Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	36,413	C→T	9.5%	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	9.5%	114.8 / 2.7	51	V47I (GTC→ATC)	tpn	IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base C (22/24);  new base T (3/2);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 6.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

CACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGT  >  CP000730/36278‑36547                                                                                                                                        |                                                                                                                                       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)                                             ttcgcaATGCGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGatata                                                                                       <  1:83435/137‑1 (MQ=255)                                             tcatcaATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGatata                                                                                       >  1:59382/1‑141 (MQ=255)                                                tcaATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAAAGATTAAAGCTCGCGCTCTTAATATTTCAGATATATCa                                                                                    >  1:406835/1‑141 (MQ=11)                                                   aTACGGCAGTTGTAATAAGCTTTTTTATGCTTGTTCTTCCAAATTTGGTACAAAATTGGGGCATATTCTTGAACCCGACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGa                                                                                 <  2:11958/141‑1 (MQ=14)                                                     aCGCCATTTGTAATAAGCCTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCTTATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACTTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATa                                                                               <  2:268284/141‑1 (MQ=11)                                                      cGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATaa                                                                              >  1:345551/1‑141 (MQ=40)                                                        ccATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGatatacccccagagcc                                                                            >  2:249490/1‑130 (MQ=11)                                                        ccATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCATGATAACt                                                                            >  2:368227/1‑141 (MQ=255)                                                        ccATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAAcc                                                                            >  2:66669/1‑140 (MQ=255)                                                         cATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTc                                                                           >  1:188629/1‑141 (MQ=40)                                                           tttGTAATAAGCTTTTTTAGGCTTTTGCTTGCAAATGTGATACGAAATTGGGGCATATTCTTGAACCCAACGGGAGACCGATGAATGATGAACGGGTTCACCAAGTTCCCTTAATATTTCAGCTAAATCagggatacacaa                                                                         >  2:231197/1‑130 (MQ=14)                                                            ttGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAAt                                                                        <  1:372056/141‑1 (MQ=40)                                                             tGTAAGAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATCCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATg                                                                       <  1:439835/141‑1 (MQ=255)                                                                 ataaGCTTTTTCATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCCATGtatt                                                                   >  2:332872/1‑140 (MQ=255)                                                                    aGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCt                                                                <  2:345551/141‑1 (MQ=38)                                                                             aTGCTTTTTCTTCCACATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGAtagta                                                       >  1:342785/1‑141 (MQ=25)                                                                              tGCTTTTTCTCCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTCTGGAACTGGTCCTTAATATTTCAGATATATCACGATAACTCAATGTATATTTTAGAtagtag                                                      >  1:335742/1‑141 (MQ=11)                                                                                     tcttcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATCGTAGCCAACgg                                               >  1:83020/1‑141 (MQ=25)                                                                                       ttcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCCGATATATCACGATAACTCAATGTATATCTTAGATAGTAGccgttggct                                             <  1:66669/141‑8 (MQ=255)                                                                                          taaaTTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACa                                          >  2:180122/2‑141 (MQ=21)                                                                                           aaaTTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAg                                         >  1:114869/1‑141 (MQ=34)                                                                                            aaTTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGt                                        <  2:112489/141‑1 (MQ=35)                                                                                             aTTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGta                                       >  1:83901/1‑140 (MQ=25)                                                                                              tttGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGa                                      <  2:15677/141‑1 (MQ=34)                                                                                                  aTACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAAc                                  <  2:250608/141‑1 (MQ=35)                                                                                                       aaaGTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCt                             <  1:359524/141‑1 (MQ=17)                                                                                                          ttGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGt                          <  2:423593/141‑1 (MQ=32)                                                                                                             gggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTaa                       >  1:384228/1‑141 (MQ=32)                                                                                                              ggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCACCGGCTACAGTGATAACCTCCTTGttcca                      >  2:200829/1‑138 (MQ=12)                                                                                                                    ttCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTGGTTAAATTGttt                >  1:144317/1‑141 (MQ=17)                                                                                                                     tCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTta               <  1:155169/141‑1 (MQ=32)                                                                                                                       ttGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCTAACGGCTACAGTGATAACATCCTTGTTAAATTGTTtata             <  1:12353/141‑1 (MQ=17)                                                                                                                       ttGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTtata             <  1:178699/141‑1 (MQ=32)                                                                                                                       ttGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTtata             <  2:330927/141‑1 (MQ=32)                                                                                                                           aCCCAACTGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTACTATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTg         <  1:152274/141‑1 (MQ=17)                                                                                                                            cccAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTCAAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGa        >  1:13805/1‑141 (MQ=17)                                                                                                                              cAACGGTAGACCGTTGAATGATGAACGTTTACCCCCCGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGaaa      <  1:85203/141‑1 (MQ=17)                                                                                                                                aCGGGAGACCGTTGAAGGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATa    <  2:182092/141‑1 (MQ=17)                                                                                                                                  ggtctaCCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGt  >  1:229193/6‑141 (MQ=17)                                                                                                                                        |                                                                                                                                       CACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGT  >  CP000730/36278‑36547

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: ‑