Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,122,677	Δ1 bp	8.7%	intergenic (‑42/+9)	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	4,122,677	0	C	.	8.7%	140.9 / 7.3	46	intergenic (‑42/+9)	PP_3625/PP_3626	LysE family transporter/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (23/18);  new base . (2/2);  total (26/20)
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

CATGGGCAAGGCTGTTGTTGATAGCCATCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTCGTCACGGGTACGGCCGCAGC  >  NC_002947/4122533‑4122822                                                                                                                                                  |                                                                                                                                                  cATGGGCAAGGCTGTTGTTGATAGCCATCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACg                                                                                                                                                >  3:33174/1‑148 (MQ=255)                    gATAGCCATCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCa                                                                                                                                 >  1:127940/1‑144 (MQ=255)                    gATAGCCATCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCa                                                                                                                                 <  2:127940/144‑1 (MQ=255)                            tCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTg                                                                                                                     >  6:74356/1‑148 (MQ=255)                            tCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTg                                                                                                                     <  5:74356/148‑1 (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                                                                                                                      <  2:99265/117‑1 (MQ=255)                                                          cgATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCtt                                                                                                                      >  1:99265/1‑117 (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                                                                                <  8:170730/90‑1 (MQ=255)                                                                                                                           aCAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTcgccg                                                                                >  7:170730/1‑90 (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                      >  1:220473/1‑138 (MQ=255)                                                                                                                                     cTGCGTGCAATTG‑ACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTc                      <  2:220473/138‑1 (MQ=255)                                                                                                                                        cGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCGTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTCGTCACGGGTACGGc        >  1:247363/1‑149 (MQ=255)                                                                                                                                             aaTTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTCg                     >  1:44930/1‑132 (MQ=255)                                                                                                                                             aaTTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTCg                     <  2:44930/132‑1 (MQ=255)                                                                                                                                             aaTTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTCGTCACGGGTACGGCCg      >  2:210581/1‑147 (MQ=255)                                                                                                                                               ttGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTCGTCACGGGTACGGCCGCAGc  >  6:343282/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                  CATGGGCAAGGCTGTTGTTGATAGCCATCAAGGTGGCAGGGCCTGGGCTGGCGATCGCGATGGCGGCGACCAGGGTAAACGCGAACAGCGAGTGAGAATCCATTTTCAGGCTCGTCAGACAAACAGGAAAGGCTGCGT‑CAATTGCACGCAGGTTCAGCCGGCATTCTGCCGCTTGGCCGCCTTTTTGGCGATAGCCTTCATTCGCGTCGCCGCACGCTGCACAGTGGCCATTTTCTCGGGCCGCTTCATGCCCCGCCACTTGCGGATTTCGTCACGGGTACGGCCGCAGC  >  NC_002947/4122533‑4122822

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