Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,794,662	G→A	E226K (GAA→AAA)	rfaD →	ADP‑L‑glycero‑D‑mannoheptose 6‑epimerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,794,662	0	G	A	90.0%	40.9 / ‑2.2	20	E226K (GAA→AAA)	rfaD	ADP‑L‑glycero‑D‑mannoheptose 6‑epimerase
Reads supporting (aligned to +/- strand):  ref base G (2/0);  new base A (10/8);  total (12/8)
Fisher's exact test for biased strand distribution p-value = 4.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTTATTTCAACGTTTATGGACCGCGTGAAGGCCATAAAGGCAGCATGGCGAGCGTCGCTTTCCATCTCAACACCCAGCTTAACAACGGTGAATCACCGAAGCTGTTTGAAGGTAGCGAGAACTTCAAACGCGACTTCGTCTATGTGGGCGACGTGGCTGATGTGAATCTGTGGTTCCTGGAAAATGGCGTTTCCGGCATCTTCAATCTCGGTACTGGTCGTGCGGAATCCTTCCAGGCGGTAGCTGATGCTACGCTGGCTTATCACAAGAAAGGCCAGATCGAATACATTCCGTTCCCGGATAAACTGAAAGGCCGCTATCAGGCGTTCACTCAGGCAGATCTGACAAATCTGCGCGCGGCGGGTTACGACAAACCGTTCAAAACCGTTG  >  NC_000913/3794482‑3794872                                                                                                                                                                                     |                                                                                                                                                                                                                   ngTTATTTCAACGTTTATGGACCGCGTGAAGGCCATAAAGGCAGCATGGCGAGCGTCGCTTTCCATCTCAACACCCAGCTTAACAACGGTGAATCACCGAAGCTGTTTGAAGGTAGCGAGAACTTCAAACGCGACTTCGTCTATGTGGGCGACGTGGCTGATGTGAATCTGTGGTTCCTGAAAAATGGCGTTTCCGGCATCTTCAATCTCGGTACTGGTCGTGCGGAATCCTTCCAGGCGGTAGCTGATGc                                                                                                                                              >  1:84885/2‑251 (MQ=255)            cGTTTATGGACCGCGTGAAGGCCATAAAGGCAGCATGGCGAGCGTCGCTTTCCATCTCAACACCCAGCTTAACAACGGTGAATCACCGAAGCTGTTTGAAGGTAGCGAGAACTTCAAACGCGACTTCGTCTATGTGGGCGACGTGGCTGATGTGAATCTGTGGTTCCTGAAAAATGGCGTTTCCGGCATCGTCAATCTCGGTACTGGTCGTGCGGAATCCTTCCAGGCGGTAGCTGATGCTACGCTg                                                                                                                                       <  1:114926/247‑1 (MQ=255)                 aTGGACCGCGTGAAGGCCATAAAGGCAGCATGGCGAGCGTCGCTTTCCATCTCAACACCCAGCTGAACAACGGTGAATCACCGAAGCTGTTTGAAGGTAGCGAGAACTTCAAACGCGACTTCGTCTATGTGGGCGACGTGGCTGATGTGAATCTGTGGTTCCTGAAAAATGTCGTTTCCGGCATCTTCAATCTCGGTACTGGTCGTGCGGAATCCTTCCAGGCGGTAGCTGATGCTACGCTGGCTTATca                                                                                                                               <  1:285900/250‑1 (MQ=255)                       ngcgTGAAGGCCATAACGGCAGCATGGCGCGCGTCGCTTTCCATCTCAACACCCAGCTTAACAACGGTGAATCACCGAAGCTGTTTGAAGGTAGCGAGAACTTCAAACGCGACTTCGTCTATGTGGGCGACGTGGCTGATGTGAATCTGTGGTTCCTGGAAAATGGCGTTTCCGGCATCTTCAATCTCGGTACTGGTCGTGCGGAATCCTTCCAGGCGGTAGCTGATGCTACGCTGGCTTATCACAAGaa                                                                                                                         >  1:96423/2‑250 (MQ=255)                          gTGAAGGCCATAAAGGCAGCATGGCGAGCGTCGCTTTCCATCTCAACACCTAGCTTAACAACGGTGAATCACCGACGCTGTTTGAAGGTAGCGAGAACTTCAAACGCGACTTCGTCTATGTGGGCGACGTGGCTGATGTGAATCTGTGGTTCCTGAAAAATGGCGTTTCCGGCATCTTCAATCTCGGTAc                                                                                                                                                                                  >  1:112549/1‑190 (MQ=255)                                        ggCAGCATGGCGAGCGTCGCTTTCCATCTCAACACCCAGACTAACAACGGTGAATAACCGAAGCTGTTTGAAGGTAGCGAGAACTTCAAACGCGACTTCGTCTATGTGGGCGACGTGGCTGATGTGAATCTGCGGTTCCTGAAAAATGGCGTTTCCGGCATCTTCAATCTCGGTACTGGTCGTGCGGAATCCTTCCAGGCGGTAGCTGATGCTACGCTGGCTTATCACAAGAAAGGCAAGATCGAATACAt                                                                                                       >  1:212924/1‑251 (MQ=255)                                                                                      acGGTGAATCACCGAAGCTGTTTGACNGTAGCGNNAANTTCAAACGCGACTTCGTCTNTGNNNGNNNCNTGGCTNATNNGAATCTGTGNTTCCTGAAAAATGGCGTTTCCGGCATCTTCAATCTCGGTACTGGTCGTGCGGANTCCTTCCAGNNg                                                                                                                                                         >  2:77988/1‑155 (MQ=255)                                                                                      acGGTGAATCACCGAAGCTGTTTGAAGGTAGCGAGAACTTCAAACGCGACTTCGTCTATGTGGGCGACGTGGCTGATGTGAATCTGTGGTTCCTGAAAAATGGCGTTTCCGGCATCTTCAATCTCGGTACTGGTCGTGCGGAATCCTTCCAGGCg                                                                                                                                                         <  1:77988/155‑1 (MQ=255)                                                                                           gAATCACCGCAGCTGTTTGCAGGTCGCGAGAACTTCAAACGCGACTTCGTCTATGTGGGCGACGTGGCTGATGTGAATCTGTGGTTCCTGGAAAATGGCGTTTCCGGCATCTTCAATCTCGGTAc                                                                                                                                                                                  >  1:106558/1‑125 (MQ=255)                                                                                           gAATCACCGAAGCTGTTTGAAGGTAGCGAGAACTTCAAACGCGACTTCGTCTATGTGGGCGACGTGGCTGATGTGAATCTGTGGTTCCTGAAAAATGGCGTGTCCGGCATCTTCAATCGCGGTACCTGTCGTGCGGAAGCCTTCCAGGCGGTAGCTGATGCTACGCTGGCTTATCACAAGAAAGGCCAGATCGAATACATTCCGTTCCCGGATAAACTGAAAGGCCGCTATCAGGCGTTCACTCAGGCAg                                                     <  1:169981/250‑1 (MQ=255)                                                                                                 ccGAAGCTGTTTGAAGGTAGCGAGAACTTCAAACGCGACTTCGTCTATGTGGGCGACGTGGCTGATGTGAATCTGTGGTTCCTGAAAAATGGCGTTTCCGGCATCTTCAATCTCGGTACTGGTCGTGCGGAATCCTTCCAGGCGGTAGCTGATGCTACGCTGGCTTATCACAAGAAAGGCCAGATCGAATACATTCCGTTCCCGGATAAACTGAAAGGCCGCTATCAGGCGTTCACTCAGGCAGATCTGan                                              <  1:205964/251‑2 (MQ=255)                                                                                                         gTTTGAAGGTAGCGAGAACTTCAAACGCGACTTCGTCTATGTGGGCGACGTGGCTGATGTGAATCTGTGGTTACTGAAAAATGGAGTTTACGGCATCTTCAATCTCGGTACTGGTCGTGCGGAATCCTTCCCGGCGGTAGCTGCTGCTACGCTGGCTTATCACAAGAACGGc                                                                                                                     >  1:182338/1‑172 (MQ=255)                                                                                                                ggTAGCGAGAACTTCAAACGCGACTTCGTCTATGTGGGCGACGTGGCTGACGTGACTCTGTGGTTCCTGAAAAATGGCGTTTCCGGCATCTACAATCTCGGTACTGGTCGGGCGGAATCCTTCCAGGCGGTAGCTGATGCTACGCTGGCTTATCACAAGAAAGGCCAGATCGAATACATTCCGTTCCCGGATAAACTGAAAGGCCGCTATCAGGCGTTCACTCAGACAGATCTGACAAATCTGCGCgcggc                               >  1:137883/1‑251 (MQ=255)                                                                                                                    gCGATAACTTCAAACGCGACTTCGTCNATGTGGNNGANGTGGCTGATGTGAATCTGTNGTNNNTNNNANATGGCNTTNNCGGCATCTTNAATCTCGGTCCTGGTCGTGCGGAATCCTTCCAGTCGGTAGCTGATGCTACGCTNGCTTATCACNNGAAAGGCCAGATCGAATACATNCCGNNCNNGNGTanaa                                                                                      >  2:77932/1‑191 (MQ=255)                                                                                                                       agaACTTCAAACGCGACTTCGTCTATGTGGGCGACGTGGCTGATGTGAATCTGTGGTTCCTGAAAAATGGCGTTTCCGGCATCTTCAATCTCGGTACTGGTCGTGCGGAATCCTTCCAGGCGGTAGCTGATGCTACGCTGGCTTATCACAAGAAAGGCCAGATCGAATACATTCCGTTCCCGGATAAACTGAAAGTCCGCTATCAGGCGTTCACTCAGGCAGATCTGACAAATCTGCGCGCGGCGGGTTAc                        <  1:138816/251‑1 (MQ=255)                                                                                                                          aCTTCAAACGCGACTTCGTCTATGTGGGCGACGTTGCTGATGTGAATCTGTGGTTCCTGAAAAATGGCGTTTCCGGCATCTTCAATCTCg                                                                                                                                                                                      <  1:141209/90‑1 (MQ=255)                                                                                                                                     gACTTCGTCTATGTGGGCGACGTGGCTGATGTGAATCTGTGGTTCCTGAAAAATGGCGTTTCCGGCATCTTCAATCTCGGTACTGGTCGTGCGGAATCCTTCCAGGCGGTAGCTGATGCTACGCTGGCTTATCACAAGAAAgg                                                                                                                      >  1:3262/1‑143 (MQ=255)                                                                                                                                             cTATGTGGGCGACGTGGCTGATGTGAATCGGTGGTTCCTGAAAAAGGGCGTTTCCGGCATCTTCCATCTCGGTACTGGTCGTGCGAAATCCTTCCAGGCGGAAGCTGATGCTACGCTGTCTTATCACAAGAAAGGCCAGATCGAATACATTCCGTTCCAGGATAAACTGAAAGGCCGCTATCAGGCGTTCACTCAGGCAGATCTGACAAATATGCGCGCGGCGGGTTACGACAAACCGTGCAAAAACGTTg  >  1:142818/1‑251 (MQ=255)                                                                                                                                                           tGGCTGATGTGAATCTGTTGTTCCTGAAAAATGGCGTTTCCGGCATCTTCAATCGCGGTACTGGTCGTGCGGAATCCGTCCAGGCGGTAGCTGATGCTACGCTGGCTTATCACAAGAAAGGCCAGATCGAATACATTCCTTTCCCGGATAATCTGAAAGGCCGCTATCAGGCGTTCACTCAGGCAGATCTGACAAATCTgcgc                                    <  1:190394/203‑1 (MQ=255)                                                                                                                                                              cTGATGTGAATCTGTGGTTCCTGAAAAATGGCGTTTCCGGCCTCTTCAATCTCGGTACTGGTCGTGCGGAATCCTTCCAGGCGGTCGCTGATGCTACGCTGGCTTATc                                                                                                                                >  1:177599/1‑108 (MQ=255)                                                                                                                                                                   gtgAATCTGTGGTTCCTGAAAAATGGCGTTTCCGGCATCTTCAATCTCGGTACTGGTCGTGCGGAATCCTTCACGGCGGTCGCTGCTGCTACGCTGGCTTATCACAAGAAAGCCCAGATc                                                                                                               >  1:162685/1‑120 (MQ=255)                                                                                                                                                                                     |                                                                                                                                                                                                                   CGTTATTTCAACGTTTATGGACCGCGTGAAGGCCATAAAGGCAGCATGGCGAGCGTCGCTTTCCATCTCAACACCCAGCTTAACAACGGTGAATCACCGAAGCTGTTTGAAGGTAGCGAGAACTTCAAACGCGACTTCGTCTATGTGGGCGACGTGGCTGATGTGAATCTGTGGTTCCTGGAAAATGGCGTTTCCGGCATCTTCAATCTCGGTACTGGTCGTGCGGAATCCTTCCAGGCGGTAGCTGATGCTACGCTGGCTTATCACAAGAAAGGCCAGATCGAATACATTCCGTTCCCGGATAAACTGAAAGGCCGCTATCAGGCGTTCACTCAGGCAGATCTGACAAATCTGCGCGCGGCGGGTTACGACAAACCGTTCAAAACCGTTG  >  NC_000913/3794482‑3794872

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑