Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	REL606	3,147,053	G→A	R397H (CGT→CAT)	rpoD →	RNA polymerase sigma factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	REL606	3,147,053	0	G	A	100.0%	246.0 / NA	61	R397H (CGT→CAT)	rpoD	RNA polymerase sigma factor
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (30/31);  total (30/31)

CGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAAT  >  REL606/3146980‑3147124                                                                          |                                                                        cgccgTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATg                                                                       <  1:363590/76‑1 (MQ=255) cgccgTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATg                                                                       <  1:1391921/76‑1 (MQ=255) cgccgTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAACAAATACACCAACCATg                                                                       <  2:1888796/76‑1 (MQ=255)    cgTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCt                                                                    <  1:1871276/76‑1 (MQ=255)      tGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTg                                                                  <  2:451144/76‑1 (MQ=255)       gCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGc                                                                 <  2:430542/76‑1 (MQ=255)          aagaaagaGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGt                                                              >  1:795999/1‑76 (MQ=255)           agaaagaGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGtt                                                             <  2:1733515/76‑1 (MQ=255)            gaaagaGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTc                                                            <  2:1897976/76‑1 (MQ=255)            gaaagaGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTc                                                            <  2:1372214/76‑1 (MQ=255)             aaagaGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTcc                                                           >  2:1154497/1‑76 (MQ=255)              aagaGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCt                                                          <  2:1881869/76‑1 (MQ=255)               agagATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCtt                                                         <  2:367545/76‑1 (MQ=255)               agagATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCtt                                                         <  2:766716/76‑1 (MQ=255)                gagaTGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTg                                                        >  2:1013353/1‑76 (MQ=255)                gagaTGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTg                                                        >  1:204943/1‑76 (MQ=255)                gagaTGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTg                                                        <  1:1575551/76‑1 (MQ=255)                      gTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGa                                                  >  2:1755685/1‑76 (MQ=255)                      gTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGa                                                  <  2:48071/76‑1 (MQ=255)                        tGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGAtt                                                >  2:1058519/1‑76 (MQ=255)                         gAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTc                                               <  1:1915871/76‑1 (MQ=255)                          aaGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCa                                              >  2:1238286/1‑76 (MQ=255)                              gAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGaa                                          >  2:490206/1‑76 (MQ=255)                                 cTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAGCCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGc                                       <  2:852261/76‑1 (MQ=255)                                 cTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGc                                       >  1:940486/1‑76 (MQ=255)                                 cTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGc                                       >  2:574126/1‑76 (MQ=255)                                 cTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGc                                       >  2:503838/1‑76 (MQ=255)                                  ttACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCa                                      <  2:1905736/76‑1 (MQ=255)                                  ttACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCa                                      <  1:379426/76‑1 (MQ=255)                                   tACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCaa                                     >  2:805949/1‑76 (MQ=255)                                     cGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACa                                   >  2:1302689/1‑76 (MQ=255)                                      gTCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACAt                                  <  2:1501761/76‑1 (MQ=255)                                       tCTGGTTATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATc                                 <  1:1565874/76‑1 (MQ=255)                                            ttATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCt                            >  1:1181437/1‑76 (MQ=255)                                            ttATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCt                            >  2:273197/1‑76 (MQ=255)                                            ttATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCt                            >  2:1753016/1‑76 (MQ=255)                                             tATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCtg                           >  1:728962/1‑76 (MQ=255)                                             tATTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCtg                           <  1:961909/76‑1 (MQ=255)                                              aTTTCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCtga                          >  1:168454/1‑76 (MQ=255)                                               tttCTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCtgat                         <  1:622738/76‑1 (MQ=255)                                                  cTATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGaa                      >  1:1830638/1‑76 (MQ=255)                                                   tATCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGaaa                     <  2:1914779/76‑1 (MQ=255)                                                    aTCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAg                    >  1:371458/1‑76 (MQ=255)                                                    aTCGCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAg                    <  1:519916/76‑1 (MQ=255)                                                       gCTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCgg                 <  2:1309513/76‑1 (MQ=255)                                                        cTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGt                <  1:697849/76‑1 (MQ=255)                                                        cTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGt                >  1:590738/1‑76 (MQ=255)                                                        cTAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGCCTGATAAAGGCGGt                >  1:202004/1‑76 (MQ=38)                                                         tAAGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGtt               <  1:1575453/76‑1 (MQ=255)                                                          aaGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTg              >  1:237566/1‑76 (MQ=255)                                                          aaGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTg              >  2:1451766/1‑76 (MQ=255)                                                          aaGAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTg              >  1:860292/1‑76 (MQ=255)                                                            gAAATACACCAACCATGGCTTGNAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGAt            >  2:263593/1‑76 (MQ=255)                                                            gAAATACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGAt            >  1:1318937/1‑76 (MQ=255)                                                             aaaTACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa           >  2:1870663/1‑76 (MQ=255)                                                             aaaTACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa           >  2:372830/1‑76 (MQ=255)                                                              aaTACACCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaa          <  2:1406899/76‑1 (MQ=255)                                                                  cacCAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTc      >  1:1852198/1‑76 (MQ=255)                                                                   accaaccaTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg     >  1:893379/1‑76 (MQ=255)                                                                     cAACCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGaa   <  1:32718/76‑1 (MQ=255)                                                                      aaCCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAAt  <  1:295839/76‑1 (MQ=255)                                                                      aaCCATGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAAt  <  1:1659303/76‑1 (MQ=255)                                                                          |                                                                        CGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAAT  >  REL606/3146980‑3147124

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑