Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,778,863	A→T	18.6%	T82S (ACT→TCT)	gpmM →	phosphoglycero mutase III, cofactor‑independent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,778,863	0	A	T	18.6%	41.2 / 2.7	21	T82S (ACT→TCT)	gpmM	phosphoglycero mutase III, cofactor‑independent
Reads supporting (aligned to +/- strand):  ref base A (8/9);  new base T (2/2);  total (10/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

GGTTTCTAAAAAACCTAT‑GGTACTGGTGATTCTGGATGGCTATGGCTATCGCGAAGAACAGCAGGATAACGCCATTTTTAGTGCTAAAACCCCGGTAATGGATGCACTGTGGGCCAATCGTCCGCATACCCTAATCGACGCTTCCGGTCTGGAAGTCGGTCTGCCTGACCGTCAGATGGGTAACTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTGGACGTTGAAATCAAAGATCGCGCTTTCTTTGCTAATCCGGTGCTGACTGGCGCGGTAGATAAAGCGAAAAACGCAGGCAAAGCGGTACACATTATGGGTCTGCTCTCCGCAGGCGGCGTACACAGCCACGAAGATCACATCATGGCGATGGTAGAACTGGCAGCTGAACGCGGCGCAGAAAAAA  >  CP009273/3778625‑3779055                                                                                                                                                                                                                                                |                                                                                                                                                                                                 ctgttagaaaaaaCGTTG‑GGTACGGTTGTGTCTGGATGGCTATGGCTTTCACGAAGAACTGGATGATAACGCCTTTTTTAGTGCTAAAACCCCGGTAAGGGATGCACTGGCGGCCAATCGTCCGCATACCCTAATAGACGCTTCCGGTCTGGAAGTCGGTCTGCCTGACCGTCAGAGGGGTAACTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTGGACGTTGAAATCAAAGATCGCGctttc                                                                                                                                                               <  2:445911/267‑1 (MQ=255)  gTTTTTAAAAAATCTTTGGGTGATGNTGTTTCTTGTTGGCTATGGCTATCGCGAAGAACAGCAGGATAACGCCATTTTTAGTGCTAAAACCCCGGTAATGGATGCACTGTGGGCCACTCGTCCGCATACCCTAATCGACGCTTCCGGTCTGGAAGTCGGTCTGCCTGACCGTCAGATGGGTAACTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTGGACGTTGAAATCAAAGATCGCGctttc                                                                                                                                                               <  2:338559/274‑1 (MQ=255)                                                   cgcgAAGAACAGCAGGATAACGCCATTTTTAGTGCTAAAACCCCGGTAATGGATGCACTGTGGGCCAATCGTCCGCATACCCTAATCGACGCTTCCGGTCTGGAAGTCGGTCTGCCTGACCGTCAGATGGGTAACTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTgg                                                                                                                                                                                         >  1:118026/1‑199 (MQ=255)                                                       aagaaCAGCAGGATAACGCGATTTTTAGTGCTAAAACCCCGGTAATGGATGCACTGTGGGCCAATCGTCCGCATACCCTAATCGACGCTTCCGGTCTGGAAGTCGGTCTGCCTGACCGTCAGATGGGTAACTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTGGACGt                                                                                                                                                                                     <  2:118025/199‑1 (MQ=255)                                                          aaCAGCAGGATAACGCCTTTTTTAGTGCTAAACCCCCGGTAATGAATGCACTGGGGGCCAATCGTCCGCATACCCTATTCGACGCTTCCGGTCTGGAAGTCGGTCTGCCTGACCGTCAGATGAGTAACTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTGGACGTTGAAATCAAAGATCGCGCTTTCTTTGCTAATCCGGTGCTGACTGGCGCGGTAGATAAAGCGAAAAACGCAGGCAAAGc                                                                                                       <  1:18959/274‑1 (MQ=255)                                                                    tAACGCCATTTTTAGTGCTAAAAACCCGGTACTGGAGGCACTGTGTGCCTATCGTCCGCATACCCGAATCGTCGCTTCCGGTCTGGAAGTCGGTCTGCCTGACCGTCAGATGGGTAGGTCCGAAGTAGGCCACGTTAACCAGGGTGGCGGCCGCATCGTGTTTCAGGATCTGACTCGTCAGGCAGTGGAAACCAAAGATCGTACCTTCTGTACTAACCCGGCGATACATGGCGCGGCAGTATCAGTGAANAACTCACGCAANNNNGTaa                                                                                                  >  2:18959/1‑268 (MQ=255)                                                                            tttttAGTGCTAAAACCCCGGTAATGGATGCACTGTGGGCCAATCGTCCGCATACCCTAATCGACGCTTCCGGTCTGGAAGTCGGTCTGCCTGACCGTCAGATGGGTAACTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGTCTCGTCTGGACGTTGAAATCAAAGATCGCGCTTTCTTTGCTAATCCGGTGCTGACTGGCGCGGTAGATAAAGCGAAAAACGCAGGCAAAGCGGTACACATTATGGGACt                                                                                     >  2:151398/1‑274 (MQ=255)                                                                                tAGTGCTAAAACCCCGGTAATGGATGCACTGTGGGCCAATCGTCCGCATACCCTAATCGACGCTTCCGGTCTGGAAGTCGGTCTGCCTGACCGTCAGATGGGTAACTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGTCTCGTCTGGACGTTGAAATCAAAGATCGCGCTTTCTTTGCTAATCCGGTGCTGACTGGCGCGGTAGATAAAGCGAAAAACGCAGGCAAAGCGGTACACATTATGGGTCTGc                                                                                   <  1:151399/272‑1 (MQ=255)                                                                                                                           ccGCATACCCTAATCGACGCTTCCGGTCTGGTAGTCGGTCTGACTGACCGTCCGATGGGTAACTCCGAAGTAGGCCACGTTAACCTGGGTCCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTGGACGTTGAAATCAAAGATCGCGCTTTCTTTGCTAATCCGGTGCTGACTGGCGCGGTAGATAAAGCGAAAAACGCAGGCAAAGCGGTACACATTATGGGTCTGCTCTCCGCAg                                                                          <  1:501837/238‑1 (MQ=255)                                                                                                                                       aTCGACGCTTCCGGTCTGGAAGTCGGTCTGCCTGACCGTCAGATGGGTAACTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTGGAc                                                                                                                                                                                       >  1:491782/1‑117 (MQ=255)                                                                                                                                             gCTTCCGGTCTGGAAGTCGGTCTGCCTGACCGTCAGATGGGTAACTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGTCTCGTCTGGACGTTGAAATCAAAGATCGCGCTTGCTTTGCTAATCCGGTGCTGACTGGCGCGGTAGATAAAGCGAAAAACGCAGGCAAAGCGGTACACATTATGGGTCTGCTCTCCGCAGGCGGCGTACACAGCCACGAAGATAACATCATGGCGATGGAAGAACTGGCAGCTGa                   >  1:204791/1‑275 (MQ=255)                                                                                                                                                                 tCTGCCTGACCGTCAGATGGGTAACTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTGGAc                                                                                                                                                                                       >  2:340789/1‑91 (MQ=255)                                                                                                                                                                   tGCCTGACCGTCAGATGGGTAACTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGAc                                                                                                                                                                                                 <  1:383290/79‑1 (MQ=255)                                                                                                                                                                     ccTGACCGTCAGATGGGTAACTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGa                                                                                                                                                                                                  <  2:312005/76‑1 (MQ=255)                                                                                                                                                                     ccTGACCGTCAGATGGGTAACTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTGGACGTTg                                                                                                                                                                                   <  1:340794/91‑1 (MQ=255)                                                                                                                                                                                     gTAACTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTGGACGTTGAAATCAAAGATCGCGCTTTCTTTGCTAATCCGGTGCTGACTGGCGCGGTAGATAAAGCGAAAAACGCAGGCAAAGc                                                                                                       >  2:189063/1‑151 (MQ=255)                                                                                                                                                                                         cTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTGGACGTTGAAATCAAAGATCGCGCTTTCTTTGCTAATCCGGTGCTGACTGGCGCGGTAGATAAAGCGAAAAACGCAGGCAAAGCGGTa                                                                                                   <  1:189066/151‑1 (MQ=255)                                                                                                                                                                                                    gCCACGTTAATCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTGGACGTTGAAATCAAAGATCGCGCTTTCTTTGCTAATCCGGTGCTGACTGGCGCGGTAGATAAAGCGAAAAACGCAGGCAAAGCGGTATACATTATGGGTCTGCTCTCCGCAGGCGGCGTACACAGCCACGAAGATCACATCATGGCGATGGTAGAACTGGCAGCTGAACGCGGCGCAGaaaaaa  >  1:511955/1‑237 (MQ=255)                                                                                                                                                                                                        cGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTGGACGTTGAAATCAAAGATCGCGCTTTCTTTGCTAATCCGGTGCTGACTGGCGCGGTAGATAAAGCGAAAAACGCAGGCAAAGc                                                                                                       >  2:328933/1‑132 (MQ=255)                                                                                                                                                                                                         gTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTGGACGTTGAAATCAAAAATcgcg                                                                                                                                                                    >  2:345275/1‑70 (MQ=255)                                                                                                                                                                                                            aaCCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTGGACGTTGAAATCAAAGATCGCGCTTTCTTTGCTAATCCGGTGCTGACTGGCGCGGTAGATAAAGCGAAAAACGCAGGCAAAGCGGTa                                                                                                   <  1:328938/132‑1 (MQ=255)                                                                                                                                                                                                             aCCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGTCTCGTCTTGACGTTGAAATCAAAGATCGCGcttt                                                                                                                                                                <  1:345280/70‑1 (MQ=255)                                                                                                                                                                                                                                                |                                                                                                                                                                                                 GGTTTCTAAAAAACCTAT‑GGTACTGGTGATTCTGGATGGCTATGGCTATCGCGAAGAACAGCAGGATAACGCCATTTTTAGTGCTAAAACCCCGGTAATGGATGCACTGTGGGCCAATCGTCCGCATACCCTAATCGACGCTTCCGGTCTGGAAGTCGGTCTGCCTGACCGTCAGATGGGTAACTCCGAAGTAGGCCACGTTAACCTGGGTGCCGGCCGCATCGTGTATCAGGACCTGACTCGTCTGGACGTTGAAATCAAAGATCGCGCTTTCTTTGCTAATCCGGTGCTGACTGGCGCGGTAGATAAAGCGAAAAACGCAGGCAAAGCGGTACACATTATGGGTCTGCTCTCCGCAGGCGGCGTACACAGCCACGAAGATCACATCATGGCGATGGTAGAACTGGCAGCTGAACGCGGCGCAGAAAAAA  >  CP009273/3778625‑3779055

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑