Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,443,447	G→A	A562T (GCG→ACG)	mnmC →	fused tRNA 5‑aminomethyl‑2‑thiouridylate methyltransferase and tRNA 5‑aminomethyl‑2‑thiouridylate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,443,447	0	G	A	95.5%	52.9 / NA	22	A562T (GCG→ACG)	mnmC	fused tRNA 5‑aminomethyl‑2‑thiouridylate methyltransferase and tRNA 5‑aminomethyl‑2‑thiouridylate synthase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (11/10);  minor base C (1/0);  total (12/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

TATCTCACGCCACAAAATCCGGCGAATCAACATCATTGTATTGGTGCCAGTTATCATCGCGGCAGCGAAGATACGGCGTACAGTGAGGACGATCAGCAGCAGAATCGCCAGCGGTTGATTGATTGTTTCCCGCAGGCACAGTGGGCAAAAGAGGTTGATGTCAGTGATAAAGAGGCGCGCTGCGGTGTGCGTTGTGCCACCCGCGATCATCTGCCAATGGTAGGCAATGTTCCCGATTATGAGGCAACACTCGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGTTTGTGTTCTGCCCCGCTGTGTGCCGAGATTCTGGCGGCGCAGATGAGCGACGAACCGATTCCGATG  >  NC_000913/2443273‑2443686                                                                                                                                                                               |                                                                                                                                                                                                                                                tATCTCACGCCACAAAATCCGGCGAATCAACATCATTGTATTGGTGCCAGTTATCATCGCGGCAGCGAAGATACGGCGTACAGTGAGGACGATCAGCAGCAGAATCGCCAGCGGTTGATTGATTGTTTCCCGCAGGCACAGTGGGCAAAAGAGGTTGATGTCAGTGATAAAGAGACGCGCTGCGGTGTGCGTTGTGCCACCCGCGATCATCTGCCAATGGTAGGCAATGTTCCCGATTATGAGGCAacac                                                                                                                                                                      <  1:378883/250‑1 (MQ=255)         gCCACAAAATCCGGCGAATCAACATCATTGTCTTGGTGCCAGTTATCATCGCGGCAGCGAAGATACGGCGTACAGTGAGGACGATCAGCAGCAGAATCGCCAGCGGGTGATTGATTGTTTCCCGCAGGCACAGTGGGCAAAAGAGGTTGATGTCAGAGATAAAGAGACGCGCTGCGGTGTGCGTTGTGCCACCCGCGATCATCTGCCACTGGTAGGCAATGTTCCCGATTATGAGGAAACACTCGTGGAat                                                                                                                                                             >  1:313515/1‑251 (MQ=255)         gCCACAAAATCCGGCGAATCAACATCATTGTATTGGTGCCAGTTATCATCGCGGCAGCGAAGATACGGCGTACAGTGAGGACGATCAGCAGCAGAATCGCCAGCGGTTGATTGATTGTTTCCCGCAGGCACAGTGGGCAAAAGAGGTTGATGTCAGAGATAAAGAGACGCGCTGCGGTGTGCGTTGTGCCACCCGCGATCATCTGCCAATGGTAGGCAATGTTCCCGATTATGAGGCAACACTCGTGGAat                                                                                                                                                             >  1:313502/1‑251 (MQ=255)                           tCAACATCNTNNNANNGGTGCCAGTTATCATCGCGGCAGCGAAGATACGGCGTACAGTGANGACGATCAGAAGCAGNATNGCCANCGGNTGGTTGATTGTTTCCGGCAGGCACAGTGGGCAAAAGAGGTTGATGTCAGTAATAAAGAGACGCGCTGCGGTGGGCGTTGTGCCACCTGCGCTCATCTTCCAATTGNAGGNCATGTNNCNGagctcnnna                                                                                                                                                                            >  2:321425/1‑210 (MQ=255)                           tCAACATCATTGTATTGGTGCCAGTTATCATCGCGGCAGCGAAGATACGGCGTACAGTGAGGACGATCAGCAGCAGAATCGCCAGCGGTTGATTGATTGTTTCCCGCAGCCACAGTGGGCAAAAGAGGTTGATGGCAGTGATAAAGAGACGCGCTGCGGTGTGCGTTGTTCCACCCGCGATCATCTGCCAATGGTAGGCAATGTTCCCg                                                                                                                                                                                     <  1:321425/209‑1 (MQ=255)                                     tGTATTGGTGCCAGTTAACAGCGCGGCAGCGAAGATGCGGCGTACAGTGAGGACGAGCAGCAGCAGAAGCGCCAGCGGTTGATTGATTGTTTCCCGCAGGCACAGTGGGCAAAAGAGGTTGATGTCAGTGATAAAGAGACACGCTGCGGTGTGCGTGGTGCCTCCCGCGATCATCTGCCAAGGGTAGGCAATGCTCCCGATTATGAGGCAACACGCGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATg                                                                                                                                  <  1:293710/250‑1 (MQ=255)                                                nagtgatcatcGCGGCAGCGAAGATACGGCGTACAGTGAGGACGATCAGCAGCAGAATCGCCAGAGGTTGATTGATTGTTTCCCGTAGGCACAGTGGGCAAAAGAGGTTGATGTCAGTGATAAAGAGACGCGCTGCGGTGTGCGTTGTGCCACCCGCGATCATCTGCCAATGGTAGGCAATGTTCCCGATTATGAGGCAACACTCGTGGAata                                                                                                                                                            >  1:55423/6‑213 (MQ=255)                                                        atcGCGGCAGCGAAGATACGGCGTACAGTGAGGACGATCAGCAGCAGAATCGCCAGCGGTTGATTGATTGTTTCCCGCAGGCACAGTGGGCAAAAGAGGTTGATGTCAGTGATAAAGAGACGCGCTGCGGTGTGCGTTGTGc                                                                                                                                                                                                                           <  1:23321/142‑1 (MQ=255)                                                                       aTACGGAGTACAGTGAGGACGATCAGCAGCAGAATCGCCAGCGGTTGATTGCTTGTTTCAAGAAGGCACAGTGGGAAAAAGAGATTGATGTCAGTGAGAAAGCGCCGCACAGCGGTGTGCGTTGTGCGACCCGCGCTCCTCTGTCAAAGGGAGGCAATGTTCCCGATTATGAGGCAACACACGTGGAATATTCGTCTTTGGCGGAGCAGAAAGATAAGGCGGGGAGCGCGCCGGTTTTTTACGGTCTCttt                                                                                               >  1:68894/1‑251 (MQ=255)                                                                                   gTGAGGACGATCAGCAGCAGAATCTGCAGCGGTTGATTGATTGTTTCCCGCAGGCACAGTGGGCAAAAGATGTTGATGTCAGTGATAAAGAGACGCGCTGCGATGTGCGGTGTGCCACCCGCTATCAGCTGCCAATGTTAGGCAATGTTCCCGATTATGAGGCAACACTCGTGGAATTTGCGTCGTCGGCGGATCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCt                                                                                   <  1:431207/251‑1 (MQ=255)                                                                                          cGATCAGCAGCAGAATCGCCAGCGGTTGATTGATTGTTTCCCGCAGGCACAGTGGGCAAAAGAGGTTGATGTCAGTGATAAAGAGACGCGCTGCGGTGTGCGTTGTGCCACCCGCGATCATCTGCCAATGGTATGCAATGTTCCCGATTATGAGGCAACACGCGTGGAATATGCGTCGTTGGTGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCTTTAGGtt                                                                            <  1:253827/251‑1 (MQ=255)                                                                                               agcagcagAATCGCCAGCGGTTGATTGATTGTTTCCCGCAGGCACAGTGGGCAACAGAGGTTGATGTCAGTGATAAAGAGACGCGCTGCGGTGTGCGTTGTGCCACCCGCGATCATCTGCCAATGGTAGGCAATGTTCCCg                                                                                                                                                                                     >  1:222472/1‑141 (MQ=255)                                                                                                 cagcagAATCGCCAGCGGTTGATTGATTGTTTCCCGCAGGCACAGTGGGCAAACGAGGTTGATGTCCGTGATAAAGAGACGCGCTGCGGTGTGCGTTGTGc                                                                                                                                                                                                                           >  1:430092/1‑101 (MQ=255)                                                                                                       aaTCGCCAGCGGTTGATTGATTGTTTCCCGCAGGCACAGTGGGCAAAAGAGGTTGATGTCAGTGATAAAGAGACGCGCTGCGGTGTGCGTGGTGCCACCCGCGATCATCTGCCAATGGTAGGCAATGTTCCCGATTATGAGGCAACACTCGTGGAATATGCGTCGTTGGCTGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGc                                                                                    <  1:303117/230‑1 (MQ=255)                                                                                                                     gattgattGTTTCCCGCAGGCACAGTGGGCAAAAGAGGTTGATGTCAGTGATAAAGAGACGCGCTGCGGTGTGCGTTGTGCCACCCGCNNTCATCTNnc                                                                                                                                                                                                         >  2:28900/1‑99 (MQ=255)                                                                                                                     gattgattGTTTCCCGCAGGCACAGTGGGCAAAAGAGGTTGATGTCAGTGATAAAGAGACGCGCGGCGGTGTGCGTTGTGCCACCCGCGATCATCTGCCAATGGTAGGCAATGTTCCCGATTATGAGGCAACACTCGTGGAATATGCGTCGTTGGCGGAg                                                                                                                                            <  1:28900/160‑1 (MQ=255)                                                                                                                          attgTTTCCCGCAGGCACAGTGGGCAAAAGAGGTTGATGTCAGTGATAAAGAGACGCGATGCGGTGTGCGTTGTGCCACCCGCGATCATCTGCCAATGGTAGGCAATGTTCCCGATTATGAGGCAACACTCGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTACGCGCGCCGGATTTTGACGATATCTTTATGTTTGCGGCTTTAGTTTCTCGCGGTTTGTGTTCTGCCCCGCTGTGTGcc                                            >  1:393161/1‑251 (MQ=255)                                                                                                                                     cAGGCACAGTGGGCAAAAGAGGTTGATGTCAGTGATAAAGAGACGCGCTGCGGTGTGCGTTGTGCCACCCGCGATCATCTGCCAATGGTAGGCAATGTTCCCGATTATGAGGCAACACTCGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGTTTGTGTTCTGCCCCGCTGTGTGCCGAGATTCTggg                                 <  1:17424/251‑2 (MQ=255)                                                                                                                                      aGGCACAGGGGGCTAAAGAGGATGAAGTCAGTGATAAAGAGACGCGCTGCGGTGTGCGTTGTGCCACCCGCGATCATCTGCCAATg                                                                                                                                                                                                     >  1:354165/1‑86 (MQ=255)                                                                                                                                                         ggTTGATGTCAGAGATAAAGAGACGCGCTGCGGTGTGCGTTGTGCCACCCGCGATCATCCGCCAATGGTAGGCAATGTTCCCGCTTATAAGGAAACACTCGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCgg                                                                                                                            >  1:437195/1‑140 (MQ=255)                                                                                                                                                                   ngTGATAAAGAGACGCGCTGCGGTGTGCGTTGTGCCACCAGCGATCATATGCCAATGGTAGGCAATGTTCCCGGTTATGAGGCAACACTCGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTCAGCGAGCCGGTTTTTGACGATCTCTTTATGTTTGCGGGTTTAGGTTCTCGCGGTTTGTGtttt                                                           >  1:39261/2‑193 (MQ=255)                                                                                                                                                                    gTGATAAAGAGACGCGCTGCGGTGTGCGTTGTGCCACCCGCGATCATCTGCCAAGGGTAGGCAATGTTCCCGATTATGAGGCAACACTCGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGTTTGTGTTCTGCCCCGCTGTGTGCCGAGATTCTGGCGGCGCAGATGAGCGACGAACCGATTCCgatn  <  1:358977/251‑2 (MQ=255)                                                                                                                                                                               |                                                                                                                                                                                                                                                TATCTCACGCCACAAAATCCGGCGAATCAACATCATTGTATTGGTGCCAGTTATCATCGCGGCAGCGAAGATACGGCGTACAGTGAGGACGATCAGCAGCAGAATCGCCAGCGGTTGATTGATTGTTTCCCGCAGGCACAGTGGGCAAAAGAGGTTGATGTCAGTGATAAAGAGGCGCGCTGCGGTGTGCGTTGTGCCACCCGCGATCATCTGCCAATGGTAGGCAATGTTCCCGATTATGAGGCAACACTCGTGGAATATGCGTCGTTGGCGGAGCAGAAAGATGAGGCGGTAAGCGCGCCGGTTTTTGACGATCTCTTTATGTTTGCGGCTTTAGGTTCTCGCGGTTTGTGTTCTGCCCCGCTGTGTGCCGAGATTCTGGCGGCGCAGATGAGCGACGAACCGATTCCGATG  >  NC_000913/2443273‑2443686

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑