Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,651,537	G→A	pseudogene (693/693 nt)	insD1 →	IS2 transposase TnpB,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,651,537	0	G	A	100.0%	183.5 / NA	57	pseudogene (693/693 nt)	insD1	IS2 transposase TnpB,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (27/30);  total (27/30)

CAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAAC  >  NC_000913/1651413‑1651666                                                                                                                             |                                                                                                                                  cAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAg                                                                                                                     <  1:822170/139‑1 (MQ=14)             aGCATTATAACGAATGGCATGCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGct                                                                                                         <  2:705280/139‑1 (MQ=255)               cATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGctcc                                                                                                       <  1:1472208/139‑1 (MQ=255)                           tGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACg                                                                                                           >  1:275577/1‑123 (MQ=255)                           tGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACg                                                                                                           <  2:275577/123‑1 (MQ=255)                           tGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTAc                                                                                           <  2:1164689/139‑1 (MQ=255)                            ggCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACg                                                                                          >  2:977862/1‑139 (MQ=255)                            ggCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACg                                                                                          <  2:3544/139‑1 (MQ=255)                              cATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGctc                                                                                                        <  2:541372/123‑1 (MQ=255)                              cATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGctc                                                                                                        >  1:541372/1‑123 (MQ=255)                                tCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAAt                                                                                      >  1:1276706/1‑139 (MQ=255)                                tCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAAt                                                                                      <  1:988382/139‑1 (MQ=255)                                        gTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTg                                                                              <  2:703834/139‑1 (MQ=255)                                             cTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTTTGGAAATATAAGGGCAAATCCAGAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGtt                                                                         <  1:238538/139‑1 (MQ=255)                                                  ttATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTGATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCGCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGa                                                                    <  2:984273/139‑1 (MQ=255)                                                  ttATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGa                                                                    <  2:1276706/139‑1 (MQ=255)                                                     tcgctcgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTa                                                                 >  1:844208/1‑139 (MQ=255)                                                            ccACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCctct                                                                                                    <  2:325298/97‑1 (MQ=255)                                                            ccACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCctct                                                                                                    >  1:325298/1‑97 (MQ=255)                                                                 ggAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGtt                                                     <  1:424908/139‑1 (MQ=255)                                                                    atatCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTcc                                                  <  1:1293119/139‑1 (MQ=255)                                                                     tatCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGt                                                                                                                   >  1:139043/1‑73 (MQ=255)                                                                     tatCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGt                                                                                                                   <  2:139043/73‑1 (MQ=255)                                                                       tCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCtgtttg                                                                                               >  1:1358092/1‑91 (MQ=255)                                                                       tCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCtgtttg                                                                                               <  2:1358092/91‑1 (MQ=255)                                                                            ggCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCAc                                          >  1:829760/1‑139 (MQ=255)                                                                             gCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACg                                         <  2:829760/139‑1 (MQ=255)                                                                             gCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACg                                         >  2:1329300/1‑139 (MQ=255)                                                                                 cGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAAt                                     <  1:902251/139‑1 (MQ=255)                                                                                 cGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAAt                                     >  1:458079/1‑139 (MQ=255)                                                                                     cTTGTAATGGGTTAAGTGATAACAGATGTCTTGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTgg                                 <  1:977862/139‑1 (MQ=255)                                                                                     cTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTgg                                 >  2:1306947/1‑139 (MQ=255)                                                                                             gggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACCCTCCTCTGTTTGTTACGCAATAAAAACTGCTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAAttt                         >  1:446198/1‑139 (MQ=255)                                                                                               gTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTATTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTgg                       >  1:977738/1‑139 (MQ=255)                                                                                                ttAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGt                      >  2:1135468/1‑139 (MQ=255)                                                                                                ttAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGt                      >  2:835561/1‑139 (MQ=255)                                                                                                   aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAAt                                                                                      >  1:935404/1‑72 (MQ=255)                                                                                                   aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAAt                                                                                      <  2:935404/72‑1 (MQ=255)                                                                                                   aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAg                   >  2:569609/1‑139 (MQ=255)                                                                                                   aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAg                   >  2:408346/1‑139 (MQ=255)                                                                                                    gTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAgg                  <  1:1306947/139‑1 (MQ=255)                                                                                                       aTAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGccc               >  1:628897/1‑139 (MQ=255)                                                                                                        tAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTg                                                                              <  1:236283/75‑1 (MQ=255)                                                                                                        tAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTg                                                                              >  2:652543/1‑75 (MQ=255)                                                                                                        tAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTg                                                                              <  1:652543/75‑1 (MQ=255)                                                                                                        tAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTg                                                                              >  2:236283/1‑75 (MQ=255)                                                                                                        tAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTc                                                   >  2:431728/1‑102 (MQ=255)                                                                                                        tAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTc                                                   <  1:431728/102‑1 (MQ=255)                                                                                                        tAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCg              >  1:704844/1‑139 (MQ=255)                                                                                                         aaCAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGa             <  2:977738/139‑1 (MQ=255)                                                                                                              aTGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGa                    <  2:627011/127‑1 (MQ=255)                                                                                                              aTGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGa                    >  1:627011/1‑127 (MQ=255)                                                                                                              aTGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGa        >  1:804103/1‑139 (MQ=255)                                                                                                                gTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGAtt      <  1:351885/139‑1 (MQ=255)                                                                                                                gTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACCCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGAtt      >  2:983296/1‑139 (MQ=255)                                                                                                                    ggAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAAc  <  1:1135468/139‑1 (MQ=255)                                                                                                                    ggAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAAc  <  2:367415/139‑1 (MQ=255)                                                                                                                             |                                                                                                                                  CAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAAC  >  NC_000913/1651413‑1651666

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑