Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,645,063	G→A	intergenic (‑161/+56)	rem ← / ← hokD	Qin prophage, uncharacterized protein/Qin prophage, small toxic polypeptide

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,645,063	0	G	A	100.0%	114.4 / NA	36	intergenic (‑161/+56)	rem/hokD	Qin prophage, uncharacterized protein/Qin prophage, small toxic polypeptide
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (17/19);  total (17/19)

CCCCTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGCGACCTCCGTCTGGCCGGTTCGGATTCGTACCTCGCAGAGGTCTT  >  NC_000913/1644929‑1645195                                                                                                                                       |                                                                                                                                     ccccTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGa                                                                                                                                  >  2:178469/1‑139 (MQ=255)  cccTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAg                                                                                                                                 >  1:894265/1‑139 (MQ=255)  cccTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGAGTTAAGTGCGGGTGCATTGAg                                                                                                                                 <  2:365630/139‑1 (MQ=255)            gACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGAtgcctgcc                                                                                                                       >  1:312305/1‑139 (MQ=255)                aTCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACAt                                                                                                                   <  2:312305/139‑1 (MQ=255)                  cccTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCa                                                                                                                 <  2:894265/139‑1 (MQ=255)                               gcgcgcTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAggg                                                                                                    >  2:654947/1‑139 (MQ=255)                               gcgcgcTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAggg                                                                                                    >  2:1037495/1‑139 (MQ=255)                               gcgcgcTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAggg                                                                                                    >  1:487678/1‑139 (MQ=255)                                        ttAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTccc                                                                                           <  1:31415/139‑1 (MQ=255)                                             tATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCccgcc                                                                                      <  2:345258/139‑1 (MQ=255)                                               tttttGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGAtg                                                                                                                             >  2:429927/1‑98 (MQ=255)                                               tttttGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGAtg                                                                                                                             <  1:429927/98‑1 (MQ=255)                                                ttttGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCggg                                                                                   <  1:432113/139‑1 (MQ=255)                                                 tttGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGa                                                                                                       <  2:1030807/118‑1 (MQ=255)                                                 tttGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGa                                                                                                       >  1:1030807/1‑118 (MQ=255)                                                 tttGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGt                                                                                  >  1:469012/1‑139 (MQ=255)                                                                     gTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGAtg                                                                                                                             >  2:950121/1‑76 (MQ=255)                                                                     gTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGAtg                                                                                                                             <  1:950121/76‑1 (MQ=255)                                                                     gTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGGCACATCAGAGGTGGCGa                                                                                                       <  1:672335/98‑1 (MQ=255)                                                                     gTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGa                                                                                                       >  2:672335/1‑98 (MQ=255)                                                                     gTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCgg                                                                                    <  2:1067286/117‑1 (MQ=255)                                                                     gTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCgg                                                                                    >  1:1067286/1‑117 (MQ=255)                                                                     gTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGt                                                              >  2:770058/1‑139 (MQ=255)                                                                         aGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGc                                                          <  1:654947/139‑1 (MQ=255)                                                                                cAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTctct                                                                              >  1:43480/1‑112 (MQ=255)                                                                                cAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTctct                                                                              <  2:43480/112‑1 (MQ=255)                                                                                cAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAg                                                   >  2:396514/1‑139 (MQ=255)                                                                                                   aacaaaaacCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGCGACCTCCGTCTGGc                                <  1:1036641/139‑1 (MQ=255)                                                                                                        aaacCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTctct                                                                              <  2:380496/88‑1 (MQ=255)                                                                                                        aaacCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTctct                                                                              >  1:380496/1‑88 (MQ=255)                                                                                                        aaacCCGCCGAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGCGACCTCCGTCTGGCCGGtt                           <  1:178469/139‑1 (MQ=255)                                                                                                               ccgAAGCGGGTTAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGCGACCTCCGTCTGGCCGGTTCGGATTc                    <  1:1037495/139‑1 (MQ=255)                                                                                                                         ttAAGTGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGCGACCTCCGTCTGGCCGGTTCGGATTCGTACCTCGCa          >  2:599597/1‑139 (MQ=255)                                                                                                                              tGCGGGTGCATTGAGGACGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGCGACCTCCGTCTGGCCGGTTCGGATTCGTACCTCGCAGAGGt     <  1:661855/139‑1 (MQ=255)                                                                                                                                 gggTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGCGACCTCCGTCTGGCCGGTTCGGATTCGTACCTCGCAGAGGTCtt  <  2:487678/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                                     CCCCTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGCGACCTCCGTCTGGCCGGTTCGGATTCGTACCTCGCAGAGGTCTT  >  NC_000913/1644929‑1645195

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑