Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,187,415	G→A	*302* (TAG→TAA)	insD1 →	IS2 transposase TnpB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,187,415	0	G	A	100.0%	145.6 / NA	45	*302* (TAG→TAA)	insD1	IS2 transposase TnpB
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (29/16);  total (29/16)

TCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCC  >  NC_000913/3187300‑3187543                                                                                                                    |                                                                                                                                 tCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCAtt                                                                                                           <  2:452026/139‑1 (MQ=255)                  tGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTa                                                                                          >  1:736192/1‑139 (MQ=255)                  tGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTa                                                                                          <  1:667930/139‑1 (MQ=255)                  tGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTa                                                                                          >  1:409999/1‑139 (MQ=255)                         cGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGtt                                                                                   >  1:221989/1‑139 (MQ=255)                            aTAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGaa                                                                                <  2:409999/139‑1 (MQ=255)                            aTAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGaa                                                                                <  1:629846/139‑1 (MQ=255)                                tGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTca                                                                            >  2:1061769/1‑139 (MQ=255)                                  cgcTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTcaac                                                                          <  2:1278141/139‑1 (MQ=255)                                        gTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGAt                                                                    >  2:11583/1‑139 (MQ=255)                                               ctcgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCg                                                             <  2:445142/139‑1 (MQ=255)                                                                 gCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGaaa                                           >  2:103149/1‑139 (MQ=255)                                                                        cGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTaa                                    >  1:1349865/1‑139 (MQ=255)                                                                        cGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTaa                                    >  1:536119/1‑139 (MQ=255)                                                                        cGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTaa                                    >  1:558901/1‑139 (MQ=255)                                                                                     ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTa                                                                                                                   <  1:180861/47‑1 (MQ=255)                                                                                     ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTa                                                                                                                   >  2:180861/1‑47 (MQ=255)                                                                                     ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGtt                                                                                                       <  2:1224845/59‑1 (MQ=255)                                                                                     ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGtt                                                                                                       >  1:1224845/1‑59 (MQ=255)                                                                                     ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAAttt                       >  2:887220/1‑139 (MQ=255)                                                                                     ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAAttt                       >  2:328210/1‑139 (MQ=255)                                                                                     ggTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAAttt                       >  1:227455/1‑139 (MQ=255)                                                                                      gTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGa                                             >  1:603491/1‑116 (MQ=255)                                                                                      gTTAAGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGa                                             <  2:603491/116‑1 (MQ=255)                                                                                          aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTa                                                                                                                   >  2:638357/1‑42 (MQ=255)                                                                                          aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTa                                                                                                                   <  1:638357/42‑1 (MQ=255)                                                                                          aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCg                                                             <  2:920897/96‑1 (MQ=255)                                                                                          aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCg                                                             >  1:920897/1‑96 (MQ=255)                                                                                          aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAAc                  >  1:241840/1‑139 (MQ=255)                                                                                          aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAAc                  >  1:238968/1‑139 (MQ=255)                                                                                          aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAAc                  >  1:1271898/1‑139 (MQ=255)                                                                                          aGTGATAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAAc                  >  2:1118554/1‑139 (MQ=255)                                                                                               tAACAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATg             <  2:1271898/139‑1 (MQ=255)                                                                                                aaCAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGATTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAATTGATgg            >  2:1135857/1‑139 (MQ=255)                                                                                                 aCAGATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGc           >  1:834298/1‑139 (MQ=255)                                                                                                    gATGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCaa        >  1:67916/1‑139 (MQ=255)                                                                                                     aTGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCg                                                             <  1:1115982/85‑1 (MQ=255)                                                                                                     aTGTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCg                                                             >  2:1115982/1‑85 (MQ=255)                                                                                                       gTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGaa                                                                                >  1:1293180/1‑64 (MQ=255)                                                                                                       gTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGaa                                                                                <  2:438660/64‑1 (MQ=255)                                                                                                       gTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGaa                                                                                <  2:1293180/64‑1 (MQ=255)                                                                                                       gTCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGaa                                                                                >  1:438660/1‑64 (MQ=255)                                                                                                        tCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTAc    <  2:221989/139‑1 (MQ=255)                                                                                                        tCTGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTAc    >  2:189032/1‑139 (MQ=255)                                                                                                          tGGAAATATAAGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTAccc  >  2:898967/1‑139 (MQ=255)                                                                                                                    |                                                                                                                                 TCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGTTATCATCATTGGTTGTGCGTCAGCTTATGCCGTTGAATTCAACAAAGATTTAATCGAAGCCGAAGATCGTGAAAACGTTAACCTTTCCCAATTTGAAACTGATGGCCAATTACCC  >  NC_000913/3187300‑3187543

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑