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%	140.1 / NA	44	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 (23/21);  total (23/21)

GTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAAC  >  NC_000913/1651420‑1651666                                                                                                                      |                                                                                                                                  gTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACt                                                                                                              <  1:1823600/139‑1 (MQ=37)      aGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGct                                                                                                         <  2:586213/139‑1 (MQ=255)             taACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCtgt                                                                                                  >  2:518380/1‑139 (MQ=255)                     ggCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACg                                                                                          >  2:1016748/1‑139 (MQ=255)                     ggCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACg                                                                                          >  2:705151/1‑139 (MQ=255)                                    cgcTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGaa                                                                                                                >  2:1416323/1‑102 (MQ=255)                                    cgcTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGaa                                                                                                                <  1:1416323/102‑1 (MQ=38)                                    cacTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTg                                                                              <  2:133461/134‑1 (MQ=255)                                    cacTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTg                                                                              >  1:133461/3‑136 (MQ=255)                                        gggTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGtttt                                                                       >  1:1667913/1‑139 (MQ=255)                                             aTCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACt                                                                  <  1:518380/139‑1 (MQ=255)                                              tcgctcgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGa                                                                    >  2:383842/1‑136 (MQ=255)                                              tcgctcgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGa                                                                    <  1:383842/136‑1 (MQ=255)                                                      cACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAAc                                                         <  2:1667913/139‑1 (MQ=255)                                                                   gCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCctcctc                                            >  1:540417/1‑139 (MQ=255)                                                                    cGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGa                                                                    <  1:1421344/114‑1 (MQ=255)                                                                    cGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGa                                                                    >  2:1421344/1‑114 (MQ=255)                                                                     ggCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACg                                                                                                           <  1:1716910/74‑1 (MQ=255)                                                                     ggCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACg                                                                                                           >  2:1716910/1‑74 (MQ=255)                                                                     ggCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTg                                                                              >  1:940356/1‑103 (MQ=255)                                                                     ggCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTg                                                                              <  2:940356/103‑1 (MQ=255)                                                                        aGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACg                                         >  2:644757/1‑137 (MQ=255)                                                                        aGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACg                                         <  1:644757/137‑1 (MQ=255)                                                                          cGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGctcct                                                                                                      <  1:1202952/74‑1 (MQ=255)                                                                          cGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGctcct                                                                                                      >  2:1202952/1‑74 (MQ=255)                                                                                       ggTTAAGTGATACCAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTg                        >  1:1465942/1‑139 (MQ=255)                                                                                       ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTAc                                                                                           <  1:1675124/72‑1 (MQ=255)                                                                                       ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTAc                                                                                           >  2:1675124/1‑72 (MQ=255)                                                                                            aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAAt                                                                                      >  1:1598175/1‑72 (MQ=255)                                                                                            aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAAt                                                                                      <  2:1598175/72‑1 (MQ=255)                                                                                            aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATaaaaa                                                                                 <  2:456455/77‑1 (MQ=255)                                                                                            aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATaaaaa                                                                                 >  1:456455/1‑77 (MQ=255)                                                                                            aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGt                      >  2:1345503/1‑136 (MQ=255)                                                                                            aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGt                      <  1:1345503/136‑1 (MQ=255)                                                                                               gATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGcc                >  1:1042032/1‑139 (MQ=255)                                                                                                    cAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACa           <  2:540417/139‑1 (MQ=255)                                                                                                       aTGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACg                                                                                                           <  2:1605707/40‑1 (MQ=255)                                                                                                       aTGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACg                                                                                                           >  1:1605707/1‑40 (MQ=21)                                                                                                       aTGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGa        >  1:685094/1‑139 (MQ=255)                                                                                                       aTGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGa        >  2:1104912/1‑139 (MQ=255)                                                                                                         gTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACg                                         >  1:534797/1‑104 (MQ=255)                                                                                                         gTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACg                                         <  2:534797/104‑1 (MQ=255)                                                                                                             ggAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAAc  <  2:1463634/139‑1 (MQ=255)                                                                                                             ggAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAAc  <  2:1042032/139‑1 (MQ=255)                                                                                                                      |                                                                                                                                  GTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAAC  >  NC_000913/1651420‑1651666

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑