Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,770,404	G→A	*234* (TAG→TAA)	yfjR →	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	2,770,404	0	G	A	100.0%	192.1 / NA	60	*234* (TAG→TAA)	yfjR	CP4‑57 prophage, putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (29/31);  total (29/31)

TGCAGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAGCGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGCCCTGACACTTG  >  NC_000913/2770268‑2770535                                                                                                                                         |                                                                                                                                    tGCAGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAacg                                                                                                                                   >  2:34188/1‑139 (MQ=255)       agaCTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCg                                                                                                                             <  2:1166970/139‑1 (MQ=255)        gaCTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCgt                                                                                                                            <  2:587547/139‑1 (MQ=255)                          cAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAAc                                                                                                          <  1:394161/139‑1 (MQ=255)                              cTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATgg                                                                                                      <  1:1268206/139‑1 (MQ=255)                                 tgtCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATggagg                                                                                                   >  1:57656/1‑139 (MQ=255)                                   tCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGgaggag                                                                                                 >  2:398052/1‑139 (MQ=255)                                      ccTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGccc                                                                                              >  1:566080/1‑139 (MQ=255)                                        tGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATc                                                                                                                     >  2:1150260/1‑114 (MQ=255)                                        tGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATc                                                                                                                     <  1:1150260/114‑1 (MQ=255)                                          gTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTg                                                                                          <  1:398052/139‑1 (MQ=255)                                           ttGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAacgc                                                                                                                                  >  2:232632/1‑98 (MQ=255)                                           ttGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAacgc                                                                                                                                  <  1:232632/98‑1 (MQ=255)                                           ttGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAg                                                                                                                                <  2:475204/100‑1 (MQ=255)                                           ttGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAg                                                                                                                                >  1:475204/1‑100 (MQ=255)                                           ttGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGc                                                                                         <  2:566080/139‑1 (MQ=255)                                           ttGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGc                                                                                         >  1:653244/1‑139 (MQ=255)                                           ttGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGc                                                                                         >  2:768636/1‑139 (MQ=255)                                                 aCCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTa                                                                                   <  2:1171425/139‑1 (MQ=255)                                                     ggTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCATCGGAATAACGCAGGCGTTGTTATCAACCCg                                                                                                               >  1:981689/1‑107 (MQ=255)                                                     ggTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCg                                                                                                               <  2:981689/107‑1 (MQ=255)                                                      gTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGcc                                                                              >  1:1152491/1‑139 (MQ=255)                                                             ttcaGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCg                                                                       <  1:501169/139‑1 (MQ=255)                                                             ttcaGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCg                                                                       <  2:284046/139‑1 (MQ=255)                                                                       aCCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTg                                                                                <  1:1238065/120‑1 (MQ=255)                                                                       aCCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTg                                                                                >  2:1238065/1‑120 (MQ=255)                                                                       aCCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTat                                                             >  2:1200312/1‑139 (MQ=255)                                                                          ccATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTatcat                                                          <  2:57656/139‑1 (MQ=255)                                                                            aTTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCGCCGGAATAACGCAg                                                                                                                                <  1:264738/67‑1 (MQ=255)                                                                            aTTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAg                                                                                                                                >  2:264738/1‑67 (MQ=255)                                                                            aTTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGcc                                                                     <  2:441379/126‑1 (MQ=255)                                                                            aTTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGcc                                                                     >  1:441379/1‑126 (MQ=255)                                                                            aTTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCg                                                        >  2:132573/1‑139 (MQ=255)                                                                                         ccAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGaa                                           <  2:653244/139‑1 (MQ=255)                                                                                             cATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTAt                                                                         <  1:666947/105‑1 (MQ=255)                                                                                             cATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTAt                                                                         >  2:666947/1‑105 (MQ=255)                                                                                                 cACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCg                                   <  1:768636/139‑1 (MQ=255)                                                                                                  aCTGCTTACGTTTGTTCCGGTCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCgg                                  >  2:145325/1‑139 (MQ=255)                                                                                                  aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTAt                                                                         >  2:1102427/1‑100 (MQ=255)                                                                                                  aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTAt                                                                         <  1:1102427/100‑1 (MQ=255)                                                                                                  aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGaa                                           <  1:637207/130‑1 (MQ=255)                                                                                                  aCTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGaa                                           >  2:637207/1‑130 (MQ=255)                                                                                                      cTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAgtg                              >  2:557895/1‑139 (MQ=255)                                                                                                        tACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGcc                                                                                               <  1:164231/72‑1 (MQ=255)                                                                                                        tACGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGcc                                                                                               >  2:164231/1‑72 (MQ=255)                                                                                                         aCGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGcc                                                                                               <  2:1095636/71‑1 (MQ=255)                                                                                                         aCGTTTGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGcc                                                                                               >  1:1095636/1‑71 (MQ=255)                                                                                                              tGTTCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAg                      <  2:1152491/139‑1 (MQ=255)                                                                                                                ttCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGc                                                                                         >  2:1149704/1‑70 (MQ=255)                                                                                                                ttCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGc                                                                                         <  1:1149704/70‑1 (MQ=255)                                                                                                                ttCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGcc                    >  2:1308429/1‑139 (MQ=255)                                                                                                                ttCCGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGcc                    >  1:222223/1‑139 (MQ=255)                                                                                                                  ccGGCTGACAGCCCGCCGGAGTAACGCAGGAGTTGTTATCAACCTGGCTACTCGGAAGAGCCCGGTGCCTGTTATTGCCATTATCGCGAGTTTTATTATCATCATCATACTGAACAAAACCGAATTGTCCGACAGCCTc                  <  1:1308429/139‑1 (MQ=255)                                                                                                                   cGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCa                 <  1:3913/139‑1 (MQ=255)                                                                                                                   cGGCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCa                 <  1:132573/139‑1 (MQ=255)                                                                                                                     gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                              <  1:565634/44‑1 (MQ=255)                                                                                                                     gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCgg                                                                                                              >  2:565634/1‑44 (MQ=255)                                                                                                                     gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCa                 >  2:1083568/1‑137 (MQ=255)                                                                                                                     gCCGACAGCCCACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCa                 <  1:1083568/137‑1 (MQ=255)                                                                                                                               cACCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGCCCTGacac     >  1:1370374/1‑139 (MQ=255)                                                                                                                                aCCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCa                                                                    >  1:189298/1‑75 (MQ=255)                                                                                                                                aCCGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCa                                                                    <  2:189298/75‑1 (MQ=255)                                                                                                                                  cGGAATAACGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGCCCTGACACTTg  >  2:73533/1‑139 (MQ=255)                                                                                                                                         |                                                                                                                                    TGCAGGAGACTTTTCGCCGCAATGACAGTCTGTGTCGCCTGGTTGAAGACCCGGTCTTCATTCAGGCCTTACCCCATTTTCGCTTTATCCAGCATTCACTGCTTACGTTTGTTCCGGCCGACAGCCCACCGGAATAGCGCAGGCGTTGTTATCAACCCGGCAACATGGAGGAGCCCAGTGCCCGTTATTGCCATTATCGCCATTGTTATCATCGTCATCATTCTGAACAAAACCGGAGTGTCCGACAGCCTCACGGCCCTGACACTTG  >  NC_000913/2770268‑2770535

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑