Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,769,648	(C)6→7	intergenic (+162/‑55)	yfjQ → / → yfjR	CP4‑57 prophage; protein YfjQ/CP4‑57 prophage; putative DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,769,642	1	.	C	100.0%	134.6 / NA	38	intergenic (+156/‑61)	yfjQ/yfjR	CP4‑57 prophage; protein YfjQ/CP4‑57 prophage; putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (23/15);  total (23/15)

TAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGG  >  NC_000913/2769509‑2769776                                                                                                                                        |                                                                                                                                       tAATATCGGACCCCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccccc                                                                                                                                  <  2:224671/140‑1 (MQ=255) tAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑ccccc                                                                                                                                   <  1:212748/140‑1 (MQ=255)     atCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑ccccc                                                                                                                                   <  1:684215/135‑1 (MQ=255)     atCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑ccccc                                                                                                                                   >  2:684215/1‑135 (MQ=255)         gACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTaa                                                                                                                           >  1:538292/1‑140 (MQ=255)         gACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTaa                                                                                                                           >  2:631287/1‑140 (MQ=255)               accTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAAt                                                                                                                     <  1:53771/140‑1 (MQ=255)                ccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATc                                                                                                                    >  2:727870/1‑140 (MQ=255)                 cTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATca                                                                                                                   >  1:107293/1‑140 (MQ=255)                            gCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTtca                                                                                                        <  1:758379/140‑1 (MQ=255)                                tgtgCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTtcagtca                                                                                                    <  1:894328/140‑1 (MQ=255)                                   gCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGtt                                                                                                 >  1:435131/1‑140 (MQ=255)                                     tCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTaa                                                                                               >  2:706175/1‑140 (MQ=255)                                       gtgtGCCTCAATCCCCCGGTTATAGCTTTTAC‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACt                                                                                             <  2:435131/140‑1 (MQ=255)                                       gtgtGCCTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACt                                                                                             <  2:538292/140‑1 (MQ=255)                                        tgtgCCTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACtt                                                                                            >  1:940610/1‑140 (MQ=255)                                            ccTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGAAATCACATCATTTTCAGTCAGTTAACTTTCCt                                                                                        >  2:424558/1‑140 (MQ=255)                                                   cccccGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAAt                                                                                 <  1:329199/140‑1 (MQ=255)                                                              aGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGaca                                                                      <  2:415096/140‑1 (MQ=255)                                                               gCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGacac                                                                     <  1:631287/140‑1 (MQ=255)                                                                   ttAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGaa                                                                                  >  2:924625/1‑123 (MQ=255)                                                                   ttAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGaa                                                                                  <  1:924625/123‑1 (MQ=255)                                                                   ttAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGc                                                                 >  1:103384/1‑140 (MQ=255)                                                                   ttAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGc                                                                 >  1:407012/1‑140 (MQ=255)                                                                    tAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCa                                                                >  2:456558/1‑140 (MQ=255)                                                                           ccGTTACATTTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAAcgc                                                          >  2:354852/1‑140 (MQ=255)                                                                           ccGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAAcgc                                                          >  2:946662/1‑140 (MQ=255)                                                                            cGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAAcgcc                                                         >  2:511626/1‑140 (MQ=255)                                                                                       gCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCgg                                              >  1:960383/1‑140 (MQ=255)                                                                                         ttttGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCggct                                            <  2:107293/140‑1 (MQ=255)                                                                                              cAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGgctggctg                                       >  1:174240/1‑140 (MQ=255)                                                                                                   aTAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTggctgtcagg                                  <  2:174240/140‑1 (MQ=255)                                                                                                                 cTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAAt                    <  1:946662/140‑1 (MQ=255)                                                                                                                    cGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAg                 <  2:151774/140‑1 (MQ=255)                                                                                                                    cGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAg                 <  1:727870/140‑1 (MQ=255)                                                                                                                                ccTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGc     >  1:526732/1‑140 (MQ=255)                                                                                                                                  tGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCgg   <  2:459977/140‑1 (MQ=255)                                                                                                                                   gTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTGACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  2:980137/1‑140 (MQ=255)                                                                                                                                   gTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  2:594590/1‑140 (MQ=255)                                                                                                                                   gTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  2:346899/1‑140 (MQ=255)                                                                                                                                   gTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  2:962175/1‑140 (MQ=255)                                                                                                                                   gTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  1:1042778/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                       TAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAA‑CCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGG  >  NC_000913/2769509‑2769776

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑