Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,464,811	G→A	T457I (ACC→ATC)	treB ←	trehalose‑specific PTS enzyme IIBC component

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,464,811	0	G	A	91.7%	18.1 / ‑6.2	12	T457I (ACC→ATC)	treB	trehalose‑specific PTS enzyme IIBC component
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (6/5);  minor base T (0/1);  total (6/6)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.85e-01

CCAGGTGTTGGATAACGCCACGTAAATCGCCGGTACCGCTACCCGTGGTGTCCTGAAAACTCTTTGGATAAATCTGGTAGATAACGCCGTTTTGCCACCAGTGGGGAAGATGAGTCATTACGTTATTCCTGCGAATGCGAGGGGGCGCAATTGCGCCCCGAAGAAAATTAAACAATGTCCAGCGTGCCCAGGCGGTATTTCCGCTGATAGATAAACGAGGTGAGTACAATCGGGATGATGATGGCGATAGCCATTGCCAGCGCAAACACCTGCCAGTAGCTCGGTTGAATCGAGAGAATTCCCGGCAGGCCGCCTACGCCGATGCCATTCGCCATAACGCCGTTCAGGCCGCATAGCAATCCTGCCAGACCAGAACCAATCATCGCGCACAGCATC  >  NC_000913/4464592‑4464987                                                                                                                                                                                                                            |                                                                                                                                                                                 ccAGGTGTTGGATAACGCCACGTAAATCGCCGGTACCGCTACCCGTGGTGTCCTGAAAACTCTTTGGATAAATCTGGTAGATAACGCCGTTTTGCCACCAGTGGGGAAGATGAGTCATTACGTTATTCCTGCGAATGCGAGGGGGCGCAATTGCGCCCCGAAGAAAATTAAACAATGTCCAGCGTGCCCAGGCGGTATTTCCGCTGATAGATAAACGAGATGAGTACAATCGGGATGATGATGGCGATAgn                                                                                                                                                   <  1:153006/251‑2 (MQ=255)          ggATAACGCCACTTAAATCGCCGGTCCCGCTACCCGTGGTGTCCTGAAAACTCGTTGGATAAATCTGGTAGATAACGCCGTGTTGCCACCAGTGGGGAAGATGAGTCATTACTTTATTCCCGCCAATCCGAGGGGTCGCAAGTGCTCCCCTAAGAAAATTAAACAATCTCCCGCGTGCCCAGGCTGTATTTCCTCGGATACATAAACGAGATTAGTTCAATCGGTATGATGATGGCGATAGCCATTGCCAg                                                                                                                                          <  1:192141/251‑1 (MQ=255)          ggATAACGCCACGTAAATCGCCGGTACCGCTACCCGTGGTGTCCTGAAAACTCTTTGGATAAATCTGGTAGATAACGCCGTTTTGCCACCAGTGGGGAAGATGAGTCATTACGTGATTCCGGCGAATGCGAGGGGGCGCAATTGCGCCCCGAAGAAAATTAAACAATGTCCAGCGTGCCCAGGCGGTATTTCCGCTGATAGATAAACGAGATGAGTACAATCGGGATGATGATGGCGATAGCCATTGCCAg                                                                                                                                          <  1:175194/251‑1 (MQ=255)                                                                          ntGGTAGATAACGCCGTTTTGCCACCAGTGGGGAAGATGAGTCATTACGTTATTCCTGCGAATGCGAGGGGGCGCAATTGCGCCCCGAAGAAAATTAAACAATGTCCAGAGTGCCCAGGCGGTATTTCCGCTGATAGATAAACGAGATGAGTACAATCGGGATGATGATGGCGATAGCCATTGCCAGCGCAAACACCTGCCAGTAGCTCg                                                                                                                   >  1:32790/2‑210 (MQ=255)                                                                               aGATAACGCCGTTTTGCCACCAGTGGGGAAGATGAGTCATTACGTTATTCCTGCGAATGCGAGGGGGCGCAATTGCGCCCCGAAGAAAATTAAACAATGTCCAGCGTGCCCAGGCGGTATTTCCGCTGATAGATAAACGAGATGAGTACAATCGGGATGATGATGGCGATAGCCATTGCAAGCGCAAACACCTGCCAGTAGCTCGGTTGAATCGAGAGAATTCCCGGCAGGCCGCCTACGCCGATGCCAtt                                                                     >  1:8446/1‑251 (MQ=255)                                                                                gATAACGCCATTTTGCCACCAGTGGGGAAGATGAGTCATTACGTTATTACTGCGAATGCGAGGGGGCGCAATTGCGACCCGAAGAAAATTAAACAATGTCCAGCGGGCCCAGGCGGTATTTCCGCTGATAGATAAACGAGATGCGTACAATCGGGATGATGATGGCGATAGCCATTGCCAGCGCAAACAACTGCCAGTAGCTCGGTTGAATCGAGAGAATTCCCGGCAGGCCGCCTACGc                                                                               >  1:84248/1‑240 (MQ=255)                                                                                      tccGTTTGGCCACCAGTGGGGAAGATGAGTTATTACTTTATTCCTGCGAAGGCGAGGGGGCGCAATTGCGCCCCGAAGAAAATTAAACAAGGTCCAGCTTTCCCAGTCTGTATTTCCGCTTATAGATAAACGAGATGAGTACATTCGGGATGATGATGGCGATAGCCATTGCCAGCGCAACCACCTGCCAGTAGCTCGGTTGAATCgaga                                                                                                       <  1:101932/209‑1 (MQ=255)                                                                                               ccaccaGTGGGGAAGATGAGTCATTACGTTATTCCTGCGAATGCGAGGGAGCGCACTTGCGCCCCGAAGAAAATTAAACCATGTCCAGCGTGCCCAGGCGGTATTTCCGCTGATAGATAAACGCGATGAGTACAATCGGGATGATGATGGCGATAGCCATTGCCAGCGCAAACACCTGCCAGTAGCTCGGTTGAATCGAGAGAATTCCCGGCAGGCCGCCTACGCCGATGCCATTCGCCATAACGCCGTTc                                                     >  1:248077/1‑251 (MQ=255)                                                                                                     gttgggAAGATGAGTCATTACGTGATTCCTGCGAATGCGAGGGGGCGCAATGGCTCCCCGAAGAAAATTAAACAATGTCCAGCGTGCCCAGGCGTGATGTCCGCTGATAGATAACCGAGTTGAGTGCAATCGGGATGAGGATGGCGATAGCCATTGCCAGCGCa                                                                                                                                      <  1:238680/161‑1 (MQ=255)                                                                                                                     aTTACTTTATTCCTGCGAAGGCGGGGGGGCGCAATTGCGCTCCGAAGAAAATTAAACAATGTCCAGCGTGCCCAGGCGGTATTTCCGCTTAGAGATAAACGAGATGAGTACAATCGGGATGATGATGGCGATAGCCATTGCCAGCGCaaa                                                                                                                                    <  1:114489/150‑1 (MQ=255)                                                                                                                                                 gcgcAATTGCGCCCCGAAGAAAATTAAACAATGTCCAGCGTGCCCAGGCGGTATTTCCGCTGATAGATAACCGCGATGAGTACAATCGGGATGCTGATGGCGATAGCCATTGCCAGCGCAAACACCTGCCAGTAGCTCGGTTGACTAGAGAGCATTCCCGGCCGGCCGCCTACGCCGCTGCCATTCGCCATAACg                                                           >  1:215351/1‑195 (MQ=255)                                                                                                                                                  cgcAATTGCGCCCCGAAGAAAATTAAACAATGTCCAGCGTGCCCAGGCGGTATTTCCGCTGATAGATAAACGAGATGAGTACAATCGGGATGATGATGGCGATAGCCATTGCCAGCGCAAACACCTGCCAGTAGCTCGGTTGAATCGAGAGAATTCCCGGCAGGCCGCCTACGCCGATGCCATTCGCCATAACGCCGTTCAGGCCGCATAGCAATCCTGCCAGACCAGAACCAATCATCGCGCACAGCATc  >  1:3103/1‑251 (MQ=255)                                                                                                                                                                                                                            |                                                                                                                                                                                 CCAGGTGTTGGATAACGCCACGTAAATCGCCGGTACCGCTACCCGTGGTGTCCTGAAAACTCTTTGGATAAATCTGGTAGATAACGCCGTTTTGCCACCAGTGGGGAAGATGAGTCATTACGTTATTCCTGCGAATGCGAGGGGGCGCAATTGCGCCCCGAAGAAAATTAAACAATGTCCAGCGTGCCCAGGCGGTATTTCCGCTGATAGATAAACGAGGTGAGTACAATCGGGATGATGATGGCGATAGCCATTGCCAGCGCAAACACCTGCCAGTAGCTCGGTTGAATCGAGAGAATTCCCGGCAGGCCGCCTACGCCGATGCCATTCGCCATAACGCCGTTCAGGCCGCATAGCAATCCTGCCAGACCAGAACCAATCATCGCGCACAGCATC  >  NC_000913/4464592‑4464987

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑