Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,533,592	G→A	intergenic (‑36/+150)	unknown ← / ← unknown	DNA‑directed RNA polymerase specialized sigma subunit, sigma24‑like/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,533,592	0	G	A	100.0%	77.4 / NA	30	intergenic (‑36/+150)	unknown/unknown	DNA‑directed RNA polymerase specialized sigma subunit, sigma24‑like/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (13/17);  total (13/17)

TTCTTCAAAATGGCAAAAAACCAGGTTTTCAGCGCAGAAGCCCCTTTAAATGAGGTCGCATGTTGATACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAGAGTATTCTACCATCATATAATACAATGCACCTATAATATCTTAAAAATAAATAATTAAATTCAGCAGCAGGCTAAGATTTTTGCAAAAAAAGGACTTGTTCACCACAAGTCCAAAATAAGTGATTATTTATAATGACTTGGAGTGAAAATTACATTTTGTGATCTTTCATTTCCTTGTCCATTTTATGGTCCATGGACTTACCGTCTTTCATCATTTTGTCTTTTTTATGA  >  1/1533354‑1533823                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                        ttcttcAAAATGGCAAAAAACCAGGTTTTCAGCGCAGAAGCCCCTTTAAATGAGGTCGCATGTTGATACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACca                                                                                                                                                                                                                             <  1:59185/251‑1 (MQ=255)          aTGGCAAAAAACCAGGTTTTCAGCGCAGAAGCCCCTTTAAATGAGGTCGCATGTTGATACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATataat                                                                                                                                                                                                                    <  1:624021/251‑1 (MQ=255)             gCAAAAAACCCGGTTTTCAGCGCAGAAGCCCCTTTAAATGAGGTCGCATGTTGATACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTACCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATAc                                                                                                                                                                                                                  <  1:31479/250‑1 (MQ=255)             gCAAAAAACCAGGTTTTCAGCGCAGAAGCCCCTTTAAATGAGGTCGCATGTTGATACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATAc                                                                                                                                                                                                                  <  1:545403/250‑1 (MQ=255)             gCAAAAAACCAGGTTTTCAGCGCAGAAGCCCCTTTAAATGAGGTCGCATGTTGATACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATAc                                                                                                                                                                                                                  <  1:649643/250‑1 (MQ=255)             gCAAAAAACCAGGTTTTCAGCGCAGAAGCCCCTTTAAATGAGGTCGCATGTTGATACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATAc                                                                                                                                                                                                                  <  1:343255/250‑1 (MQ=255)             gCAAAAAACCAGGTTTTCAGCGCAGAAGCCCCTTTAAATGAGGTCGCATGTTGATACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATAc                                                                                                                                                                                                                  <  1:357017/250‑1 (MQ=255)                          ttttCAGCGCAGAAGCCCCTTTAAATGAGGTCGCATGTTGATACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATACAATGCACCTataat                                                                                                                                                                                                    <  1:527794/251‑1 (MQ=255)                           tttCAGCGCAGAAGCCCCTTTAAATGAGGTCGCATGTTGATACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATAc                                                                                                                                                                                                                  >  1:795259/1‑236 (MQ=255)                             tCAGCGCAGAAGCCCCTTTAAATGAGGTCGCATGTTGATACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATACAATGCACCTATAATATc                                                                                                                                                                                                 <  1:36186/251‑1 (MQ=255)                                  gcAGAAGCCCCTTTAAATGAGGTCGCATGTTGATACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATACAATGc                                                                                                                                                                                                             <  1:285062/234‑1 (MQ=255)                                           ccTTTAAATGAGGTCGCATGTTGATACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATAc                                                                                                                                                                                                                  >  1:747875/1‑220 (MQ=255)                                                           cATGTTGATACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCatat                                                                                                                                                                                                                       >  1:253411/1‑199 (MQ=255)                                                               ttGATACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATAc                                                                                                                                                                                                                  >  1:247026/1‑200 (MQ=255)                                                                   tACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATACAATGCACCTATAATATCTTAAAAATAAATAATTAAATTCAGCAGCAGGCTAAGAt                                                                                                                                                           <  1:736334/251‑1 (MQ=255)                                                                    aCGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATAc                                                                                                                                                                                                                  >  1:346638/1‑195 (MQ=255)                                                                           cACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTAt                                                                                                                                                                                                                                    <  1:713729/170‑1 (MQ=255)                                                                           cACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATACAATGCACCTATAATATCTTAAAAATAAATAATTAAATTCAGCAGCAGGCTAAGATTTTTGCaa                                                                                                                                                   >  1:53960/1‑251 (MQ=255)                                                                                 ggTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTAc                                                                                                                                                                                                                               <  1:296062/169‑1 (MQ=255)                                                                                    ttCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATAc                                                                                                                                                                                                                  <  1:765219/179‑1 (MQ=255)                                                                                              aCATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATAc                                                                                                                                                                                                                  >  1:693683/1‑169 (MQ=255)                                                                                                  cTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATAc                                                                                                                                                                                                                  >  1:776000/1‑165 (MQ=255)                                                                                                      cGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATACAATGCACCTATAATATCTTAAAAATAAATAATTAAATTCAGCAGCAGGCTAAGATTTTTGCAAAAAAAGGACTTGTTCACCACAAGTCCa                                                                                                                        >  1:544493/1‑251 (MQ=255)                                                                                                          aaaTCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATACAATGCGCCTATAATATCTTAAAAATAAATAATTAAATTCAGCAGCAGGCTAAGATTTTTGCAAAAAAAGGACTTGTTCACCACAAGTCCAAAAt                                                                                                                    <  1:176938/251‑1 (MQ=255)                                                                                                          aaaTCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATACAATGCACCTATAATATCTTAAAAATAAATAATTAAATTCAGCAGCAGGCTAAGATTTTTGCAAAAAAAGGACTTGTTCACCACAAGTCCAAAAt                                                                                                                    <  1:104889/251‑1 (MQ=255)                                                                                                                   tCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATACAATGCACCTATAATATCTTAAAAATAAATAATTAAATTCAGCAGCAGGCTAAGATTTTTGCAAAAAAAGGACTTGTTCACCACAAGTCCaaaa                                                                                                                     >  1:726767/1‑241 (MQ=255)                                                                                                                     ccTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATACAATGCACCtata                                                                                                                                                                                                      >  1:850337/1‑158 (MQ=255)                                                                                                                         aaCTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATACAATGCACCTataat                                                                                                                                                                                                    >  1:360031/1‑156 (MQ=255)                                                                                                                                  gTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCatat                                                                                                                                                                                                                       >  1:263096/1‑128 (MQ=255)                                                                                                                                                                 ccTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAAAGTATTCTACCATCATATAATACAATGCACCTATAATATCt                                                                                                                                                                                                <  1:173089/120‑1 (MQ=255)                                                                                                                                                                                                                                          aaagaaagTATTCTACCATCATATAATACAATGCACCTATAATATCTTAAAAATAAATAATTAAATTCAGCAGCAGGCTAAGATTTTTGCAAAAAAAGGACTTGTTCACCACAAGTCCAAAATAAGTGATTATTTATAATGACTTGGAGTGAAAATTACATTTTGTGATCTTTCATTTCCTTGTCCATTTTATGGTCCATGGACTTACCGTCTTTCATCATTTTGTCTTTTTTATGa  >  1:830770/1‑237 (MQ=255)                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                        TTCTTCAAAATGGCAAAAAACCAGGTTTTCAGCGCAGAAGCCCCTTTAAATGAGGTCGCATGTTGATACGCTTTCACTAAGGTTTCCTGCACGACATCTTCCGCTAAATCTTCGTCCCTTAACTGTAAAGTGGCAAATTTCAGCATCTGCCGGCGAATATCCTCAATTTCTTGAGATGAAATGTGTTGAAAAGAAAATTGCATTGTTGAGTCCATTTTATTTTAATGAGTAGAAAAGAGAGTATTCTACCATCATATAATACAATGCACCTATAATATCTTAAAAATAAATAATTAAATTCAGCAGCAGGCTAAGATTTTTGCAAAAAAAGGACTTGTTCACCACAAGTCCAAAATAAGTGATTATTTATAATGACTTGGAGTGAAAATTACATTTTGTGATCTTTCATTTCCTTGTCCATTTTATGGTCCATGGACTTACCGTCTTTCATCATTTTGTCTTTTTTATGA  >  1/1533354‑1533823

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑