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%	134.3 / NA	39	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 (22/17);  total (22/17)

TGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGG  >  NC_000913/2769506‑2769776                                                                                                                                          |                                                                                                                                       tgttAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑ccc                                                                                                                                     >  1:65344/1‑140 (MQ=255)             acacCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTaaa                                                                                                                          >  2:821984/1‑140 (MQ=255)             acacCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTaaa                                                                                                                          >  1:223315/1‑140 (MQ=255)                 caccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTaa                                                                                                                           >  1:494267/1‑135 (MQ=255)                 caccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTaa                                                                                                                           <  2:494267/135‑1 (MQ=255)                  accTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAAt                                                                                                                     <  1:550246/140‑1 (MQ=255)                   ccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccccc                                                                                                                                  >  1:441085/1‑125 (MQ=255)                   ccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccccc                                                                                                                                  <  2:441085/125‑1 (MQ=255)                     tGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATcac                                                                                                                  <  1:696917/140‑1 (MQ=255)                               gCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTtca                                                                                                        <  2:65344/140‑1 (MQ=255)                                        tCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTaa                                                                                               >  2:687960/1‑140 (MQ=255)                                        tCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTaa                                                                                               <  2:699346/140‑1 (MQ=255)                                        tCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTaa                                                                                               <  1:687960/140‑1 (MQ=255)                                           tgtgCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTaa                                                                                               <  2:627678/137‑1 (MQ=255)                                           tgtgCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTaa                                                                                               >  1:627678/1‑137 (MQ=255)                                              gCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCAGATCATTTTCAGTCAGTTAACTTTcc                                                                                         <  1:204434/140‑1 (MQ=255)                                                             ttATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCAt                                                                          <  1:653009/140‑1 (MQ=255)                                                               ataGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGa                                                                        >  1:653835/1‑140 (MQ=255)                                                                      ttAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGc                                                                 >  2:837432/1‑140 (MQ=255)                                                                       tAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCa                                                                >  1:486395/1‑140 (MQ=255)                                                                            cccGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAAcg                                                           <  2:798699/140‑1 (MQ=255)                                                                                     tCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGa                                                  >  2:157194/1‑140 (MQ=255)                                                                                        ggCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCg                                               >  1:623150/1‑140 (MQ=255)                                                                                           ttttGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCggct                                            <  1:157194/140‑1 (MQ=255)                                                                                             ttGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCggctgg                                          >  2:1643/1‑140 (MQ=255)                                                                                              tGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGa                                                  >  2:223105/1‑131 (MQ=255)                                                                                              tGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGa                                                  <  1:223105/131‑1 (MQ=255)                                                                                                            aTAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCAc                           <  2:486395/140‑1 (MQ=255)                                                                                                                      cGTTGTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAg                 <  1:837432/140‑1 (MQ=255)                                                                                                                          gTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGt             <  1:1643/140‑1 (MQ=255)                                                                                                                          gTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGt             >  1:307130/1‑140 (MQ=255)                                                                                                                          gTCCATACCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGt             >  1:245073/1‑140 (MQ=255)                                                                                                                                aCCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATc                   >  2:340474/1‑128 (MQ=255)                                                                                                                                aCCCTGTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATc                   <  1:340474/128‑1 (MQ=255)                                                                                                                                     gTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAg                 <  1:551650/125‑1 (MQ=255)                                                                                                                                     gTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAg                 >  2:551650/1‑125 (MQ=255)                                                                                                                                     gTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  1:596529/1‑140 (MQ=255)                                                                                                                                     gTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  2:798547/1‑140 (MQ=255)                                                                                                                                     gTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  1:37836/1‑140 (MQ=255)                                                                                                                                     gTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  1:548165/1‑140 (MQ=255)                                                                                                                                     gTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  2:427801/1‑140 (MQ=255)                                                                                                                                     gTCCGCCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  1:708470/1‑140 (MQ=255)                                                                                                                                          |                                                                                                                                       TGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGG  >  NC_000913/2769506‑2769776

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: ‑