Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,649,041	G→A	*73* (TAG→TAA)	ydfC →	uncharacterized protein, Qin prophage

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,649,041	0	G	A	100.0%	167.6 / NA	52	*73* (TAG→TAA)	ydfC	uncharacterized protein, Qin prophage
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (26/26);  total (26/26)

CGCAGGATCTGAAATGGGCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAGTAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGATATTTCCCTGAAAAGTCAGACCATA  >  NC_000913/1648908‑1649176                                                                                                                                      |                                                                                                                                        cgcAGGATCTGAAATGGGCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCt                                                                                                                                    <  2:939069/139‑1 (MQ=255)      gATCTGAAATGGGCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATca                                                                                                                               >  1:1105751/1‑139 (MQ=255)              aTGGGCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCt                                                                                                                       >  1:117956/1‑139 (MQ=255)                 ggCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCt                                                                                                                       >  1:587662/1‑136 (MQ=255)                 ggCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCt                                                                                                                       <  2:587662/136‑1 (MQ=255)                  gCTAACGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTACGCTCTGGCGCAGGATATCACCAATGTGGAAAAAGCAGCGGCATTAAGCATTCCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGcacagg                                                                                                                   >  2:610507/1‑134 (MQ=255)                   cTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGt                                                                                                                  >  2:158575/1‑139 (MQ=255)                    tAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGtt                                                                                                                 <  2:1349352/139‑1 (MQ=255)                    tAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGtt                                                                                                                 <  1:430558/139‑1 (MQ=255)                           gCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAAtt                                                                                                          >  1:123642/1‑139 (MQ=255)                                ggCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCt                                                                                                                       <  1:1212968/121‑1 (MQ=255)                                ggCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCt                                                                                                                       >  2:1212968/1‑121 (MQ=255)                                 gCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAg                                                                                                    <  2:1105751/139‑1 (MQ=255)                                     aGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATcaac                                                                                                                             <  2:1020644/110‑1 (MQ=255)                                     aGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATcaac                                                                                                                             >  1:1020644/1‑110 (MQ=255)                                     aGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTtct                                                                                                >  2:572155/1‑139 (MQ=255)                                         ggCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCAc                                                                                            <  1:158575/139‑1 (MQ=255)                                          gCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTtaatag                                                                                                                                      <  2:1262851/96‑1 (MQ=255)                                          gCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTtaatag                                                                                                                                      >  1:1262851/1‑96 (MQ=255)                                          gCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAg                                                                                                    <  2:639395/130‑1 (MQ=255)                                          gCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAg                                                                                                    >  1:639395/1‑130 (MQ=255)                                           cTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACgg                                                                                          <  1:572155/139‑1 (MQ=255)                                                  tCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGt                                                                                   <  2:123642/139‑1 (MQ=255)                                                    tGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTgg                                                                                 <  2:1074895/139‑1 (MQ=255)                                                              ggAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGtgcgtgcg                                                                       <  2:1376627/139‑1 (MQ=255)                                                                    ggATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGac                                                                 >  2:212691/1‑139 (MQ=255)                                                                      atatCACCAATCTGGAAAAAGCAGCGGCATTAAGCAGTGCCAGAATGATTACATACCCGCGTTAATAGCGAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGAGCGTGCGCCGGacac                                                               <  1:610507/139‑1 (MQ=255)                                                                         tCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACggg                                                            >  1:397696/1‑139 (MQ=255)                                                                               aTCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAAt                                                                                                                                 <  1:770003/64‑1 (MQ=255)                                                                               aTCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAAt                                                                                                                                 >  2:770003/1‑64 (MQ=255)                                                                               aTCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATcaaca                                                                                                                            <  1:153380/69‑1 (MQ=255)                                                                               aTCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATcaaca                                                                                                                            >  2:153380/1‑69 (MQ=255)                                                                                tCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATcaa                                                                                                                              >  1:1179614/1‑66 (MQ=255)                                                                                tCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATcaa                                                                                                                              <  2:1179614/66‑1 (MQ=255)                                                                                          gcagcGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAgtgc                                                                            <  2:1386045/106‑1 (MQ=255)                                                                                          gcagcGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAgtgc                                                                            >  1:1386045/1‑106 (MQ=255)                                                                                                       gCATTGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGaaa                              <  2:397696/139‑1 (MQ=255)                                                                                                           tGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTtctc                                                                                               <  1:1072581/70‑1 (MQ=255)                                                                                                           tGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTtctc                                                                                               >  2:1072581/1‑70 (MQ=255)                                                                                                           tGCCAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGat                          >  1:823692/1‑139 (MQ=255)                                                                                                             ccAGAATGATTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGatat                        >  2:130519/1‑139 (MQ=255)                                                                                                                     aTTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGa                                <  1:358718/123‑1 (MQ=255)                                                                                                                     aTTACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGa                                >  2:358718/1‑123 (MQ=255)                                                                                                                       tACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCAc                                                                                            >  2:1264292/1‑61 (MQ=255)                                                                                                                       tACATACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCAc                                                                                            <  1:1264292/61‑1 (MQ=255)                                                                                                                           tACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCAc                                                                                            >  1:355533/1‑57 (MQ=255)                                                                                                                           tACCCGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCAc                                                                                            <  2:355533/57‑1 (MQ=255)                                                                                                                             cccGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAAtt                                                                                                          >  1:822185/1‑41 (MQ=255)                                                                                                                             cccGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAAtt                                                                                                          <  2:822185/41‑1 (MQ=255)                                                                                                                             cccGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAAtt                                                                                                          <  2:751632/41‑1 (MQ=255)                                                                                                                             cccGCGTTAATAGCTAATCAACAAAGCTAAGGTTAGTAAtt                                                                                                          >  1:751632/1‑41 (MQ=255)                                                                                                                                   ttAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGtgcgtgcg                                                                       <  2:261472/70‑1 (MQ=255)                                                                                                                                   ttAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGtgcgtgcg                                                                       >  1:261472/1‑70 (MQ=255)                                                                                                                                   ttAATAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGATATTTCCCTGAAAAGTCAGACCATa  >  2:445795/1‑139 (MQ=255)                                                                                                                                      |                                                                                                                                        CGCAGGATCTGAAATGGGCTAATGAAGCCAGGGCTAAGCAGGCTGAAAATCTGTCCGCTCTGGAGCAGGATATCACCAATCTGGAAAAAGCAGCGGCATTAAGCATTGCCAGAATGATTACATACCCGCGTTAGTAGCTAATCAACAAAGCTAAGGTTAGTAATTAAGGAGTTCTCCACGGGTGAGGTGGAGTGCGTGCGCCGGACACGGGTGCGCATCCGGAACTGACAGTTTACTGAAAGGATATTTCCCTGAAAAGTCAGACCATA  >  NC_000913/1648908‑1649176

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: ‑