Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,486,885	A→C	Q320P (CAG→CCG)	tsgA →	MFS transporter TsgA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,486,885	0	A	C	93.8%	45.9 / ‑3.5	16	Q320P (CAG→CCG)	tsgA	MFS transporter TsgA
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base C (7/8);  total (7/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

TGGCGTGGTCAATTCTCGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACAGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTACTATGTTGACCTTTG  >  NZ_CP009273/3486813‑3486962                                                                         |                                                                              tGGCGTGGTCAATTCTCGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGt                                                              >  2:252268/1‑90 (MQ=255)    cGTGGTCAATTCTCGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGc                                                           >  1:331975/1‑90 (MQ=255)        gTCAATTCTCGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCaaa                                                       <  1:49933/90‑1 (MQ=255)               ctcGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGtt                                                <  1:252268/90‑1 (MQ=255)                                  ccAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCg                             >  1:131650/1‑90 (MQ=255)                                  ccAGCGCGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCg                             >  1:236669/1‑90 (MQ=255)                                     gcgcGATCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGaa                          <  1:282941/90‑1 (MQ=255)                                          aTCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATc                     <  1:308044/90‑1 (MQ=255)                                          aTCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATc                     <  1:389518/90‑1 (MQ=255)                                          aTCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATc                     <  2:17776/90‑1 (MQ=255)                                          aTCTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATc                     >  2:70957/1‑90 (MQ=255)                                            cTATACCACCATCATCACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCgg                   <  2:242455/90‑1 (MQ=255)                                               taCCACCATCATCACCCTGGGTTCACAGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTAc                <  1:346912/90‑1 (MQ=255)                                                      atcatcACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATc                     >  1:235646/1‑78 (MQ=255)                                                      atcatcACCCTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATc                     <  2:235646/78‑1 (MQ=255)                                                             cccTGGGTTCACCGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTACTATGTTGACCTTtg  >  1:142088/1‑90 (MQ=255)                                                                         |                                                                              TGGCGTGGTCAATTCTCGCTCTGGGCTTCTTCTCCAGCGCGATCTATACCACCATCATCACCCTGGGTTCACAGCAGACCAAAGTACCGTCGCCAAAACTGGTTAACTTTGTCCTGACCTGCGGAACCATCGGTACTATGTTGACCTTTG  >  NZ_CP009273/3486813‑3486962

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑