Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,725,176	T→G	E48A (GAG→GCG)	glyQ ←	glycine‑‑tRNA ligase subunit alpha

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,725,176	0	T	G	92.9%	31.3 / ‑5.2	14	E48A (GAG→GCG)	glyQ	glycine‑‑tRNA ligase subunit alpha
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base G (5/8);  total (6/8)
Fisher's exact test for biased strand distribution p-value = 4.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

AACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGACCACCTGGAACTGATAGTAGTGCTGTAAACGGTTGGGGTTTTCGCCGTAGCGACCATCGGTCGGGCGACGAGAAGGCTGAACATAAGCAGCCGCCATCGGTTCTGGCCCCAGCTCGCGCAGACAGGTCATTGGGTGAGAGGTTCCCGCGCCGACTTCCATGTCCAATGGTTGAACAATGGTGCAGCCCTGGCGAGCCCAGTAATCCTGTAAGGTCAGGATCAAGCCCTGGAAGGTCCTGGTATCAAACTTTTGCATATTATTTCGTGCTGGATACGTGTGGATTTAAAGGAAGGGATCAGTATACCCGCTGGATGGAAGATATACAGT  >  NC_000913/3724973‑3725390                                                                                                                                                                                                            |                                                                                                                                                                                                                       aaCGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGACCACCTGGAACTGATAGTAGTGCTGTAAACGGTTGGGGTTTTCGCCGTAGCGACCATCGGTCGGGCGACGAGAAGGCTGAACATAAGCAGCCGCAATCGGTTCTGGCCCCAGCGCGCGCAGACAGGTCATTGGGTGAGAGGTTCCCGCGCCGACTTCCATg                                                                                                                                                                         <  1:120419/251‑1 (MQ=255)   cGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGACCACCTGGAACTGATAGTAGTGCTGTAAACGGTTGGGGTTTTCGCCGTAGCGACCATCGGTCGGGCGACGAGAAGGCTGAACATAAGCAGCCGCCATCGGTTCGTGCCCCAGCGCGCGCAGACAGGTCATTGGGTGAGAGGTTCCCGCGCCGACTTCCATGtn                                                                                                                                                                       <  1:90826/251‑2 (MQ=255)               aTAGTCGGGTCCATACCCAGCTCTTTCAGAGAACCGAGGTACAGCCCCTGAATATTGTCCGGCGATGGCTTAATGACCACCTGGAACTGATAGTAGTGCTGGAAACGGTTGGGGTTTTCGCCGTAGCGACCATCGGTCGGGCGACGAGAAGGCTGAACATAAGCAGCCGCCATCGGTTCTGGCCCCAGCGCGCGCAGACAgg                                                                                                                                                                                                            <  1:227792/202‑1 (MQ=255)                  gTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTACGGGGGTGGCTTAATGACCACCTGGACCTGATAGTAGTGCTGTAAACGGTTGGGGTTTTCGCCGTAGCGACCCTAGGTAGGGCGACGAGAAGGCTGAACATAAGCAGCCGCCACAGGTTCTGGCCCCAGCGCGCGCAGACAGGGCATTGGGGGAGAGGTTTCCGCGCCGACTTTCCTGTCCAATGGTTGAACaa                                                                                                                                                         >  1:333537/1‑250 (MQ=255)                       gTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGACCACCTGGAACTGATAGTAGTGCTGTAAACGGTTGGGGTTTTCGCCGTAGCGACCATCGGTCGGGCGACGAGAAGGCTGAACATAAGCAGCCGCCATCGGTTCTGGCCCCAGCGCGCGCAGACAGGTCATTGGGTGAGAGGTTCCCGCGCCGACTTCCATGTCCAATGGTTGAACAATGGTgn                                                                                                                                                   <  1:50950/251‑2 (MQ=255)                                       ttCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGAGATGGCTTAATGAACACCTGGAACTGATAGTAGTGCTGTAAACGGTTGGGGTTTTAGCCGTAGCGACCATCCGTCGGGCGACGAGAAGGCTGAACATAAGCAGCCGCCATCGGTTCTGGCCCCAGCGCGCGCAGACAGGTCATTGGGTGAGAGGTTCCCGCGCCGACTTCCATGTCCAATGGTTGAACAATGGTGCAGCCCTGGCGAGccc                                                                                                                                    >  1:222134/1‑250 (MQ=255)                                                                                   cTTAATGACCACCTGGAACTGATAGTAGTGCTGTAAACGGTTGGGGTTTTCGCCGTAGCGACCATCGGTCGGGCGACGAGAAGGCTGAACATAAGCAGCCGCCATCGGTTCTGGCCCCAGCGCGCGCAGACAGGTCATTGGGTGAGAGGTTCCCGCGCCGACTTCCATGTCCAATGGTTGAACAATGGTGCAg                                                                                                                                                 <  1:372137/193‑1 (MQ=255)                                                                                              ccTGGAACTTATAGTAGTTCTGTAAACGGTGTGGGTTGTCGCCGTAGCGACCAGCGGTCGGGTGACGAGAAGGCTGAACATAAGCATCCGCCAGCGGTTCTGGCCCCAGCGCGCGCAGACAGGTCATTGGGTGAGAGGTTCCcgcg                                                                                                                                                                                     <  1:75617/146‑1 (MQ=255)                                                                                                              gtGCTGTAAACGGTTGGGGTTTTCGCCGTAGCGACCATCGGTCGGGCGACGAGAAGGCTGAACATAAGCAGCCGCCATCGGTTATGGCTCCAGCGCGCGCAGACCGGTCATTGGGTGAGAGGTTCCCGCGCCGACTTCCATGTCCAATGGTTGAACACTGGTGCAGACCTGGCGAGCCCAGTAATCCTGTAAGGTCAGGATCAAGCCCTGGAAGGTCCTGGTATCAAACTTTTGCATATTATTTAGTGCTg                                                            >  1:364868/1‑251 (MQ=255)                                                                                                                                                            cgacgaGAAGGCTGAACATAAGCAGCCGCCATCGGTTCTGGTCCCAGCTCGCGCAGACAGCCCATTGGGTGAGAGGTTCCCGCGCCGACTTCCATGTCCAATGGTTGAACAATGGTGCAGCCCTGGCGAGCCCAGTAATCCTGTAAGGTCAGGATCAAGCCCTGGCAGGTCCTGGTATCAACCTTTTGCATATTATTTCGTGCTGGATACGTGTGGATTTCATGGAAGGGATCAGTATACCCGCtggatgg              >  1:231422/1‑251 (MQ=255)                                                                                                                                                                            cATAAGCAGCCGCCATCGGTTCTGGCCCCAGCGCGCGCAGACAGGTCATCGGGTGAGAGGTTCCCGCGCCGACTTCCATGTcc                                                                                                                                                                      >  1:259830/1‑83 (MQ=255)                                                                                                                                                                                  cagcCGCCATCGGTTCTGGCCCCAGCGCGCGCAGACAGGTCAGTGGGTGAGAGGTTCCCGCGCCGACTTCCATGTGCAATGTTGGAACAATGGTGCAGCCCTGGCGAGCCCAGTAATCCTGTAAGGTCAGGATCAAGc                                                                                                         <  1:71388/138‑1 (MQ=255)                                                                                                                                                                                              gtgcTGGCCCCAGCGCGCGCAGACAGGTCATTGGGTGAGCGGTTCCCGCGCCGCCTTCCATGTCCAATGGTTGACCAATGGTGCAGCCCTGGCGAGCCCAGTAATCCTGTAAGGTCAGGATCAAGCCCTGGAAGGTCCTGGTATCAAACTTTTGCATATTATTTCGTGCTGGATACGTGAGGATTTAAAGGAAGGGATCAGTATACCCGCTGGATGGAAGATATACAGt  >  1:173135/4‑229 (MQ=255)                                                                                                                                                                                                  tGGCCNCANCNCGNNCNGACANGTCATTGGGTGAGAGGTTCCCGCGCCGACTTCCATGTCNANt                                                                                                                                                                   >  2:225841/1‑64 (MQ=255)                                                                                                                                                                                                  tGGCCCCAGCGCGCGCAGACAGGTCATTGGGTGAGAGGTTCCCGCGCCGACTTCCATGTCCAATGGTTGAACAATGGTGCAGCCCTg                                                                                                                                            <  1:225841/87‑1 (MQ=255)                                                                                                                                                                                                            |                                                                                                                                                                                                                       AACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGACCACCTGGAACTGATAGTAGTGCTGTAAACGGTTGGGGTTTTCGCCGTAGCGACCATCGGTCGGGCGACGAGAAGGCTGAACATAAGCAGCCGCCATCGGTTCTGGCCCCAGCTCGCGCAGACAGGTCATTGGGTGAGAGGTTCCCGCGCCGACTTCCATGTCCAATGGTTGAACAATGGTGCAGCCCTGGCGAGCCCAGTAATCCTGTAAGGTCAGGATCAAGCCCTGGAAGGTCCTGGTATCAAACTTTTGCATATTATTTCGTGCTGGATACGTGTGGATTTAAAGGAAGGGATCAGTATACCCGCTGGATGGAAGATATACAGT  >  NC_000913/3724973‑3725390

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑