Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,064,564	A→G	Y185H (TAT→CAT)	yihS ←	sulfoquinovose isomerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,064,564	0	A	G	85.7%	60.3 / 5.2	28	Y185H (TAT→CAT)	yihS	sulfoquinovose isomerase
Reads supporting (aligned to +/- strand):  ref base A (1/3);  new base G (11/13);  total (12/16)
Fisher's exact test for biased strand distribution p-value = 6.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01

TATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGG  >  NZ_CP009273/4064483‑4064647                                                                                  |                                                                                    tattTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCa                                                                             >  2:327105/1‑90 (MQ=255) tattTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCa                                                                             >  1:138867/1‑90 (MQ=255)   tttCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAg                                                                           >  2:687101/1‑90 (MQ=255)   tttCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAg                                                                           >  1:67762/1‑90 (MQ=255)    ttCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGa                                                                          <  1:687101/90‑1 (MQ=255)    ttCTGGCGACGCCGTGGATAATCCCGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGa                                                                          <  1:492888/90‑1 (MQ=255)     tCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGaa                                                                         >  2:534562/1‑90 (MQ=255)      cTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGaaa                                                                        <  1:470938/90‑1 (MQ=255)      cTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGaaa                                                                        <  1:616812/90‑1 (MQ=255)      cTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGaaa                                                                        <  2:134649/90‑1 (MQ=255)               tcgtGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCAcc                                                               <  2:470100/90‑1 (MQ=255)                    gATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTg                                                          <  2:71729/90‑1 (MQ=255)                     aTAATCGCGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGc                                                         <  2:98493/90‑1 (MQ=255)                        aTCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCata                                                      >  2:147494/1‑90 (MQ=255)                                aGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCAtt                                              <  1:527795/90‑1 (MQ=255)                                    aCGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTgccg                                          >  2:757660/1‑90 (MQ=255)                                        gAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCcgccgc                                      >  1:644433/1‑90 (MQ=255)                                        gAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCcgccgc                                      <  2:796449/90‑1 (MQ=255)                                           tCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGt                                   <  2:80601/90‑1 (MQ=255)                                                       gCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGttt                       >  1:809409/1‑90 (MQ=255)                                                       gCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGttt                       <  2:809409/90‑1 (MQ=255)                                                       gCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGttt                       >  1:28592/1‑90 (MQ=255)                                                                   cGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCtt           <  1:597561/90‑1 (MQ=255)                                                                    gtgagtgaCGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTc          >  1:312783/1‑90 (MQ=255)                                                                      gagtgaCGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGt        >  1:574125/1‑90 (MQ=255)                                                                           aCGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAg   <  2:148052/90‑1 (MQ=255)                                                                           aCGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAg   <  2:754617/90‑1 (MQ=255)                                                                            cGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAgg  <  1:357044/90‑1 (MQ=255)                                                                                  |                                                                                    TATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGG  >  NZ_CP009273/4064483‑4064647

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑