Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,798,171	C→T	D258N (GAC→AAC)	pheS ←	phenylalanine‑‑tRNA ligase subunit alpha

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,798,171	0	C	T	94.1%	46.7 / ‑5.4	18	D258N (GAC→AAC)	pheS	phenylalanine‑‑tRNA ligase subunit alpha
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (10/6);  total (11/7)
Fisher's exact test for biased strand distribution p-value = 4.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGTTCACTGAATTTCATAATCTATTCCTGCCTTATTTAAACTGTTTGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGTTACGCAACACGTTCGGATGCACCATCCCGCAGCCCAGCACTTCCAGCCATTTACCGTTTTTACCCATGACGTCCACTTCTGCAGAAGGTTCGGTAAACGGGAAGTAGGAAGGACGGAAGCGAATCTGCAAATCTTCCTCAAAGAAGTTACGCAGGAAGTCGTGCAGCGTGCCTTTCAGGTTGGTAAAGCTGATGTTGGTATCAACAATCAGACCTTCCATCTGATGGAACATCGGCGTGTGAGTCTGGTCGTAGTCGTTACGATAAACACGGCCAGGCGCGATGATACGAATCGGTGGCTGCTGGGCTTTCATG  >  NC_000913/1797927‑1798412                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                  caGTTCACTGAATTTCATAATCTATTCCTGCCTTATTTAAACTGTTTGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGTTACGCAACACGTTCGGATGCACCATCCCGCAGCCCAGCACTTCCAGCCATTTACCGTTTTTACCCATGACGTTCACTTc                                                                                                                                                                                                                                             <  2:254042/251‑1 (MQ=255)   gTTCACTGAATTTCATAATCTATTCCTGCCTTATTTAAACTGTTTGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGTTACGCAACACGTTCGGATGCACCATCCCGCAGCCCAGCACTTCCAGCCAGGTACCGTTTTTACCCATGACGTTCACTTCTg                                                                                                                                                                                                                                           <  1:275165/251‑1 (MQ=255)    ttCACTGAATTTCATAATCTATTCCTGCCTTATTTAAACTGTTTGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGTTACGCAACACGTTCGGATGCACCATCCCGCAGCCCAGCACTTCCAGCCATTTACCGTTTTTACCCATGACGTTCACTTCTGc                                                                                                                                                                                                                                          >  2:106876/1‑251 (MQ=255)            aTTTCATAATCTATTCCTGCCTTATTTAAACTGTTTGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGTTACGCAACACGTTCGGATGCACCATCCCGCAGCCCAGCACTTCCAGCCATTTACCGTTTTTACCCATGACGTTCACTTCTGCAGAAGGtt                                                                                                                                                                                                                                  >  1:213744/1‑251 (MQ=255)               tCATAATCTATTCCTGCCTTATTTAAACTGTTTGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGTTACGCAACACGTTCGGATGCACCATCCCGCAGCCCAGCACTTCCAGCCATTTACCGTTTTTACCCATGACGTTCACTTCTGCAGACGGTTCgg                                                                                                                                                                                                                               >  2:199712/1‑251 (MQ=255)                  tAATCTATTCCTGCCTTATTTAAACTGTTTGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGTTACGCAACACGTTCGGATGCACCATCCCGCAGCCCAGCACTTCCAGCCATTTACCGTTTTTACCCATGACGTTCACTTCTGCAGAAGGTTCGGTa                                                                                                                                                                                                                             >  1:248026/1‑250 (MQ=255)                                        aaCTGTTTGAGGAAACGCCGATCGTTTTCGCAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGACACCAGAGTAAACTTCCGGGTCGATGCCAACGTTACGCAACACGTTCGGATGCACCATCCCGCAGCCCAGCACTTCCAGCCATTTACCGTTTTTACCCATGACGTTCACTTCTGCAGACGGTTCGGTAATCGGGAAGTAGGAAGGCCGGa                                                                                                                                                                                                       >  2:283659/1‑250 (MQ=255)                                             tttGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGTTACGCAACACGTTCGGATGCACCATCCCGCAGCCCAGCACTTCCAGCCATTTACCGTTTTTACCCATGACGTTCACTTCTGCAGAAGGTTCGGTAAACGGGAAGTAGGAAGGACGGAAGCGa                                                                                                                                                                                                  >  1:237584/1‑250 (MQ=255)                                                       cGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGTTACGCATCACGTTCGGATGCACCATCCCGCAGCCCAGCACTTCCAGCCATTTACCGTTTTTACCCATGACGTTCACTTCTGCAGAAGGTTCGGTAAACGGGAAGTAGGAAGGACGGAAGCGAATCTGCAAATc                                                                                                                                                                                       >  2:207401/1‑251 (MQ=255)                                                                                                                         atccccatcccGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGTTACGCAACACGTTCGGATGCACCATCCCGCAGCCCAGCACTTCCAGCCATTTACCGTTTTTACCCATGACGTTCACTTCTGCAGAAGGTTCGGTAAACGGGAAGTAGGAAGGACGGAAGCGAATCTGCAAATCTTCCTCAAAGAAGTTACGCAGGAAGTCGTGCAGCGTGCCTTTCAGGTTGGTAAAGCTGATGTTGGt                                                                                                                     >  1:165664/1‑251 (MQ=255)                                                                                                                                                     aaaCTTCCGGGTCGATGCCAACGTTACGCAACACGTTCGGATGCACCATCCCGCAGCCCAGCACTTCCAGCCATTTACCGTTTTTACCCATGACGTTCACTTCTGCAGAAGGTTCGGTAAACGGGAAGTAGGAAGGACGGAAGCGAATCTGCAAATCTTCCTCAAAGAAGTTACGCAGGAAGTCGTGCAGCGTGCCTTTCAGGTTGGTAAAGCTGATGTTGGTATCAACAATCAGACCTTCCATCTGATgg                                                                                         <  2:128705/251‑1 (MQ=255)                                                                                                                                                      aaCTTCCGGGTCGATGCCAACGTTACGCAACACGTTCGGATGCACCATCCCGCAGCCCAGCACTTCCAGCCATTTACCGTTTTTACCCATGACGTTCACTTCTGCAGAAGGTTCGGTAAACGGGAAGTAGGAAGGACGGAAGCGAATCTGCAAATCTTCCTCAAAGAAGTTACGCAGGAAGTCGTGCAGCGTGCCTTTCAGGTTGGTAAAGCTGATGTTGGTATCAACAATCAGACCTTCCATCTGATGGa                                                                                        <  2:104730/251‑1 (MQ=255)                                                                                                                                                                              aCGCAACACGTTCGGATGCACCATCCCGCAGCCCAGCACTTCCAGCCATTTACCGTTTTTACCCATGACGTTCACTTCTGCAGAAGGTTCGGTAAACGGGAAGTAGGAAGGACGGAAGCGAATCTGCAAATCTTCCTCAAAGAAGTTACGCAGGAAGTCGTGCAGCGTGCCTTTCAGGTTGGTAAAGCTGATGTTGGTATCAACAATCAGACCTTCCATCTGATGGAACATCGGCGTGTGAGTCTGGTCGt                                                                <  2:237584/251‑1 (MQ=255)                                                                                                                                                                                 cAACACGTTCGGATGAACCACCCCGCAGCCCAGCACTTCCTGCCATTTACCGTTTTTACCCATGCCGTACACTTCTGCAGAAGGTCCGGAAAACGGGAAGTAGGAAGGACGGAAGCGAATCTGCAAATCTTCCTCACAGAAGTTACGCAGGAAGTCGTGCAGCGTGCCTTTCAGGTTGGTAAAACTGATGTTGGTATCAACAATCAGACCTTCCATCTGATGGAACATCGGCGTGTGAGTCTGATCGTAGt                                                             >  2:180834/1‑251 (MQ=255)                                                                                                                                                                                                                       ccAGCCATTTACCGTTTTTACCCATGACGTTCACTTCTGCAGAAGGTTCGGTAAACGGGAAGTAGGAAGGACGGAAGCGAATCTGCAAATCTTCCTCAAAGAAGTTACGCAGGAAGTCGTGCAGCGTGCCTTTCAGGTTGGTAAAGCTGATGTTGGTATCAACAATCAGACCTTCCATCTGATGGAACATCGGCGTGTGAGTCTGGTCGTAGTCGTTACGATAAACACGGCCAGGCGCGATGATACGAATc                       >  1:21815/1‑251 (MQ=255)                                                                                                                                                                                                                                    gTTTTTACCCATGACGTTCACTTCTGCAGAAGGTTCGGTAAACGGGAAGTAGGAAGGACGGAAGCGAATCTGCAAATCTTCCTCAAAGAAGTTACGCAGGAAGTCGTGCAGCGTGCCTTTCAGGTTGGTAAAGCTGATGTTGGTATCAACAATCAGACCTTCCATCTGATGGAACATCGGCGTGTGAGTCTGGTCGTAGTCGTTACGATAAACACGGCCAGGCGCGATGATACGAATCGGTGGCTGCTggg          <  2:2455/251‑1 (MQ=255)                                                                                                                                                                                                                                        ttACCCATGACGTCCACTTCTGCAGAAGGTTCGGTAAACGGGAAGTAGGAAGGACGGAAGCGAATCTGCAAATCTTCCTCAAAGAAGTTACGCAGGAAGTCGTGCAGCGTGCCTTTCAGGTTGGTAAAGCTGATGTTGGTATCAACAATCAGACCTTCCATCTGATGGAACATCGGCGTGTGAGTCTGGTCGTAGTCGTTACGATAAACACGGCCAGGCGCGATGATACGAATCGGTGGCTGCTGGGCtt       <  1:173250/250‑1 (MQ=255)                                                                                                                                                                                                                                            ccATGACGTTCACTTCTGCAGAAGGTTCGGTAAACGGGAAGTAGGAAGGACGGAAGCGAATCTGCAAATCTTCCTCAAAGAAGTTACGCAGGAAGTCGTGCAGCGTGCCTTTCAGGTTGGTAAAGCTGATGTTGGTATCAACAATCAGACCTTCCATCTGATGGAACATCGGCGTGTGAGTCTGGTCGTAGTCGTTACGATAAACACGGCCAGGCGCGATGATACGAATCGGTGGCTGCTGGGCTTTCATg  >  2:143669/1‑251 (MQ=255)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                  CAGTTCACTGAATTTCATAATCTATTCCTGCCTTATTTAAACTGTTTGAGGAAACGCAGATCGTTTTCGAAGAATGAACGCAGGTCGGTGACGCCGTAACGCAACATAGTCAGACGCTCCATCCCCATCCCGAAGGCGAAACCAGAGTAAACTTCCGGGTCGATGCCAACGTTACGCAACACGTTCGGATGCACCATCCCGCAGCCCAGCACTTCCAGCCATTTACCGTTTTTACCCATGACGTCCACTTCTGCAGAAGGTTCGGTAAACGGGAAGTAGGAAGGACGGAAGCGAATCTGCAAATCTTCCTCAAAGAAGTTACGCAGGAAGTCGTGCAGCGTGCCTTTCAGGTTGGTAAAGCTGATGTTGGTATCAACAATCAGACCTTCCATCTGATGGAACATCGGCGTGTGAGTCTGGTCGTAGTCGTTACGATAAACACGGCCAGGCGCGATGATACGAATCGGTGGCTGCTGGGCTTTCATG  >  NC_000913/1797927‑1798412

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑