Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	634,122	A→T	23.6%	Q142L (CAG→CTG)	PP_0546 →	sigma‑54 dependent transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	634,122	0	A	T	23.6%	27.1 / 6.1	17	Q142L (CAG→CTG)	PP_0546	sigma‑54 dependent transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (5/8);  new base T (2/2);  total (7/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01

GGGGTGATCCTCAATTGCGTCAGTGCCCCCGCCGAGCGGCGCAGCTTCGAGCGTGCCGGGCTGTGGCTGGGCGCTGACTGGAGCGAGGCGCGCGAGGGCACCAATGGCATCGGCACATGTCTGGTCGAGCGCCAGGCGCT‑GACCATCCATCAGAACGAGCACTTCCGTGGCCGTCACACCGGGCTGACCTGCTCGGCCAGCCCGGTGTTCGACCCGCATGGCGACCTGCTGGCGGTGCTCGACGTGTCCTCTGCGCGCCCCGACGTATCGCGGCAAAGCCAGT  >  NC_002947/633989‑634271                                                                                                                                      |                                                                                                                                                       ggggTGATCCTCAATTGCGTCAGTGCCCCCGCCGAGCGGCGCATCTTCGAGCGTGCCGGGCTGTGGCTGGGCGCTGACTGGAGCGAGGCGCGCGAGGGCACCAATGGCATCGGCACATGTCTGGTCGAGCGCCAGGCGCT‑GAccatccat                                                                                                                                       <  2:368634/150‑1 (MQ=255)      gATCCTCAATTGCGTCAGTGCCCCCGCCGAGCGGCGCAGCTTCGAGCGTGCCGGGCTGTGGCTGGGCGCTGACTGGAGCGAGGCGCGCGAGGGCACCAATGGCATCGGCACATGTCTGGTCGAGCGCCAGGCGCT‑GACCATCCATCAGaa                                                                                                                                  <  1:31316/150‑1 (MQ=255)                    tCAGTGCCCCCGCCGAGCGGCGCAGCTTCGAGCGTGCCGGGCTGTGACTGGGCGCTGACTGGAGCGAGGCGCGCGAGGGCACCAATGGCATCGGCACATGTCTGGTCGAGCGCCAGGCGCT‑GACCATCCATCAGAACGAGCACTTCCGTg                                                                                                                    >  2:167101/1‑150 (MQ=255)                       gTGCCCCCGCCGAGCGGCGCAGCTTCGAGCGTGCCGGGCTGTGGCTGGGCGCTGACTGGAGCGAGGCGCGCGAGGGCACCAATGGCATCGGCACATGTCTGGTCGAGCGCCAGGCGCT‑GACCATCCATCAGAACGAGCACTTCCGTGGcc                                                                                                                 >  2:546085/1‑150 (MQ=255)                       gTGCCCCCGCCGAGCGGCGCAGCTTCGAGCGTGCCGGGCTGTGGCTGGGCGCTGACTGGAGCGAGGCGCGCGAGGGCACCAATGGCATCGGCACATGTCTGGTCGAGCGCCAGGCGCT‑GACCATCCATCAGAACGAGCACTTCCGTGGcc                                                                                                                 <  2:199026/150‑1 (MQ=255)                                  gAGCGGCGCAGCTTCGAGCGTGCCGGGCTGTGGCTGGGCGCTGACTGGAGCGAGGCGCGCGAGGGCACCAATGGCATCGGCACATGTCTGGTCGAGCGCCAGGCGCT‑GACCATCCATCAGAACGAGCACTTCCGTGGCCGTCACACCggg                                                                                                      <  2:487382/150‑1 (MQ=255)                                       gcgcAGCTTCGAGCGTGCCGGGCTGTGGCTGGGCGCTGACTGGAGCGAGGCGCGCGAGGGCACCAATGGCATCGGCACATGTCTGGTC‑AGCGCCTGGCGCTCGAcca                                                                                                                                            >  1:404616/1‑107 (MQ=255)                                       gcgcAGCTTCGAGCGTGCCGGGCTGTGGCTGGGCGCTGACTGGAGCGAGGCGCGCGAGGGCACCAATGGCATCGGCACATGTCTGGTC‑AGCGCCTGGCGCTCGAcca                                                                                                                                            <  2:404616/107‑1 (MQ=255)                                             cTTCGAGCGTGCCGGGCTGTGGCTGGGCGCTGACTGGAGCGAGGCGCGCGAGGGCACCAATGGCATCGGCACATGTCTGGTCGAGCGCCAGGCGCT‑GACCATCCATCAGAACGAGCACTTCCGTGGCCGTCACACCGGGCTGACCTGCTc                                                                                           >  2:264471/1‑150 (MQ=255)                                                  aGCGTGCCGGGCTGTGGCTGGGCGCTGACTGGAGCGAGGCGCGCGAGGGCACCAATGGCATCGGCACATGTCTGGTC‑AGCGCCTGGCGCTCGAccagacat                                                                                                                                       <  1:15075/101‑6 (MQ=38)                                                  aGCGTGCCGGGCTGTGGCTGGGCGCTGACTGGAGCGAGGCGCGCGAGGGCACCAATGGCATCGGCACATGTCTGGTC‑AGCGCCTGGCGCTCGAccagacat                                                                                                                                       >  2:15075/1‑96 (MQ=38)                                                                                               aGGGCACCAATGGCATCGGCAAATGTGCGTTCGAGCGCCAGGCGCT‑GAACATACATCAGAACTAGCATTTTCGTGGCCGTCACACCGGGCTGACCTGCTCGGCCAGCCCGGTGTTCGACCCGCATGGCGACCTGCTGGCGGTGCTCGACg                                         <  1:167101/150‑1 (MQ=255)                                                                                                gggCACCAATGGCATCGGCACATGTCTGGTCGAGCGCCAGGCGCT‑GACCATCCATCAGAACGAGCACTTCCGTGGCCGTCACACCGGGCTGACCTGCTCGGCCAGCCCGGTGTTCGACCCGCATGGCGACCTGCTGGCGGTGCTCGACgt                                        <  1:436867/150‑1 (MQ=255)                                                                                                  gCACCAATGGCATCGGCACATGTCTGGTCGAGCGCCAGGCGCT‑GACCATCCATCAGAACGAGCACTTCCGTGGCCGTCACACCGGGCTGACCTGCTCGGACAGCCCGGTGTTCGACCCGCATGGCGACCTGCTGGCGGTGCTCGACgtgt                                      >  2:323928/1‑150 (MQ=255)                                                                                                   cACCAATGGCATCGGCACATGTCTGGTCGAGCGCCAGGCGCT‑GACCATCCATCAGAACGAGCACTTCCGTGGCCGTCACACCGGGCTGACCTGCTCGGCCAGCCCGGTGTTCGACCCGCATGGCGACCTGCTGGCGGTGCTCGACGTGTc                                     >  2:217383/1‑150 (MQ=255)                                                                                                   cACCAATGGCATCGGCACATGTCTGGTCGAGCGCCAGGCGCT‑GACCATCCATCAGAACGAGCACTTCCGTGGCCGTCACACCGGGCTGACCTGCTCGGCCAGCCCGGTGTTCGACCCGCATGGCGACCTGCTGGCGGTACTCGACGTGTc                                     <  1:523748/150‑1 (MQ=255)                                                                                                                             tCGAGCGCCAGGCGCT‑GACCATCCATCAGAACGAGCACTTCCGTGGCCGTCACACCGGGCTGACCTGCTCGGCCAGCCCGGTGTTCGACCCGCATGGCGACCTGCTGGCGGTGCTCGACGTGTCCTCTGCGCGCCCCGACGTATCGCGGc           <  2:401789/150‑1 (MQ=255)                                                                                                                                      aGGCGCT‑GACCATCCATCAGAACGAGCACTTCCGTGGCCGTCACACCGGGCTGACCTGCTCGGCCAGCCCGGTGTTCGACCCGCATGGCGACCTGCTGGCGGTGCTCGACGTGTCCTCTGCGCGCCCCGACGTATCGCGGCAAAGCCAGt  <  2:53320/150‑1 (MQ=255)                                                                                                                                      |                                                                                                                                                       GGGGTGATCCTCAATTGCGTCAGTGCCCCCGCCGAGCGGCGCAGCTTCGAGCGTGCCGGGCTGTGGCTGGGCGCTGACTGGAGCGAGGCGCGCGAGGGCACCAATGGCATCGGCACATGTCTGGTCGAGCGCCAGGCGCT‑GACCATCCATCAGAACGAGCACTTCCGTGGCCGTCACACCGGGCTGACCTGCTCGGCCAGCCCGGTGTTCGACCCGCATGGCGACCTGCTGGCGGTGCTCGACGTGTCCTCTGCGCGCCCCGACGTATCGCGGCAAAGCCAGT  >  NC_002947/633989‑634271

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑