Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,117,707	G→A	G301S (GGT→AGT)	trhO →	tRNA U34 hydroxylase TrhO

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,117,707	0	G	A	96.0%	62.1 / ‑3.9	26	G301S (GGT→AGT)	trhO	tRNA U34 hydroxylase TrhO
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (11/13);  total (12/14)
Fisher's exact test for biased strand distribution p-value = 4.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.69e-01

TCTGGCATATCGAGGGCGGAATTATTGAATACGCCCGTAAGGCGCGCGAGCAGGGCTTGCCGGTGCGTTTTATTGGCAAAAATTTTGTTTTTGACGAGCGGATGGGCGAACGTATATCGGATGAGATTATCGCGCATTGCCACCAGTGCGGCGCGCCGTGCGACAGCCATACCAACTGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAGGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGACGCCGTCGGGCAGGACGTGAAAATGGCAATAAGATCTTTAATAAGTCTCGTGGACGTCTGAATACAACACTGTGCATTCCTGATCCAACAGAATAAATATCATTGCCGGATGCGTGCCATCCGGCAACATTTCACGCTTACTTCTGCTGTACGCCTTCCACTGAAATAATCAGA  >  NC_000913/1117468‑1117937                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                       ccgtgcagatCGAGGACTGAATTTTTTAATAAGCCCGTAAGGCGCGCGAGCAGGGCTTGCCGGTGCGTTTTATTGGCAAAAATTTTGTTTTTGACGAGCGGATGGGCGAACGTATATAGGATGAGATTATCGCGCATTGCCACCAGTGCGGCGCGCCGTGCTACAGCCATACCAACTGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTTTAGt                                                                                                                                                                                                                             <  2:315195/243‑1 (MQ=255)    ggaatattgatgggtgaatgagtGAATACGCCCGTAAGGATCGCGTTCAGGGCTTGGTGGTTCTTTTTATTGGCAAAAATTTTGTTTTTGACGAGCGGATGGGCGAACGTATATCGGCTGAGATTATCGCGCATTGCCACCAGTGCGGCTCGCCGTGCGACAGCCATACCAACTGTAAAAATGA‑TTGCTGCCACCTTCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTg                                                                                                                                                                                                                            <  2:242002/227‑1 (MQ=255)     gCATATCGAGGGCGGAATTATTGAATACGCCCGTAAGGCGCGCGAGCAGGGCTTGCCGGTGCGTTTTATTGGCAAAAATTTTGTTTTTGACGAGCGGATGGGCGAACGTATATCGGATGAGATTATCGCGCATTGCCACCAGTGCGGCGCGCCGTGCGACAGCCATACCAACTGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTgaga                                                                                                                                                                                                                         <  1:286775/251‑1 (MQ=255)            gAGGGCGGAATTATTGAATACGCCCGTAAGGCGCGCGAGCAGGGCTTGCCGGTGCGTTTTATTGGCAAAAATTTTGTTTTTGACGAGCGGATGGGCGAACGTATATCGGATGAGATTATCGCGCATTGCCACCAGTGCGGCGCGCCGTGCGACAGCCATACCAACTGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTGAGATTtgctg                                                                                                                                                                                                                  >  1:342452/1‑251 (MQ=255)                                                              ggTGCGTTTTATTGGCAAAAATTTTGTTTTTGACGAGCGGATGGGCGAACGTATATCGGATGAGATTATCGCGCATTGCCACCAGTGCGGCGCGCCGTGCGACAGCCATACCAACTGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGACGCCGTCGGGCAGGAc                                                                                                                                                                <  1:10047/251‑1 (MQ=255)                                                                   gTTTTATTGGCAAAAATTTTGTTTTTGACGAGCGGATGGGCGAACGTATATCGGATGAGATTATCGCGCATTGCCACCAGTGCGGCGCGCCGTGCGACAGCCATACCAACTGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGATGTTGTAGTGCGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGACACCGTCGGGCAGGACGTgc                                                                                                                                                            >  2:150556/1‑249 (MQ=255)                                                                               aaaaTTTTGTTTTTGACGAGCGGATGGGCGAACGTATATCGGATGAGATTATCGCGCATTGCCACCCGTGCGGCGCGCCGTGCGACAGCCATACCAACTGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGACCAGCGACGCCGTCGGGCAGGACGTGAAACTGGCAATa                                                                                                                                                 >  2:287099/1‑249 (MQ=255)                                                                               aaaaTTTTGTTTTTGACGAGCGGATGGGCGAACGTATATCGGATGAGATTATCGCGCATTGCCACCAGTGCGGCGCGCCGTGCGACAGCCATACCAACTGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGACGCCGTCGGGCAGGACGTGAAAATGGCAATAAg                                                                                                                                               <  1:302940/251‑1 (MQ=255)                                                                                       gtttgtgaggagtggtgggtggAACTTATAGCGGATGAGGTTATCGCGCATTGCGACCAGTGCGGCGGTCCGTTCGACAGCAATACTAACTGTAAAAATGAGTGG‑TGTCACCTGCTGTTTATTCAGTGTCCGGTTAGCGAGGAAAAATACAAAAGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGACAGAAGAACAGCGACGCCGTCGGGCAGGACGTGAAAATGTCAATAAGATCTTtaa                                                                                                                                       <  2:282815/230‑1 (MQ=255)                                                                                                      aTGGGCGAACGTATATCGGATGAGATTATCGCGCATTGCCACCAGTGCGGCGCGCCGTGCGACAGCCATACCAACTGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGACGCCGTCGGGCAGGACGTGAAAATGGCAATAAGATCTTTAATAAGTCTCGTGGACg                                                                                                                        >  2:90684/1‑251 (MQ=255)                                                                                                                         aTGAGATTATCGCGCATTGCCACCAGTGCGGCGCGCCGTGCGACAGCCATACCAACTGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGACGCCGTCGGGCAGGACGTGAAAATGGCAATAAGATCTTTAATAAGTCTCGTGGACGTCTGAATACAACACTGTGc                                                                                                     <  1:287099/251‑1 (MQ=255)                                                                                                                                      gaaTTGCCACCATGGCGGCGCGCCGTTCGACAGCCATACCAACTGTAAAAATGA‑TGGATGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTGAGATGTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGACGCCGTCGGGCAGGACGTGAAAATGGCAATAAGATCTTTAATAAGTCTCGTGGACGTCTGTATACAACACTTTGCATTCCTGATCCaa                                                                                        <  2:23484/249‑1 (MQ=255)                                                                                                                                                     gggcgCGCCGTGCGACAGCCATACCAACTGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGACGCCGTCGGGCAGGACGTGAAAATGGCAATAAGATCTTTAATAAGTCTCGTGGACGTCTGAATACAACACTGTGCATTCCTGATCCAACAGAATAAATATCAt                                                                         <  1:173161/250‑1 (MQ=255)                                                                                                                                                             cGTGCGACAGCCATACCAACTGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGTAAAAATACAAAAGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGACGCCGTCGGGCATTACGTGAAAATGGCAATAAGATCTTTAATAAGTCTCGTGGACGTCTGAATACAACACTGTGCATTCCTGATCCAACAGAATAAATATCATTGCCGGAt                                                                 <  1:348183/251‑1 (MQ=255)                                                                                                                                                                            ccAACTGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGGAAAATACAACAGTTGTTGTAGTGCGATTTGCTGCGAAGAAAGGGCGTTACCGCCAGAAGAACAGCGACGCCGTCGGGCAGGa                                                                                                                                                                 >  2:195031/1‑140 (MQ=255)                                                                                                                                                                            ccAACTGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGACGCCGTCGGGCAGGa                                                                                                                                                                 <  1:195031/140‑1 (MQ=255)                                                                                                                                                                                cTGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGACGCCGTCGGGCAGGACGTGAAAATGGCAATAAGATCTTTAATAAGTCTCGTGGACGTCTGAATACAACACTGTGCATTCCTGATCCAACAGAATAAATATCATTGCCGGATGCGTGCCATCCGGCAACAt                                              >  1:184792/1‑251 (MQ=255)                                                                                                                                                                                 tGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGCCGCCGTCGGGCAGGACGTGAAAATGGCAATAAGATCTTTAATAAGTCTCGTGGACGTCTGAATACAACACTGTGCATTCCTGATCCAACAGCATAAATATCATTGCCGGATGCGTGCCATCCGGCAACAtt                                             >  1:299607/1‑251 (MQ=255)                                                                                                                                                                                   tAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGACGCCGTCGGGCAGGACGTGAAAATGGCAATAAGATCTTTAATAAGTCTCGTGGACGTCTGAATACAACACTGTGCATTCCTGATCCAACAGAATAAATATCATTGCCGGATGCGTGCCATCCGGCAACATTTc                                           >  2:194176/1‑251 (MQ=255)                                                                                                                                                                                       aaTGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTGCGATTTGCTGCGAAGAAAGCGCGCTACCGCCAGAAGAACAGCGACGCCGTCGGGCAGGACGTGAAAATGGCAATAAGATCTTTAATAAGTCTCGTGGACGTCTGAATACAACACTGTGCATTCCTGATCCAACAGAATAAATATCATTGCCGGATGCGTGCCATCCGGCAACGTTTCACGc                                       >  1:329878/1‑251 (MQ=255)                                                                                                                                                                                          ga‑tgGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGAGGAAAAATACAAAGGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGACGCCGTCGGGCAGGACGTGAAAATGGCAATAAGATCTTTAATAAGTCTCGTGGACGTCTGAATACAACACTGTGCATTCCTGATCCAACAGAATAAATATCATTGCCGGATGCGTGCCATCCGGCAACATTTCACGCtt                                     >  1:154616/1‑250 (MQ=255)                                                                                                                                                                                                  gCCACCTACTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTGAGATTTGCTGCGAAGCAAGCGCGTTCCCGCCAGAAGAACAGCGACGCCGTCGGGCAGGACGTGAAAATGGCAATAAGATCTTTAATAAGTCTCGTGGACGTCTGAATACAACACTGTGCATTCCTGATCCAACAGCATAAATATCATTGCCGGCTGCGTGCCATCCGGCACCATTTCACGCTTACTTatgc                             >  2:55700/1‑251 (MQ=255)                                                                                                                                                                                                   ccgcttgctgTTTATTCAGTGATCATGATGCGCGAAAATATACAAATGTGGTTTTAGTGAGATTTGCTGCGAAGAAAGCGCGTTGCCGCCAGAAGAACAGCGACTCTGTCGGGCAGGACGTGAAAATTGCAATAAGATCTTTAATAAGTCTCGTTGACGTCTGAATACAACACTGTGCATTCCTGATCCAACAGAATAAATATCATTGCCGGATGCGTGCCATCCGGCAACATTTCACGCTTACTTctgct                            <  2:313085/246‑1 (MQ=255)                                                                                                                                                                                                            gTTTAGTCAGTGTCCAGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTTAGATTTGCTGCGAAGAAATCGCGTTACCGCTAGAAGAACAGCGACGCCGTCGGGCAGGACGTGAAAATGGCAATAAGATCTTTAATAAGTCTCGTGGACGTCTGAATACAACACTGTGCATTCCTGATCCAACAGAATAAATATCATTGCCGGATGCGTGCCATCCGGCAACATTTCACGCTTACTTCTGATGTACGCCt                    <  2:184792/250‑1 (MQ=255)                                                                                                                                                                                                                           aGTATGCGCGGAAAAATACAAAAGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGACGCCGTCGGGCAGGACGTGAAAATGGCAATAAGATCTTTAATAAGTCTCGTGGACGTCTGAATACAACACTGTGCATTCCTGATCCAACAGAATAAATATCATTGCCGGATGCGTGCCATCCGGCAACATTTCACGCTTACTTCTGCTGTACGCCTTCCACTGAAATAATc     >  1:191079/1‑250 (MQ=255)                                                                                                                                                                                                                              aTGCGCGGAAAAATACAAAAGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGACGCCGTCGGGCAGGACGTGAAAATGGCAATAAGATCTTTAATAAGTCTCGTGGACGTCTGAATACAACACTGTGCATTCCTGATCCAACAGAATAAATATCATTGCCGGATGCGTGCCATCCGGCAACATTTCACGCTTACTTCTGCTGTACGCCTTCCACTGAAATAATCAGa  <  1:90684/250‑1 (MQ=255)                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                       TCTGGCATATCGAGGGCGGAATTATTGAATACGCCCGTAAGGCGCGCGAGCAGGGCTTGCCGGTGCGTTTTATTGGCAAAAATTTTGTTTTTGACGAGCGGATGGGCGAACGTATATCGGATGAGATTATCGCGCATTGCCACCAGTGCGGCGCGCCGTGCGACAGCCATACCAACTGTAAAAATGA‑TGGCTGCCACCTGCTGTTTATTCAGTGTCCAGTATGCGCGGAAAAATACAAAGGTTGTTGTAGTGAGATTTGCTGCGAAGAAAGCGCGTTACCGCCAGAAGAACAGCGACGCCGTCGGGCAGGACGTGAAAATGGCAATAAGATCTTTAATAAGTCTCGTGGACGTCTGAATACAACACTGTGCATTCCTGATCCAACAGAATAAATATCATTGCCGGATGCGTGCCATCCGGCAACATTTCACGCTTACTTCTGCTGTACGCCTTCCACTGAAATAATCAGA  >  NC_000913/1117468‑1117937

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑