Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	REL606	3,145,822	C→A	intergenic (+153/‑42)	dnaG → / → rpoD	DNA primase/RNA polymerase sigma factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	REL606	3,145,822	0	C	A	100.0%	227.7 / NA	57	intergenic (+153/‑42)	dnaG/rpoD	DNA primase/RNA polymerase sigma factor
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (28/29);  total (28/29)

CTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAA  >  REL606/3145752‑3145892                                                                       |                                                                       cTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCa                                                                   <  1:292257/76‑1 (MQ=255)  tCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCaa                                                                  <  2:1057153/76‑1 (MQ=255)  tCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCaa                                                                  <  2:56140/76‑1 (MQ=255)    gTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAaca                                                                <  2:797576/76‑1 (MQ=255)    gTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAaca                                                                <  1:209229/76‑1 (MQ=255)     tAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCCATAGCCCAacac                                                               >  2:570198/1‑76 (MQ=255)     tAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAacac                                                               >  2:720076/1‑76 (MQ=255)       aTTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCa                                                             >  1:1584576/1‑76 (MQ=255)       aTTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCa                                                             <  1:492884/76‑1 (MQ=255)        ttATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCaa                                                            >  2:1047471/1‑76 (MQ=255)        ttATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCaa                                                            <  2:1201521/76‑1 (MQ=255)        ttATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCaa                                                            >  1:167456/1‑76 (MQ=255)         tATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGGCAATAGCCCAACACCAAc                                                           >  1:692784/1‑76 (MQ=255)          aTCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAAcc                                                          >  2:224159/1‑76 (MQ=255)           tCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCt                                                         <  2:1166664/76‑1 (MQ=255)            cGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTc                                                        <  2:71579/76‑1 (MQ=255)             gTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCCACCTCa                                                       >  2:395315/1‑76 (MQ=255)              ttGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCAt                                                      <  1:1298911/76‑1 (MQ=255)               tGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATg                                                     >  1:1611997/1‑76 (MQ=255)                  cGGTATACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGaaa                                                  <  2:1636762/76‑1 (MQ=255)                   ggTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGaaaa                                                 >  1:607103/1‑75 (MQ=255)                   ggTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAAt                                                 <  1:746747/76‑1 (MQ=255)                     tAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATaa                                               >  2:1537528/1‑76 (MQ=255)                      aaaCAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAg                                              <  1:225576/76‑1 (MQ=255)                      aaaCAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAg                                              <  1:1498669/76‑1 (MQ=255)                       aacaacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAgt                                             >  2:1598062/1‑76 (MQ=255)                        acaacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAgtg                                            >  1:733005/1‑76 (MQ=255)                             cGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGAt                                       >  1:158112/1‑76 (MQ=255)                             cGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGAt                                       <  1:588609/76‑1 (MQ=255)                              gTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATa                                      <  2:832971/76‑1 (MQ=255)                               ttGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATAc                                     <  1:278549/76‑1 (MQ=255)                                tGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATAcc                                    <  2:765692/76‑1 (MQ=255)                                  gATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGt                                  <  2:19884/76‑1 (MQ=255)                                    tttCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCt                                <  2:582752/76‑1 (MQ=255)                                     ttCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCtt                               <  2:1103035/76‑1 (MQ=255)                                     ttCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCtt                               >  1:402538/1‑76 (MQ=255)                                      tCAGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTa                              >  2:1411709/1‑76 (MQ=255)                                        aGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATg                            >  1:84492/1‑76 (MQ=255)                                        aGCGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATg                            <  1:1566641/76‑1 (MQ=255)                                          cGTTAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGa                          >  1:1057237/1‑76 (MQ=255)                                            ttAACGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGc                        >  1:496731/1‑76 (MQ=255)                                             naaCGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCa                       >  1:278990/2‑76 (MQ=255)                                                cGGCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCaaaa                    <  1:1311702/76‑1 (MQ=255)                                                 ggCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAAc                   <  2:1092725/76‑1 (MQ=255)                                                  gCTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAAcc                  >  2:919713/1‑76 (MQ=255)                                                   cTGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAAccc                 >  1:491375/1‑76 (MQ=255)                                                    tGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCg                >  2:940666/1‑76 (MQ=255)                                                    tGAAGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCg                >  1:1132924/1‑76 (MQ=255)                                                      aaGGACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCa              >  2:608748/1‑76 (MQ=255)                                                        ggACATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGt            <  2:1255904/76‑1 (MQ=255)                                                          aCATCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTca          >  2:1110421/1‑76 (MQ=255)                                                            aTCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTcaca        >  2:371444/1‑76 (MQ=255)                                                            aTCGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTcaca        <  2:805059/76‑1 (MQ=255)                                                              cGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGc      <  2:655657/76‑1 (MQ=255)                                                              cGGGTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGc      <  1:566821/76‑1 (MQ=255)                                                               gggTCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCt     <  2:1398905/76‑1 (MQ=255)                                                                  tCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGaa  >  2:1394891/1‑76 (MQ=255)                                                                  tCAATAGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGaa  >  1:83710/1‑76 (MQ=255)                                                                       |                                                                       CTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAA  >  REL606/3145752‑3145892

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: ‑