Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,482,794	T→A	13.9%	A252A (GCT→GCA)	PP_3974 →	LysR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,482,794	0	T	A	13.9%	69.0 / 3.4	28	A252A (GCT→GCA)	PP_3974	LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (15/9);  new base A (2/2);  total (17/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.51e-01

CCGATCCCTTCGCTGAGGGTCAGGCATGGGTATCCTACTCGGGAGGCTTGTGCGGTTTGAAGGCAACAAGCTACGTCGAATGTCGGGTGCCCTCGGAGCTTATTTCTTACCGCACTGATTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCTTCAGGATGAGTTGTGGCTGCTCACCCACCAGGACATCAGAAAGTCCTGGCGGGT  >  NC_002947/4482652‑4482940                                                                                                                                               |                                                                                                                                                   ccGATCCCTTCGCTGAGGGTCAGGCATGGGTATCCTACTCGGGAGGCTTGTGCGGTTTGAAGGCAACAAGCTACGTCGAATGTCGGGTGCCCTCGGAGCTTATTTCTTCCCGCACTGATTCCGTGGCGGCAGCAAGTGCCGCTATTgcgg                                                                                                                                             >  2:327426/1‑150 (MQ=255)        cTTCGCTGAGGGTCAGGCATGGGTATCCTACTCGGGAGGCTTGTGCGGTTTGAAGGCAACAAGCTACGTCGAATGTCGGGTGCCCTCGGAGCTTATTTCTTACCGCACTGATTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGccc                                                                                                                                      >  1:640060/1‑149 (MQ=255)         ttCGCTGAGGGTCAGGCATGGGTATCCTACTCGGGAGGCTTGTGCGGGTTGAAGGCAACAAGCTACGTCGAATGTCGGGTGCCCTCGGAGCTTATTTCTTACCGCACTGATTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCCTg                                                                                                                                     >  1:199308/1‑150 (MQ=255)                aGGGTCAGGCATGGGTATCCTACTCGGTAGGCTTGTGCGGTTTGAAGGCAACAAGCTACGTCGAATGTCGGGTGCCCTCGGAGCTTATTTCTTACCGCACTGATTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCCTGGGTTTTg                                                                                                                              <  2:640060/150‑1 (MQ=255)                      ccgatctggTATCCTACTCGGGAGGCTTGTGCGGTTTGAAGGCAACAAGCTACGTCGAATGTCGGGTGCCCTCGGAGCTTATTTCTTACCGCACTGATTCCGTGGCGGCCGCCAGTGCCGCAATTGCGGCGGGCCTGGGTTTTGGTTtcc                                                                                                                        <  1:447945/143‑1 (MQ=255)                            gggTATCCTACTCGGGAGGCTTGTGCGGTTTGAATGCAACCAGCTACGTCGAATGTCGGCTGCCCTCGGAGCTTATTTCTTACCGCCCTGATTCCGGGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCt                                                                                                                  <  1:327426/150‑1 (MQ=255)                              gTATCCTACTCGGGAGGCTTGTGCGGTTTGAAGGCAACAAGCTACGTCGAATGTCGGGTGCCCTCGGAGCTTATTTCTTACCGCACTGATTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCCTGGGTTTTGGTTtcctagatcgg                                                                                                                >  2:447945/1‑143 (MQ=255)                                      cTCGGGAGGCTTGTGCGGTTTGAAGGCAACAAGCTACGTCGAATGTCGGGTGCCCTCGGAGCTTATTTCTTACCGCACTGATTCCGTGGCGGCAGCAAATGCCGCTATTACGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTgag                                                                                                        >  2:428518/1‑148 (MQ=255)                                               cTTGTGCGGTTTGAAGGCAACAAGCTACGTCGAATGTCGGGTGCCCTCGGAGCTTATTTCTTACCGCACTGATTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCAAGGGCATTGGTATCCTCCCCGGCGTGCTGGTGTACATTAc                                                                                               >  2:7444/1‑150 (MQ=255)                                                 ggtgCGGTTTGAAGGCAACAAGCTACGTCGAATGTCGGGTGCCCTCGGAGCTTATTTCTTACCGCACTGATTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTAccc                                                                                             <  2:194584/149‑1 (MQ=255)                                                                    aaGCTACGTCGAATGTCGGGTGCCCTCGGAGCTGATTTCTGACGGCACGGATTCCGTGGCGGCAGCAAGTGTCGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCgg                                                                          <  2:10920/150‑1 (MQ=255)                                                                       cTACGTCGAATGTCGGGTGCCCTCGGAGCTTATTTCTTACCGCACTGATTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGccc                                                                       >  1:197503/1‑150 (MQ=255)                                                                                      ggTGCCCTCGGAGCTTATTTCTTACCGCACTGATTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCt                                                        >  1:242531/1‑150 (MQ=255)                                                                                             tCGGAGCTTATTTCTTACCGCACTGATTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCTTCAGGAt                                                 >  1:452911/1‑150 (MQ=255)                                                                                                    ttATTTCTTACCGCACTGATTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCTTCAGGATGAGTtgt                                          <  2:242531/150‑1 (MQ=255)                                                                                                               cGCACTGATTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGAAACCGAGGTGGAAGATCTTCAGGACGAGTTGTGGCTGCTcacc                               >  2:310492/1‑150 (MQ=255)                                                                                                                gCACTGATTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCTTCAGGATGAGTTGTGGCTGCTcaccc                              >  2:766996/1‑150 (MQ=255)                                                                                                                    tGATTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCTTCAGGATGAGTTGTGGCTGCTCACccacca                          >  1:432879/1‑150 (MQ=255)                                                                                                                    tGATTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCCTGGGTTTTGCTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCTTCAGGATGAGTTGTGGCTGCTCACccacca                          <  1:428518/150‑1 (MQ=255)                                                                                                                      aTTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCTTCAGGATGAGTTGTGGCTGCTCACCCACCAgg                        >  2:697839/1‑150 (MQ=255)                                                                                                                                  cagcaAGTGCCGCTATTGCGGCGGGCCTCGGGGTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCTTCAGGATGAGTTGTGGCTGCTCACCCACCAGGACATGAGAAAGt            >  1:22543/1‑150 (MQ=255)                                                                                                                                   caggcccgCCGCAATAGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCTTCAGGATGAGTTGTGGCTGCTCACCCACCAGGACATCAGAAAGTc           >  1:789827/8‑150 (MQ=255)                                                                                                                                    aggcccgCCGCAATAGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCTTCAGGATGAGTTGTGGCTGCTCACccacca                          <  1:727081/128‑1 (MQ=255)                                                                                                                                    aggcccgCCGCAATAGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCTTCAGGATGAGTTGTGGCTGCTCACccacca                          >  2:727081/7‑134 (MQ=255)                                                                                                                                     caAGTGCCGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCTTCAGGATGAGTTGTGGCTGCTCACCCACCAGGACATCAGAAAGTCCt         <  1:127797/150‑1 (MQ=255)                                                                                                                                          gCCGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCTTCAGGATGAGTTGTGGCTGCTCACCCACCAGGACATCAGAAAGTCCTGGCgg    <  2:197503/150‑1 (MQ=255)                                                                                                                                           ccGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCTTCAGGATGAGTTGTGGCTGCTCACCCACCAGGACATCAGAAAGTCCTGGCggg   >  2:87758/1‑150 (MQ=255)                                                                                                                                            cGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCTTCAGGATGAGTTGTGGCTGCTCACCCACCAGGACATCAGAAAGTCCTGGCGGGt  <  2:452911/150‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                   CCGATCCCTTCGCTGAGGGTCAGGCATGGGTATCCTACTCGGGAGGCTTGTGCGGTTTGAAGGCAACAAGCTACGTCGAATGTCGGGTGCCCTCGGAGCTTATTTCTTACCGCACTGATTCCGTGGCGGCAGCAAGTGCCGCTATTGCGGCGGGCCTGGGTTTTGGTTTCCTCCCCTGCATGCTGGGCGACATTACCCCCGGATTGGTTCGAGCCGGCCCAGTGGTGCAGGAGCTTCAGGATGAGTTGTGGCTGCTCACCCACCAGGACATCAGAAAGTCCTGGCGGGT  >  NC_002947/4482652‑4482940

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑