Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,769,648	(C)6→5	intergenic (+162/‑55)	yfjQ → / → yfjR	CP4‑57 prophage, uncharacterized protein/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	2,769,643	0	C	.	100.0%	185.5 / NA	46	intergenic (+157/‑60)	yfjQ/yfjR	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (22/24);  total (22/24)

TTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGGT  >  NC_000913/2769505‑2769777                                                                                                                                           |                                                                                                                                       ttgttAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGc                                                                                                                                        >  1:1106965/1‑139 (MQ=255)   gttAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGccc                                                                                                                                      <  1:1201967/139‑1 (MQ=255)           cGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTa                                                                                                                             >  2:1385843/1‑139 (MQ=255)            ggACACCACCTGTCCGCATCGCTATGTGCCCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTaa                                                                                                                            >  2:517776/1‑139 (MQ=255)             gACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGcccc                                                                                                                                     >  2:1514303/1‑130 (MQ=255)             gACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGcccc                                                                                                                                     <  1:1514303/130‑1 (MQ=255)             gACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTaaa                                                                                                                           >  1:984777/1‑139 (MQ=255)              acacCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAg                                                                                                                          <  1:1414182/139‑1 (MQ=255)              acacCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAg                                                                                                                          >  1:253787/1‑139 (MQ=255)               caccacCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGt                                                                                                                         <  1:1441510/139‑1 (MQ=255)                   accTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATc                                                                                                                     <  2:410361/139‑1 (MQ=255)                    ccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATca                                                                                                                    >  2:369283/1‑139 (MQ=255)                      tGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCATAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATcaca                                                                                                                  <  2:984551/139‑1 (MQ=255)                        tCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCAcatc                                                                                                                >  2:657103/1‑139 (MQ=255)                        tCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCAcatc                                                                                                                >  1:1021939/1‑139 (MQ=255)                               cGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTtca                                                                                                         >  2:1307451/1‑139 (MQ=255)                                ggtATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTTGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTtcag                                                                                                        <  2:1021939/137‑1 (MQ=255)                                            tgtgCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACttt                                                                                            >  2:668175/1‑139 (MQ=255)                                                ccTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTtcag                                                                                                        <  2:398095/123‑1 (MQ=255)                                                ccTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTtcag                                                                                                        >  1:398095/1‑123 (MQ=255)                                                  tCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGga                                                                                      <  2:508166/139‑1 (MQ=255)                                                     aTCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGaa                                                                                   <  1:1307451/139‑1 (MQ=255)                                                          ccGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAAtctct                                                                              <  2:984777/139‑1 (MQ=255)                                                                ataGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGcccc                                                                                                                                     <  1:618521/79‑1 (MQ=255)                                                                ataGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGcccc                                                                                                                                     >  2:618521/1‑79 (MQ=255)                                                                ataGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGac                                                                        <  1:668175/139‑1 (MQ=255)                                                                       ttAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACttt                                                                                            >  1:1323133/1‑112 (MQ=255)                                                                       ttAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACttt                                                                                            <  2:1323133/112‑1 (MQ=255)                                                                        tAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGcccc                                                                                                                                     >  1:1377696/1‑71 (MQ=255)                                                                        tAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGcccc                                                                                                                                     <  2:1377696/71‑1 (MQ=255)                                                                                      tCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGAc                                                  <  2:253787/139‑1 (MQ=255)                                                                                        tGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCg                                                >  2:68102/1‑139 (MQ=255)                                                                                         ggCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCgg                                               >  2:1033901/1‑139 (MQ=255)                                                                                             tttGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCggctgg                                           <  1:1385843/139‑1 (MQ=255)                                                                                             tttGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCggctgg                                           <  1:517776/139‑1 (MQ=255)                                                                                               tGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATcac                                                                                                                   <  1:874605/65‑1 (MQ=255)                                                                                               tGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATcac                                                                                                                   >  2:874605/1‑65 (MQ=255)                                                                                               tGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGtt                                                                                                  >  2:1541040/1‑82 (MQ=255)                                                                                               tGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGtt                                                                                                  <  1:1541040/82‑1 (MQ=255)                                                                                                 cAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTggctgt                                       <  2:1106965/139‑1 (MQ=255)                                                                                                 cAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTggctgt                                       <  1:657103/139‑1 (MQ=255)                                                                                                     aaTAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTggctgtcagg                                   <  1:369283/139‑1 (MQ=255)                                                                                                                 tttCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGacac                                                                      >  2:62349/1‑92 (MQ=255)                                                                                                                 tttCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGacac                                                                      <  1:62349/92‑1 (MQ=255)                                                                                                                         ttGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAAtctctc                                                                             <  1:1700013/77‑1 (MQ=255)                                                                                                                         ttGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAAtctctc                                                                             >  2:1700013/1‑77 (MQ=255)                                                                                                                                   ccTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGgag                                                                                     >  2:1353890/1‑59 (MQ=255)                                                                                                                                   ccTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGgag                                                                                     <  1:1353890/59‑1 (MQ=255)                                                                                                                                      gTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCa                                                                 <  1:724126/76‑1 (MQ=255)                                                                                                                                      gTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCa                                                                 >  2:724126/1‑76 (MQ=255)                                                                                                                                      gTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTggctgtcagg                                   <  1:895439/106‑1 (MQ=255)                                                                                                                                      gTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTggctgtcagg                                   >  2:895439/1‑106 (MQ=255)                                                                                                                                      gTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGGt  >  1:1618530/1‑139 (MQ=255)                                                                                                                                      gTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGGt  >  1:73770/1‑139 (MQ=255)                                                                                                                                           |                                                                                                                                       TTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGGT  >  NC_000913/2769505‑2769777

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑