Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,561,159	C→A	intergenic (+261/‑209)	yffL → / → yffM	CPZ‑55 prophage; uncharacterized protein YffL/CPZ‑55 prophage; uncharacterized protein YffM

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,561,159	0	C	A	100.0%	73.2 / NA	22	intergenic (+261/‑209)	yffL/yffM	CPZ‑55 prophage; uncharacterized protein YffL/CPZ‑55 prophage; uncharacterized protein YffM
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (10/12);  total (10/12)

GGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGGTAT  >  NC_000913/2561027‑2561290                                                                                                                                     |                                                                                                                                    gggTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGc                                                                                                                              <  1:140529/140‑1 (MQ=255)  ggTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGCg                                                                                                                             <  2:48162/140‑1 (MQ=255)  ggTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGCg                                                                                                                             <  2:355844/140‑1 (MQ=255)  ggTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGCg                                                                                                                             >  2:183580/1‑140 (MQ=255)    tCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGCGAg                                                                                                                           >  1:195486/1‑140 (MQ=255)                             actaTTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAAt                                                                                                  <  1:261069/140‑1 (MQ=255)                             actaTTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAAt                                                                                                  >  1:307065/1‑140 (MQ=255)                                      aaTTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAg                                                                                         >  1:393003/1‑140 (MQ=255)                                           tAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGc                                                                                    >  1:27427/1‑140 (MQ=255)                                           tAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGc                                                                                    >  1:20824/1‑140 (MQ=255)                                           tAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGc                                                                                    <  1:183580/140‑1 (MQ=255)                                                             tAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATtcact                                                                  <  2:20824/140‑1 (MQ=255)                                                               gCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATtcactca                                                                >  2:411259/1‑140 (MQ=255)                                                                     cggtcggtCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGcaca                                                          <  2:393003/140‑1 (MQ=255)                                                                                    agTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGAc                                           <  1:411259/140‑1 (MQ=255)                                                                                      tCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACca                                         >  2:12563/1‑140 (MQ=255)                                                                                       cGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACcaa                                        <  1:12563/140‑1 (MQ=255)                                                                                                        aagaaTTATTTCGCCGCCTGATAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCAtt                       >  2:3487/1‑140 (MQ=255)                                                                                                                  tCGCCGCCTGATAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATggg             <  2:195486/140‑1 (MQ=255)                                                                                                                       gccTGATAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAgcg        <  2:307065/140‑1 (MQ=255)                                                                                                                          tGATAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCgg     >  1:34675/1‑140 (MQ=255)                                                                                                                             tAGGTCGGATGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGGtat  <  2:27427/140‑1 (MQ=255)                                                                                                                                     |                                                                                                                                    GGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGGTAT  >  NC_000913/2561027‑2561290

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑