Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,122,670:1	+G	8.9%	intergenic (‑35/+16)	PP_3625 ← / ← PP_3626	LysE family transporter/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,122,670	1	.	G	8.9%	167.4 / 7.9	45	intergenic (‑35/+16)	PP_3625/PP_3626	LysE family transporter/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (22/19);  new base G (2/2);  total (24/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

CGTTGGCCATGGGCAAGGCTGTTGTTGATAGCCATCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTCGTCACGGGTACGGC  >  NC_002947/4122526‑4122816                                                                                                                                                  |                                                                                                                                                   cGTTGGCCATGGGCAAGGCTGTTGTTGATAGCCATCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAAt                                                                                                                                                <  5:15990/149‑1 (MQ=255)        cATGGGCAAGGCTGTTGTTGATAGCCATCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACg                                                                                                                                          >  3:33174/1‑148 (MQ=255)                         ttgATAGCCATCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAAt                                                                                                                                                >  5:124804/1‑125 (MQ=255)                         ttgATAGCCATCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAAt                                                                                                                                                <  6:124804/125‑1 (MQ=255)                           gATAGCCATCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCa                                                                                                                           >  1:127940/1‑144 (MQ=255)                           gATAGCCATCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCa                                                                                                                           <  2:127940/144‑1 (MQ=255)                                   tCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTg                                                                                                               <  5:74356/148‑1 (MQ=255)                                   tCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTg                                                                                                               >  6:74356/1‑148 (MQ=255)                                             aGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCttttt                                                                                                    <  5:60337/149‑1 (MQ=255)                                             aGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGAACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCttttt                                                                                                    >  4:207545/1‑149 (MQ=255)                                              gggCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTg                                                                                                   >  4:251281/1‑149 (MQ=255)                                                          gCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCt                                                                                         <  3:251281/147‑1 (MQ=255)                                                           cGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGcc                                                                                          >  6:167881/1‑145 (MQ=255)                                                           cGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGcc                                                                                          <  5:167881/145‑1 (MQ=255)                                                            gATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCAt                                                                                     >  4:184948/1‑149 (MQ=255)                                                                 cgATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCtt                                                                                                                >  1:99265/1‑117 (MQ=255)                                                                 cgATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCtt                                                                                                                <  2:99265/117‑1 (MQ=255)                                                                                     aaCGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTg                                                            >  4:175390/1‑149 (MQ=255)                                                                                      aCGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTgg                                                           >  5:196706/1‑149 (MQ=255)                                                                                            aCAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCAttt                                                     <  1:319508/149‑1 (MQ=255)                                                                                              aGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGAt                                                                                              <  7:97399/106‑1 (MQ=255)                                                                                              aGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGAt                                                                                              >  8:97399/1‑106 (MQ=255)                                                                                                 gAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCg                                                >  2:293223/1‑149 (MQ=255)                                                                                                   gTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCggg                                              <  3:175390/149‑1 (MQ=255)                                                                                                    tGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTTCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGc                                             <  4:33174/149‑1 (MQ=255)                                                                                                        aaTCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCt                                         >  4:334254/1‑149 (MQ=255)                                                                                                            cATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCAt                                     <  3:184948/149‑1 (MQ=255)                                                                                                             aTTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCAt                                                                                     <  2:193083/100‑1 (MQ=255)                                                                                                             aTTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCAt                                                                                     >  1:193083/1‑100 (MQ=255)                                                                                                                    ggCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGc                              >  6:286755/1‑148 (MQ=255)                                                                                                                         gTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTg                        >  7:74394/1‑149 (MQ=255)                                                                                                                            aGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCAc                                                                       >  2:287456/1‑99 (MQ=255)                                                                                                                            aGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCAc                                                                       <  1:287456/99‑1 (MQ=255)                                                                                                                            aGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCg                      <  3:334254/148‑1 (MQ=255)                                                                                                                                 aaCAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTc                <  5:286755/149‑1 (MQ=255)                                                                                                                                  aCAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTcgccg                                                                          >  7:170730/1‑90 (MQ=255)                                                                                                                                  aCAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTcgccg                                                                          <  8:170730/90‑1 (MQ=255)                                                                                                                                      gAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTCGTCAc           >  2:197354/1‑149 (MQ=255)                                                                                                                                        aaGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTCGTCACgg         <  8:74394/149‑1 (MQ=255)                                                                                                                                         aaccTGCGTGCAATTG‑ACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTCGTCAc           >  1:64024/4‑146 (MQ=255)                                                                                                                                         aaccTGCGTGCAATTG‑ACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTCGTCAc           <  2:64024/143‑1 (MQ=255)                                                                                                                                           gCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTCGTCACGGGTa      >  1:167371/1‑149 (MQ=255)                                                                                                                                            cTGCGTGCAATTG‑ACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTc                <  2:220473/138‑1 (MQ=255)                                                                                                                                            cTGCGTGCAATTG‑ACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTc                >  1:220473/1‑138 (MQ=255)                                                                                                                                               cGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCGTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTCGTCACGGGTACGGc  >  1:247363/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                   CGTTGGCCATGGGCAAGGCTGTTGTTGATAGCCATCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTCGTCACGGGTACGGC  >  NC_002947/4122526‑4122816

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑