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%	118.0 / NA	37	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 (18/19);  total (18/19)

GAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATA  >  NC_000913/1651415‑1651670                                                                                                                           |                                                                                                                                      gagGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGt                                                                                                                       <  2:1503819/139‑1 (MQ=18)         cGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACg                                                                                                               <  1:639658/139‑1 (MQ=255)                  taACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCtgt                                                                                                      >  2:1160206/1‑139 (MQ=255)                          ggCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACg                                                                                              >  2:1477961/1‑139 (MQ=255)                            cATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCa                                                                                            >  2:478907/1‑139 (MQ=255)                                      gTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTg                                                                                  <  1:478907/139‑1 (MQ=255)                                                ttATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGa                                                                        <  2:332691/139‑1 (MQ=255)                                                        cgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTAc                                                                                               >  2:1392208/1‑108 (MQ=255)                                                        cgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTAc                                                                                               <  1:1392208/108‑1 (MQ=255)                                                        cgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCaa                                                                >  1:9092/1‑139 (MQ=255)                                                          ccACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCaaaa                                                              <  1:1160206/139‑1 (MQ=255)                                                          ccACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCaaaa                                                              >  1:250512/1‑139 (MQ=255)                                                                     tCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTAc                                                                                                                >  1:438869/1‑78 (MQ=255)                                                                     tCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTAc                                                                                                                <  2:438869/78‑1 (MQ=255)                                                                         cGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTc                                                       >  1:418785/1‑131 (MQ=255)                                                                         cGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTc                                                       <  2:418785/131‑1 (MQ=255)                                                                              gCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGctc                                                                                                            >  2:278874/1‑73 (MQ=255)                                                                              gCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGctc                                                                                                            <  1:278874/73‑1 (MQ=255)                                                                               cGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGGCTATGCAAAACAGTTTcc                                                      <  2:838645/126‑1 (MQ=255)                                                                               cGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTcc                                                      >  1:838645/1‑126 (MQ=255)                                                                                            ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGa                                                                        >  2:897322/1‑95 (MQ=255)                                                                                            ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGa                                                                        >  1:1075922/1‑95 (MQ=255)                                                                                            ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGa                                                                        <  2:1075922/95‑1 (MQ=255)                                                                                            ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGa                                                                        <  1:897322/95‑1 (MQ=255)                                                                                            ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTg                            >  1:1111584/1‑139 (MQ=255)                                                                                              ttAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGt                          <  1:39029/139‑1 (MQ=255)                                                                                                 aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAg                       >  1:47839/1‑139 (MQ=255)                                                                                                  gTGATAACAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAgg                      <  1:1477961/139‑1 (MQ=255)                                                                                                       aaCAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAg                       >  2:222553/1‑133 (MQ=255)                                                                                                       aaCAGATGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAg                       <  1:222553/133‑1 (MQ=255)                                                                                                             tGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTcc                                                      >  1:810939/1‑96 (MQ=255)                                                                                                             tGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTcc                                                      <  2:810939/96‑1 (MQ=255)                                                                                                             tGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGAt           <  2:250512/139‑1 (MQ=255)                                                                                                             tGTCTGGAAATATAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGAt           >  2:426422/1‑139 (MQ=255)                                                                                                                 tGGAAATATAAGGGCAAATCCACTGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTc                                                       <  2:1107839/91‑1 (MQ=255)                                                                                                                 tGGAAATATAAGGGCAAATCCACTGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTc                                                       >  1:1107839/1‑91 (MQ=255)                                                                                                                      atatAAGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATa  <  2:1111584/139‑1 (MQ=255)                                                                                                                           |                                                                                                                                      GAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATA  >  NC_000913/1651415‑1651670

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: ‑