Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,906,562	A→G	I91T (ATC→ACC)	htpX ←	protease HtpX

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,906,562	0	A	G	96.2%	80.8 / NA	26	I91T (ATC→ACC)	htpX	protease HtpX
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (9/16);  minor base C (1/0);  total (10/16)
Fisher's exact test for biased strand distribution p-value = 3.85e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCATCACGGCGCGCACCGGTTGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGATCCCCGCCTGACGAGCCTGGGTTGCTACAGTATTGACCAGCCAACGTTCCCTTTCGTTACGCGGTTGCTCGATC  >  NZ_CP009273/1906489‑1906636                                                                          |                                                                           ggCATCACGGCGCGCACCGGTTGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCTTAGCGCTCCCCGCGTGACGGGc                                                            >  2:379692/1‑90 (MQ=255)  gCATCACGGCGCGCACCGGTTGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGcc                                                           >  2:93641/1‑90 (MQ=255)  gCATCACGGCGCGCACCGGTTGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGcc                                                           <  2:137794/90‑1 (MQ=255)        cGGCGCGCACCGGTTGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGtt                                                     <  2:79895/90‑1 (MQ=255)        cGGCGCGCACCGGTTGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGtt                                                     <  1:306807/90‑1 (MQ=255)        cGGCGCGCACCGGTTGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGtt                                                     <  2:404311/90‑1 (MQ=255)        cGGCGCGCACCGGTTGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGtt                                                     <  2:399556/90‑1 (MQ=255)        cGGCGCGCACCGGTTGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGtt                                                     <  1:50636/90‑1 (MQ=255)        cGGCGCGCACCGGTTGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGtt                                                     <  2:32501/90‑1 (MQ=255)        cGGCGCGCACCGGTTGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGtt                                                     <  2:118072/90‑1 (MQ=255)        cGGCGCGCACCGGTTGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGtt                                                     <  2:135124/90‑1 (MQ=255)        cGGCGCGCACCGGTTGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGtt                                                     <  2:213414/90‑1 (MQ=255)             cgcACCGGTTGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGTTGCTAc                                                <  2:339130/90‑1 (MQ=255)               cACCGGTTGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGTTGCTACAg                                              >  2:14716/1‑90 (MQ=255)                      tGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGTTGCTACAGTATTGAc                                       >  1:316916/1‑90 (MQ=255)                                 tGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGTTGCTACAGTATTGACCa                                     >  1:109441/1‑81 (MQ=255)                                 tGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGTTGCTACAGTATTGACCa                                     <  2:109441/81‑1 (MQ=255)                                               tGGTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGTTGCTACAGTATTGACCAGCCAACGTTCCCTTTCGTTAcgc              >  1:306461/1‑90 (MQ=255)                                                 gTAGATAGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGTTGCTACAGTATTGACCAGCCAACGTTCCCTTTCGTTACGCgg            <  2:353182/90‑1 (MQ=255)                                                       aGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCt                                                          <  2:331434/38‑1 (MQ=255)                                                       aGCCACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCt                                                          >  1:331434/1‑38 (MQ=38)                                                         ccACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGTTGCTACAGTATTGACCAGCCAACGt                             <  1:461299/65‑1 (MQ=255)                                                         ccACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGTTGCTACAGTATTGACCAGCCAACGt                             >  2:461299/1‑65 (MQ=255)                                                         ccACTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGTTGCTACAGTATTGACCAGCCAACGTTCCCTTTCGTTACGCGGTTGCTCGa    >  1:151578/1‑90 (MQ=255)                                                           aCTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGTTGCTACAGTATTGACCAGCCAACGTTCCCTTTCGTTACGCGGTTGCTCGATc  <  2:33324/90‑1 (MQ=255)                                                           aCTTGCGGCATAGCGGTCCCCGCCTGACGAGCCTGGGTTGCTACAGTATTGACCAGCCAACGTTCCCTTTCGTTACGCGGTTGCTCGATc  >  1:33324/1‑90 (MQ=255)                                                                          |                                                                           GGCATCACGGCGCGCACCGGTTGCAAAAGCGTTGATGTCCGGCGCATGGTAGATAGCCACTTGCGGCATAGCGATCCCCGCCTGACGAGCCTGGGTTGCTACAGTATTGACCAGCCAACGTTCCCTTTCGTTACGCGGTTGCTCGATC  >  NZ_CP009273/1906489‑1906636

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑