  2:95185/2‑141 (MQ=12)                                                                                                                gcaattcatatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaa                        <  2:334111/134‑7 (MQ=1)                                                                                                                 cAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGtattat                       >  1:316680/1‑141 (MQ=255)                                                                                                                 cAATGCATATCGTAGATAGTAGCCAACGGCTATAGTGATAACATACTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGCCTCTGTTTTGTTAAAATTATATTATTTATGCAACTTTGCAACAGAACCGtatttt                       <  2:56836/141‑3 (MQ=11)                                                                                                                   atacaaatCTTAGATAGTAGCCAAAGGCTACAGTGATAACATCCTGTTTAAATTGTTTATATCTGAAATATTTCAAACAGAAGACTCCTTTTTGTTAAAATTATATTAGAAATTCAACTTTGCAACAGAACCGtagcttat                     <  2:132975/135‑7 (MQ=11)                                                                                                                    tGTATATCTTAGATAGTAGCCACCGGCTACAGTGATAACATCCTTGTTAAAGTGTTTATATCTGAAATAGTTCATACAGACGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCCACAGAACGGTCTTATGGa                    >  2:51190/1‑141 (MQ=14)                                                                                                                     gcatatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatga                   <  1:168875/139‑7 (MQ=255)                                                                                                                     gcatatCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAAcctcatttactat                   <  2:149216/139‑12 (MQ=11)                                                                                                                     gcatatCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAAcctcatttactat                   <  2:231688/139‑12 (MQ=11)                                                                                                                      catatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaactgtat                  <  1:55093/140‑13 (MQ=11)                                                                                                                      catatCTTAGATAGTAGCCAACAGCTACCGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATCAATTCAACTTTGCACCCGAAcctcatttactata                  >  2:62505/2‑129 (MQ=11)                                                                                                                       atatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCATTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAAcctcctaactgtatt                 >  1:32516/1‑128 (MQ=11)                                                                                                                        tatCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagta                >  1:225113/1‑132 (MQ=255)                                                                                                                        tatCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAAcctcatttactatatg                >  1:90416/1‑127 (MQ=11)                                                                                                                         atCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtaa               >  1:57724/1‑131 (MQ=255)                                                                                                                         atCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTg                                        >  1:171788/1‑116 (MQ=17)                                                                                                                         atCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTg                                        <  2:171788/116‑1 (MQ=18)                                                                                                                           cTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacac             >  1:36129/1‑129 (MQ=11)                                                                                                                             tAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGtattttatgagtacactc           <  1:169770/141‑15 (MQ=11)                                                                                                                                      gCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACa  <  2:58527/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                       TCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGTATTATGGAATAGAGATGTTGGTAACA  >  CP000730/36362‑36635

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: ‑