Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	REL606	3,147,777	G→T	intergenic (+72/+7)	rpoD → / ← ygjF	RNA polymerase sigma factor/G/U mismatch‑specific DNA glycosylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	REL606	3,147,777	0	G	T	100.0%	276.2 / NA	70	intergenic (+72/+7)	rpoD/ygjF	RNA polymerase sigma factor/G/U mismatch‑specific DNA glycosylase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (45/25);  total (45/25)

AATCGGTAGGCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGGCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTCAACCAGTTTCTCCAGTG  >  REL606/3147704‑3147848                                                                          |                                                                        aaTCGGTAGGCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCg                                                                       >  2:2214689/1‑76 (MQ=255)  aTCGGTAGGCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGt                                                                      >  2:484431/1‑76 (MQ=255)    cGGTAGGCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGttt                                                                    >  1:1433499/1‑76 (MQ=255)       tAGGCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGtttttt                                                                 <  2:110920/76‑1 (MQ=255)       tAGGCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGtttttt                                                                 <  1:1487594/76‑1 (MQ=255)        aGGCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTTGGTGTCGTTTTTTa                                                                >  1:1425911/1‑76 (MQ=255)        aGGCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTa                                                                <  1:1365911/76‑1 (MQ=255)         ggCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTAt                                                               <  1:1026114/76‑1 (MQ=255)         ggCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTAt                                                               >  1:1253706/1‑76 (MQ=255)            cGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGc                                                            >  1:2060960/1‑76 (MQ=255)             ggATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGcc                                                           >  1:183137/1‑76 (MQ=255)              gATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGccc                                                          >  1:2192071/1‑76 (MQ=255)               aTCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCa                                                         >  2:1319405/1‑76 (MQ=255)                tCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCAc                                                        <  1:1558549/76‑1 (MQ=255)                  aGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGc                                                      >  1:38836/1‑76 (MQ=255)                  aGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGc                                                      >  2:1037879/1‑76 (MQ=255)                   ggCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCa                                                     <  1:2191613/76‑1 (MQ=255)                       ttACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTAc                                                 >  1:923441/1‑76 (MQ=255)                       ttACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTAc                                                 >  2:1510774/1‑76 (MQ=255)                         aCGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCa                                               >  1:1172178/1‑76 (MQ=255)                         aCGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCa                                               <  2:698455/76‑1 (MQ=255)                          cgccgcACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAg                                              >  1:1965330/1‑76 (MQ=255)                          cgccgcACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAg                                              >  2:13912/1‑76 (MQ=255)                          cgccgcACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAg                                              <  2:1411909/76‑1 (MQ=255)                              gcACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGcc                                          >  2:881689/1‑76 (MQ=255)                               cACCCGGCACTAGGCCCTCTGCACACACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACCACCAGCGCCt                                         >  2:510855/1‑76 (MQ=255)                               cACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCt                                         >  2:761737/1‑76 (MQ=255)                               cACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCt                                         >  2:557283/1‑76 (MQ=255)                                 cccGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTgg                                       >  2:1585956/1‑76 (MQ=255)                                 cccGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTgg                                       >  2:619200/1‑76 (MQ=255)                                    ggCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTcc                                    <  1:642124/76‑1 (MQ=255)                                    ggCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTcc                                    <  2:178585/76‑1 (MQ=255)                                    ggCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTcc                                    <  2:1429021/76‑1 (MQ=255)                                      cACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGTTCCAg                                  <  1:602613/76‑1 (MQ=255)                                       gcTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGc                                 <  2:200322/75‑1 (MQ=255)                                       aCTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGc                                 >  1:1676937/1‑76 (MQ=255)                                        cTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCt                                >  1:1716498/1‑76 (MQ=255)                                        cTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCt                                >  2:441315/1‑76 (MQ=255)                                         tAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTc                               >  1:10182/1‑76 (MQ=255)                                         tAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTc                               >  1:456723/1‑76 (MQ=255)                                         tAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTc                               <  1:88540/76‑1 (MQ=255)                                         tAGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTc                               <  1:884800/76‑1 (MQ=255)                                          aGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTcg                              >  2:1018832/1‑76 (MQ=255)                                          aGGCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTcg                              <  2:1680976/76‑1 (MQ=255)                                           ggCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTcgc                             <  1:247752/76‑1 (MQ=255)                                            gCCCTCTGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTcgcg                            >  2:758753/1‑76 (MQ=255)                                                 ctGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACg                       >  2:1361305/1‑76 (MQ=255)                                                 ctGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACg                       <  2:139468/76‑1 (MQ=255)                                                  tGCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGc                      >  2:1219228/1‑76 (MQ=255)                                                  tGCACAAACGCCACCTTTTCGGNGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGc                      >  2:304530/1‑76 (MQ=255)                                                   gCACAAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCt                     >  2:1476358/1‑76 (MQ=255)                                                    cacaAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCtt                    >  1:157676/1‑76 (MQ=255)                                                    cacaAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCtt                    <  1:882537/76‑1 (MQ=255)                                                     acaAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTc                   >  1:479793/1‑76 (MQ=255)                                                     acaAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTc                   <  1:1415458/76‑1 (MQ=255)                                                     acaAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTc                   >  1:428818/1‑76 (MQ=255)                                                      caAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTCa                  >  2:1913044/1‑76 (MQ=255)                                                      caAACGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTCa                  >  2:781889/1‑76 (MQ=255)                                                       aaaCGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTCac                 >  2:1085783/1‑75 (MQ=255)                                                       aaaCGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTCaa                 >  2:246483/1‑76 (MQ=255)                                                       aaaCGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTCaa                 >  2:760924/1‑76 (MQ=255)                                                        aaCGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTCAAc                >  2:1424512/1‑76 (MQ=255)                                                        aaCGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTCAAc                >  2:1617308/1‑76 (MQ=255)                                                         aCGCCACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTCAAcc               <  2:1285685/76‑1 (MQ=255)                                                            ccACCTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTCAACCAGt            <  1:1028014/76‑1 (MQ=255)                                                               ccTTTTCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTCAACCAGTTtc         >  1:1246930/1‑76 (MQ=255)                                                                 ttttCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTCAACCAGTTtctc       <  2:1286121/76‑1 (MQ=255)                                                                    tCGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTCAACCAGTTTCTCCAg    <  2:2128764/76‑1 (MQ=255)                                                                     cGGTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTCAACCAGTTTCTCCAGt   >  1:535327/1‑76 (MQ=255)                                                                      ggTGTCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTCAACCAGTTTCTCCAGTg  <  1:2049166/76‑1 (MQ=255)                                                                          |                                                                        AATCGGTAGGCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGGCGTTTTTTATCGCCCACGCACTACCAGCGCCTGGTCCAGCTCGCGATACGCTTCAACCAGTTTCTCCAGTG  >  REL606/3147704‑3147848

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑