Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,647,558	T→C	T27A (ACG→GCG)	ydfX ←	Qin prophage; uncharacterized protein YdfX

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,647,558	0	T	C	100.0%	167.3 / NA	45	T27A (ACG→GCG)	ydfX	Qin prophage; uncharacterized protein YdfX
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (29/16);  total (29/16)

TCCAGCGTTCAAATATCTTCACTCGATTAACGCCAAGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGTCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAACCGCCCCGCCCGCTTCGTCTTACGATATTCATCATAAACTTTGGGA  >  NC_000913/1647423‑1647689                                                                                                                                        |                                                                                                                                    tCCAGCGTTCAAATATCTTCACTCGATTAACGCCAAGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCgccgcc                                                                                                                                 <  2:1353121/140‑1 (MQ=255)  ccAGCGTTCAAATATCTTCACTCGATTAACGCCAAGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCt                                                                                                                                <  1:27730/140‑1 (MQ=255)       gTTCAAATATCTTCACTCGATTAACGCCAAGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTcc                                                                                                                           >  1:609091/1‑140 (MQ=255)        ttCAAATATCTTCACTCGATTAACGCCAAGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTcc                                                                                                                           <  1:1195850/139‑1 (MQ=255)        ttCAAATATCTTCACTCGATTAACGCCAAGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTcc                                                                                                                           >  2:1195850/1‑139 (MQ=255)             atatCTTCACTCGATTAACGCCAAGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTg                                                                                                                               >  1:711872/1‑130 (MQ=255)             atatCTTCACTCGATTAACGCCAAGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTg                                                                                                                               <  2:711872/130‑1 (MQ=255)                   tCACTCGATTAACGCCAAGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCt                                                                                                               <  1:1421209/140‑1 (MQ=255)                     aCTCGATTAACGCCAAGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTgg                                                                                                             <  1:309092/140‑1 (MQ=255)                     aCTCGATTAACGCCAAGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTgg                                                                                                             <  2:609091/140‑1 (MQ=255)                       tCGATTAACGCCAAGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTc                                                                                                           >  1:24013/1‑140 (MQ=255)                          aTTAACGCCAAGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGAc                                                                                                        >  2:990311/1‑140 (MQ=255)                               cGCCAAGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATc                                                                                                   <  1:990311/140‑1 (MQ=255)                                    aGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGAc                                                                                                        >  2:850691/1‑130 (MQ=255)                                    aGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGAc                                                                                                        <  1:850691/130‑1 (MQ=255)                                     gcgcTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCa                                                                                                 >  1:1130166/1‑136 (MQ=255)                                     gcgcTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCa                                                                                             >  1:1037275/1‑140 (MQ=255)                                     gcgcTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTGTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCa                                                                                             >  1:1241993/1‑140 (MQ=255)                                     gcgcTCGCTGATCAATCGCGCCACCTTCACATGTGACACGCTGAACATCGATGTTCGGGCCCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCa                                                                                                 <  2:1130166/136‑1 (MQ=255)                                            ctGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGTGCTCTTTCAAAGCCCAGAATGCTTCGGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCagag                                                                                      <  1:450570/140‑1 (MQ=255)                                                     cgcgCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCagag                                                                                      <  2:72070/131‑1 (MQ=255)                                                     cgcgCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCagag                                                                                      >  1:1292948/1‑131 (MQ=255)                                                     cgcgCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCagag                                                                                      <  2:1292948/131‑1 (MQ=255)                                                     cgcgCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCagag                                                                                      >  1:72070/1‑131 (MQ=255)                                                     cgcgCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAg                                                                             >  1:881140/1‑140 (MQ=255)                                                       cgcCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGc                                                                            <  1:571321/139‑1 (MQ=255)                                                       cgcCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGc                                                                            >  2:571321/1‑139 (MQ=255)                                                         ccACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTg                                                                         >  1:35155/1‑140 (MQ=255)                                                                 atatGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAg                                                                 >  2:903891/1‑140 (MQ=255)                                                                   atGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTg                                                               <  1:903891/140‑1 (MQ=255)                                                                     gtgACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGAt                                                             <  2:1037275/140‑1 (MQ=255)                                                                       gACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGAttt                                                           >  1:3177/1‑140 (MQ=255)                                                                              tGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGt                                                    >  1:866748/1‑140 (MQ=255)                                                                                    tCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAAcc                                              >  2:378542/1‑140 (MQ=255)                                                                                     cGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAAccg                                             >  2:743841/1‑140 (MQ=255)                                                                                       aTGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAAccgcc                                           >  1:1333466/1‑140 (MQ=255)                                                                                          ttCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAAccgccccg                                        >  1:1126314/1‑140 (MQ=255)                                                                                                cgcTCTTTCAAACCCCAGAATGCTTCAGTAATAAATACCCCCCCCTGCCCCTGTGTCATCCCTGGTCGATTTACCCAGGCACCCAGACCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAACCGCCCCGCCCGCt                                  <  2:1241993/140‑1 (MQ=255)                                                                                                 gcTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAACCGCCCCGCCCGCtt                                 >  2:1209750/1‑140 (MQ=255)                                                                                                  ctctTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAACCGCCCCGCCCGCTTc                                >  2:1285013/1‑140 (MQ=255)                                                                                                  ctctTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAACCGCCCCGCCCGCTTc                                >  2:473715/1‑140 (MQ=255)                                                                                                     tttCAAAGCCCAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAACCGCCCCGCCCGCTTCGTc                             <  1:1285013/140‑1 (MQ=255)                                                                                                      ttCAAAGCCAAAAGTGCTAGATTGATAAATAACGCCCCCTGCACCTGTGTCATTCCTGCACACCATACCCGCAACACCAGCGCCTGAAGCACCTTTTCGGGTGTGATTTTCATTTTTCAACCGCCCCGCCCGCTTCGTCt                            <  2:289250/140‑1 (MQ=255)                                                                                                             cccAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAACCGCCCCGCCCGCTTCGTCTTACGata                     >  2:802302/1‑140 (MQ=255)                                                                                                             cccAGAATGCTTCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAACCGCCCCGCCCGCTTCGTCTTACGata                     >  1:976843/1‑140 (MQ=255)                                                                                                                       ttCAGTGATTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAACCGCCCCGCCCGCTTCGTCTTACGATATTCATCATaa           >  1:560186/1‑140 (MQ=255)                                                                                                                            tGATTAATACCCCCGCCTGCTCCTGTGTCATCCCTGGTCGACATATCCAGGCACCCAGACCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAACCGCCCCGCCCGCTTCGTCTTACGATATTCATCATAAACttt      <  2:35155/140‑1 (MQ=255)                                                                                                                              aTTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAACCGCCCCGCCCGCTTCGTCTTACGATATTCATCATAAACTTTgg    >  1:294199/1‑140 (MQ=255)                                                                                                                              aTTAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAACCGCCCCGCCCGCTTCGTCTTACGATATTCATCATAAACTTTgg    >  1:272850/1‑140 (MQ=255)                                                                                                                                tAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAACCGCCCCGCCCGCTTCGTCTTACGATATTCATCATAAACTTTGGGa  <  2:3177/140‑1 (MQ=255)                                                                                                                                tAATATCGCCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAACCGCCCCGCCCGCTTCGTCTTACGATATTCATCATAAACTTTGGGa  <  1:802302/140‑1 (MQ=255)                                                                                                                                        |                                                                                                                                    TCCAGCGTTCAAATATCTTCACTCGATTAACGCCAAGCGCTCGCTGATCAATCGCGCCACCTTCATATGTGACACGCTGAACATCGATGTTCGGGCGCTCTTTCAAAGCCCAGAATGCTTCAGTGATTAATATCGTCGCCTGCTCCTGTGTCATTCCTGGTCGACATATCCAGGCATCCAGAGCCTCACGAGCCTGTTCAGGAGTGATTTTCATTGTTCAACCGCCCCGCCCGCTTCGTCTTACGATATTCATCATAAACTTTGGGA  >  NC_000913/1647423‑1647689

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑