Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,053,218	G→A	17.5%	intergenic (+19/+27)	PP_2664 → / ← agmR	two‑component system sensor histidine kinase/response regulator/glycerol metabolism activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,053,218	0	G	A	17.5%	81.4 / 10.5	40	intergenic (+19/+27)	PP_2664/agmR	two‑component system sensor histidine kinase/response regulator/glycerol metabolism activator
Reads supporting (aligned to +/- strand):  ref base G (18/15);  new base A (3/4);  total (21/19)
Fisher's exact test for biased strand distribution p-value = 6.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.44e-01

TCAACTACAGCAACGATCTCAAGCAGCAGATCCGCGAACTGGGTCACACGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTACCCGGTTGTGCACATTGAGTTTGCGCAAAATCGCCGAAACGTGGGCCTTGACGGTGG  >  NC_002947/3053075‑3053357                                                                                                                                                |                                                                                                                                            tCAACTACAGCAACGATCTCAAGCAGCAGATCCGCGAACTGGGTCACACGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGGTTGAt                                                                                                                                        <  7:17192/149‑1 (MQ=255)        cAGCAACGATCTCAAGCAGCAGATCCGCGAACTGGGTCACACGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGGTTGATCcgcg                                                                                                                                   >  4:207602/1‑147 (MQ=255)         aGCAATGATCTCAAGCAGCAGATCGGACAACTGGGTCACAGGCTGATGCACAAGCCCTTAACACCGATGAATCTCTTGACCGCCATGAGCCTTCTGCTGGCGAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGATCAACCCGCGAAg                                                                                                                                <  8:215447/149‑1 (MQ=255)         aGCAACGATCTCAAGCAGCAGATCCGCGAACTGGGTCACACGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGAGGTTGGCCCCTTCGCGGGTTGATCCGCGAAg                                                                                                                                >  5:97372/1‑149 (MQ=255)          gCAACGATCTCAAGCAGCAGATCCGCGAACTGGGTCACACGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGGTTGATCCGCGAAGc                                                                                                                               <  3:207602/149‑1 (MQ=255)          gCAACGATCTCAAGCAGCAGATCCGCGAACTGGGTCACACGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGATCAACCCGCGAAGc                                                                                                                               <  4:328465/149‑1 (MQ=255)            aaggATCTCAAGCAGCAGTTCCGGGTTCTGGGTCACACGCTGATTCACATGCCAGTAAGACGGATGAAACTCAAGACGGCGATGAGCGATCTGCTGGCCAGTGGCTTGGCATAGCTGTTGGGCGCTTGGCGGATGAACCCGCGAAggg                                                                                                                              <  4:88894/145‑3 (MQ=255)            aaCGATCTCAAGCAGCAGATCCGCGAACTGGGTCACACGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGATCAACCCGCGAAGCgg                                                                                                                             <  8:219019/149‑1 (MQ=255)            aaCGATCTCAAGCAGCAGATCCGCGAACTGGGTCACACGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGATCAACCCGCGAAGCg                                                                                                                              >  3:88894/1‑148 (MQ=255)                   tcAAGCAGCAGATCCGCGAACTGGGTCACACGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGaa                                                                                                                       >  7:107770/1‑148 (MQ=255)                     aaGCAGCAGATCCGCGAACTGGGTCACACGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTAGCGGGTTGATACGCGAAGCGGCCGGAAccg                                                                                                                    >  8:10068/1‑147 (MQ=255)                     aaGCAGCAGATCCGCGAACTGGGTCACACGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGACGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCCCCGGTTGATCCGCGAAGCGGGCGGAACAg                                                                                                                    >  5:282922/1‑149 (MQ=255)                                  gcgAACTGGGTCACACGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGgcg                                                                                                          >  2:276378/1‑146 (MQ=255)                                          ggTCACACGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGGTTGATACGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAg                                                                                               >  1:38763/1‑149 (MQ=255)                                          ggTCACACGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGAATAGCGGTTGGCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATc                                                                                                 <  7:173207/147‑1 (MQ=255)                                              acacGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCATAGCGGGTTGATCCCCGAAGCGGCCGGAAAACCTCAACGGCGCAGATAATAAGCaa                                                                                            >  4:44820/1‑148 (MQ=255)                                                acGCTGATGCACAACACCGTAAGACCGATGAAACTCAAGACGCCGAAGACCCATCTGCTGCCCAGTGCCTTGTCATAGCGCTTCGCCGCTTCGCGGGTTGAAACGACAAGCGCCCGCAACACCACAACCTCCCACATAAACACCaaaa                                                                                          >  4:270828/1‑148 (MQ=255)                                                 cGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATc                                                                                        <  1:276378/149‑1 (MQ=255)                                                         caaaaGCACTTAAGACCGATGAAACTCAAGACGGCTATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGc                                                                                <  7:314365/146‑1 (MQ=255)                                                                  gTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCTGTGGGTTGGCATAGCGGTTGGCCGCTTCGGGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGa                                                                       <  3:270828/149‑1 (MQ=255)                                                                    aaGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCATCGCGGGTTGATCCGCCAAGCGGCCGGGAAAGCGCAACGGCCCAACTAAAAAGCAAAATAGAAATAACCAGGAcatag                                                                      >  6:137762/1‑144 (MQ=255)                                                                      gACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTAGCCGGTTTAACCCCCAAGCGGGCCGAAAAGCGCAAAGGCACAGCTAATCATCCAAAACCATATGGCAACCACAGAGGAt                                                                   >  2:233963/1‑149 (MQ=255)                                                                           aTGAACCTCAAGACGGCTAGGAGCCATCTGCGGGCCAGTGGCTTGGCATAGCGGTGGGCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCtt                                                              <  3:152636/149‑1 (MQ=255)                                                                               aaCTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTAGCGGGTTGATACGCGCAGCGGCCGGAACAGCTCAACGGCGCAGATAATCCGCAAAATAGAGTTCGCCAGCACTGAGGGTGGCTTGttc                                                          >  8:239551/1‑147 (MQ=255)                                                                               aaCTCAAGACGGCGATGAGCAATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTAc                                                          <  3:44820/149‑1 (MQ=255)                                                                                  tCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCCACGGCGCAGATAATCAGCAAAATAGAAATCGCCACCACTGAGGATGGCTTGTACCCg                                                       >  2:116127/1‑149 (MQ=255)                                                                                      gACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTACCCGGTtg                                                   >  5:170293/1‑149 (MQ=255)                                                                                          gCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTACCCGGTTGTGca                                               >  3:221337/1‑149 (MQ=255)                                                                                              tgcgCCATCTGCGTGCCAGTGGCTTGTCATAGCGGTTGGCCGCTTCGCGGGTTGATCCGCCAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTACCCGGTTGTGCACAtt                                           <  7:10068/146‑1 (MQ=255)                                                                                                         gtgGCCAGTGGCTTGGCATTGCGGTTGGCGGCTTCGCGGGTTGATCGGCGATGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTACCCGGTTGTGCACATTGAGTTTgc                                   <  5:137762/145‑1 (MQ=255)                                                                                                              cAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTACCCGGTTGTTCACATTGAGTTAGCGCAAAATc                           >  5:105579/1‑149 (MQ=255)                                                                                                                  ggCTTGGCATAGCGGTTGGCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTACCCGGTTGTGCACATTGAGTTTGCGCAAAATCGcc                        <  7:239551/148‑1 (MQ=255)                                                                                                                     ttGGCATTGCGGTTGGCCGCTTCGCGGGTTGATCCGCTAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTAc                                                          <  3:282622/111‑1 (MQ=255)                                                                                                                        gCATAGCGGTTGGCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTACCCGGTTGTGCACATTGAGTTTGCGCAAAATCGCCGAAACGt                 <  4:221337/149‑1 (MQ=255)                                                                                                                          aTAGCGGTTGGCCGCTTCGCGGGTTTATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTACCCGGTTGTGCACATTGAGTTAGCGCAAAATCGCCGAAACGTgg               <  6:105579/149‑1 (MQ=255)                                                                                                                               ggTTGGCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTACCCGGTTGTGCACATTGAGTTTGCGCAAAATCGCCGAAACGTGGGCCtt          >  5:115391/1‑149 (MQ=255)                                                                                                                                    gCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTACCCGGTTGTGCACATTGAGTTTGCGCAAAATCGCCGAAACGTGGGCCTTGACg      <  6:115391/148‑1 (MQ=255)                                                                                                                                    gCCGCTTCGCGGATCAACCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTACCCGGGTGTGCACAGTGAGTTGGCGCAAAATCGCCGAAACGTGGGCCTTGACgg     >  8:182804/1‑149 (MQ=255)                                                                                                                                      cGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTACCCGGTTGTGCACATTGAGTTTGCGCAAAATCGCCGAAACGTGGGCCTTGACggtg   >  7:329140/1‑149 (MQ=255)                                                                                                                                       gCTTCGCGGATCAACCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTACCCGGTTGTGCACATTGAGTTTGCGCAAAATCGCCGAAACGTGGGCCTTGACggtgg  >  8:267480/1‑149 (MQ=255)                                                                                                                                                |                                                                                                                                            TCAACTACAGCAACGATCTCAAGCAGCAGATCCGCGAACTGGGTCACACGCTGATGCACAAGCCCGTAAGACCGATGAAACTCAAGACGGCGATGAGCCATCTGCTGGCCAGTGGCTTGGCATAGCGGTTGGCCGCTTCGCGGGTTGATCCGCGAAGCGGCCGGAACAGCTCAACGGCGCAGATAATCAGCAAAATCGATATCGCCAGCACTGAGGATGGCTTGTACCCGGTTGTGCACATTGAGTTTGCGCAAAATCGCCGAAACGTGGGCCTTGACGGTGG  >  NC_002947/3053075‑3053357

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑