Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,708,844	C→G	20.7%	A642A (GCC→GCG)	rsxC →	SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,708,844	0	C	G	20.7%	38.4 / 4.3	28	A642A (GCC→GCG)	rsxC	SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex
Reads supporting (aligned to +/- strand):  ref base C (13/7);  new base G (3/3);  total (17/11)
Fisher's exact test for biased strand distribution p-value = 6.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.12e-01

CGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCG‑GCAGTTGC  >  NC_000913/1708611‑1709077                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                            cccgcCAAAGCCGGCAAGCTGGAACAGCAACAGGCTAAGGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTTGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGc                                                                                                                                                                                                                                         <  1:892903/236‑1 (MQ=255)   cgcCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCATAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTTCCCGTGCAAAAGCCCGCAAGCTGGAACAGCAACAGGCTAATGCAGacacac                                                                                                                                                                                                                                      >  1:881257/1‑234 (MQ=255)       aagagcgccaaacgggAGCAGCTACAGGCACATGCGAGACCAGAGAGCGAGGTGGACCGGCGAAAAGCGGCCCGCGAGGCAGCTAGGCCCCGGGCCCAAGCGCCCAAGCGGGAACAGCAGCCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCGGCCGTCGAAGCGGCTATTGCCCGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACC‑AGaaga                                                                                                                                                                                                                                 <  2:200542/225‑3 (MQ=9)                     gaaaCAGCAAAAGGCAAAGGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGGGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAAGGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCcg                                                                                                                                                                                                                    <  1:1013499/236‑1 (MQ=255)                            cAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACACAAGGACGATCCGCGCAAAGCCGCCGTAGAAGCGGCTTATGCCCAAGCCAAAGCGCCCAAGCGGTAACCACACCCGGCGAATGGGGAGCCAACAACACCAGG‑CGATcccgaaccagt                                                                                                                                                                                                            >  2:776749/1‑230 (MQ=14)                            cAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAACCCGCTATTGCCCGAGCCAAAGCACGCAAGCTGGAACATCAACACGCTAATGCCGAGCC‑AGAACAACAGGACGATCCCCGCaaac                                                                                                                                                                                                             >  1:254408/1‑237 (MQ=255)                                                                        aGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCCCGCAAACGGGAACAACAACCGCCTAATGCGGAGCC‑AGAAGAACAGGGGGATCCGCGCAAAGCGGACGGCGAAGCGGCAATGGACCGGCCCaaaaaaacaaaaggag                                                                                                                                                                >  2:588423/1‑226 (MQ=14)                                                                             ccgTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCCCCCAAACggggaaa                                                                                                                                                            >  1:608284/1‑234 (MQ=255)                                                                                          tATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCGGGAACAGCACCAGGCTAACACCGAGCC‑AGAAGAACAGGTCGATCCCCGCAAACCCGCCGCCCAACCCGCTATTTTCCGCCCCCAAGCCCCCAAACGGGCACACCAACAggggaaaa                                                                                                                                              >  2:869256/1‑233 (MQ=11)                                                                                                   tGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCTGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGGGCAAAGCCGCCGTCCAACCCGCTATTTCCCGCGCCAAACCGCGCAACCGGGAACAGCAACCGGCTAATGCGGAGccca                                                                                                                                     >  1:1015654/1‑237 (MQ=14)                                                                                                   tGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAAGAACAGGTTGATCCGCGCAAACCCCCCGTCGAACCGGCTATTGCCCACGCCAAAGACCGCAAAAGGGAAAAGaaaaagggcaaaagggaggaga                                                                                                                                     >  2:466046/1‑220 (MQ=11)                                                                                                       aaaGGGCGCAAGCTGGAAAAGCACAAGGCTAATGCGGAACCAGAAGACCAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCagaaga                                                                                                                                 <  1:769937/239‑1 (MQ=255)                                                                                                            gggcAAGGTGGAACGGCAACCGGCCAAGGCGGAACCAGAAGAACAGGCCGACCCGCACAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAgg                                                                                                                            <  1:834807/237‑1 (MQ=14)                                                                                                                                                      aCAGGGCGACCCGCGCAAAGCCGCGGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAGCC‑AGAACACCAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCAcg                                                                                    <  1:872787/237‑1 (MQ=255)                                                                                                                                                          gTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGCGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGCAGCCGCTATTGCCCGCGCCAAAGCACGCAAACTGGCACAGCAACCGGCTAATCCGGAGCCAGAAGAACCAGGTGATCCGCCAAAACCCGCCGTcacagagcaacttgccacacacaa                                                                              >  2:1088794/1‑216 (MQ=11)                                                                                                                                                               tCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTGATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCGGCTATTGCCCGAGCCAAAGCCGGCAAACGGGAAAAGCAACCGGTTAATGCCGAGCCGGAAGAACAGGATAGTCCGCCCAAACGGGCGGTCAAAGCGGCAACTGCCCGCCCCAAAGAAc                                                                         >  2:436231/1‑239 (MQ=14)                                                                                                                                                               tCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAAGCCGGAACCAGAAGAACAGGTTGATCCCCGCAAAGCTGCCGTCGAAGCGGCAATTGCACGCGCCAAGGccc                                                                         >  1:546885/1‑237 (MQ=255)                                                                                                                                                                   cgcAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAACCAGAAGAACAGGTTGATCCGCGCAAAGCGCCCGTCGAACCGGCCATTGCACGCGcccaggccccaaa                                                                     >  1:1017281/1‑228 (MQ=17)                                                                                                                                                                                              gCCCGTGCAAAAGCGCGCAAGCGGGAACAGCAACAGGTAAATGCGGAGCC‑AGAACACCAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGt                                          <  1:764141/239‑1 (MQ=255)                                                                                                                                                                                                    tccAAAGAACCGAAGCTTGAACAGCAACGGGGTAATGCCGAGCC‑AAAAAAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGTTATTGCCCGAGCCAAAGCGCCCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCag                                     <  1:776749/237‑1 (MQ=17)                                                                                                                                                                                                    gCCAAAGGCCTCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCag                                     <  1:656248/238‑1 (MQ=255)                                                                                                                                                                                                       aaaccccccAAACTGGAACAGCAACAGGCTAATGCAAACCA‑AGAGCACGAGGCCGAGCCGCGAAAAGGCGACTACGAAGCGGATATTGCACGAGCCAAAGCCCGCAAGCGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCagaaga                                 <  2:1015654/231‑1 (MQ=14)                                                                                                                                                                                                              gCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAACCTGGACCAGCAACAGGCTAATGCGGTACCAGAAGAAACGGtt                          >  1:352676/1‑239 (MQ=255)                                                                                                                                                                                                                            cAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGCGCCCAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGAAGGCAAGACGGAAAAAACACAGGCTCAAGGGGAGCACGAAGAACAGGGTGaacggggccaaga            >  2:858920/1‑227 (MQ=14)                                                                                                                                                                                                                                aGGCTAATGCCGGGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCCCGCAAACGGGCACAGCAACCGGCTAATGCGGAGCCAGAAGAACCGGTTGATCCGCGCAAAGCAGCCGCGGGAGCGGCTAGTGCACGCGGCCAATCCCCCAAGCTAGAAAGGCAAAAAGCTAAAGAGGGACAAGAAAAAAAgggagaaaacggacagaaggaa        >  2:570892/1‑219 (MQ=9)                                                                                                                                                                                                                                      aTGCGGAACC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCGGCCGTCGACGCCGCTATTGCCCGCGCCCAAGCACGAAAGACGGACCAGAAAAAGGCTAATCCGCAGCCAGCAGAACAGGCGGATACCCGCCAACCG‑GCAggcga  >  2:293334/1‑234 (MQ=11)                                                                                                                                                                                                                                      aTGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGCAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGGACAGCAACAAGCTAAAGCGGGACCCAAAGAACAGGCTGAACCGCGCAAAGCGCGCGGTTGc  >  2:647236/1‑239 (MQ=17)                                                                                                                                                                                                                                       tGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAg                                                                                                                                                                            <  1:148257/68‑1 (MQ=255)                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                            CGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCC‑AGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAACGGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGCACGCGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCG‑GCAGTTGC  >  NC_000913/1708611‑1709077

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑