Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,822	T→C	D363D (GAT→GAC)	thrC →	threonine synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,822	0	T	C	96.8%	78.9 / ‑4.3	31	D363D (GAT→GAC)	thrC	threonine synthase
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (11/19);  total (12/19)
Fisher's exact test for biased strand distribution p-value = 3.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.85e-01

GACGGTCAGTGGTCACCCAAAGCGACTCAGGCGACGTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGC‑GCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATCTGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATG  >  NC_000913/4586‑5061                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                 gacgGTCAGTGATCACCCAAAACGACTCAGGCGACGTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTACGCCGCAAAATCTGGAAACTGAAAGAGCTGGGATATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGCACTGGGCTACACCTCGGAGCCGCACGCTGCCGTAGCGTATCGTGC‑GCGGCGTGACCAGGTGAATCCAgg                                                                                                                                                                                                                                    >  2:370674/1‑251 (MQ=255)  acagcgcgagggaccccAAAACGCCTCGGGCGACTTTATACACCGCTAAGGACGTGAGTCAGCTAAACAACTGGCCGCGTGGGAAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACCTCGGAGCTGCACGCTGCCGTAGCTTATCGTGT‑GCTGCGTGACCAGTTGAATCCAGGc                                                                                                                                                                                                                                   <  2:200407/237‑1 (MQ=255)              cccccAAAGCGACTCAGGCCACGTTATCCAACGCGTTGGCCGTGATTCGGCCGAACACCTGGCCGGTTGGGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTAGCGTATCGTGC‑GCTGCGTGACCAGTTGAATCCAGGGGAATATGGCTTg                                                                                                                                                                                                                       <  2:222125/249‑1 (MQ=255)                     aGCGACTCAGGCGGCGTTATCCAACGCGAGGGACGTGAGTCAGCCGAACAACTGGCCGCGTGGGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTAGCGTATCGTGC‑GCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCg                                                                                                                                                                                                                <  1:101714/251‑1 (MQ=255)                                  aCGTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTAGCGTATCGTGC‑GCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATcc                                                                                                                                                                                                  <  1:379567/251‑1 (MQ=255)                                   cGTTATCCAACGCGATGGACGTGAGTCAGCCGAACCACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGAGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTAGAGTATCGTGC‑GCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTGCGCACC‑GCGCCTCCg                                                                                                                                                                                                 >  2:186860/1‑251 (MQ=255)                                             cgcgATGGCCGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTAGCGTATCGTGC‑GCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGAAAttt                                                                                                                                                                                        >  1:9081/1‑250 (MQ=255)                                                        tGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTAGCGTATCGTGC‑GCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGGAATTTAAagagggagtg                                                                                                                                                                            >  1:197684/1‑245 (MQ=255)                                                                   aacaacGGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTAGCGTATCGTGC‑GCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATtct                                                                                                                                                                 <  1:141914/251‑1 (MQ=255)                                                                     caacTGGCAGCGTGTGGAAGCGTTGTTCCGCCGCAAAAACTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTAGCGTATCGTGC‑GCTGCGTGACCAGTTGAATACAGGCGCATATGGAGTGTTCCTACGCACCTCCGC‑CCCGGCGAAATTTTAAGAGAGCGGGTAAGCGGTtcgcg                                                                                                                                                               >  2:35345/1‑248 (MQ=255)                                                                            ccggtgggggAAGAGTGATTCCGCCGCAAAATCTGGCAACGGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACGCCTCGGAGCCGCACGCTGCCGTAGCGTAGCGTGC‑GCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAAc                                                                                                                                                        <  2:118377/243‑1 (MQ=255)                                                                                   tggcagagTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACCTCGGAGTCGCACGCGGCCGAAGAGTATCGTGC‑GCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCATCGGCACC‑GCGCATCCGGCGAAATTTAAAAAGGGGGTGGTATCGATTCCCGGTGGAACGtaggtt                                                                                                                                                 >  2:85658/5‑246 (MQ=255)                                                                                   gggAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTAGCGTATCGTGC‑GCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGAt                                                                                                                                                 <  1:216401/250‑1 (MQ=255)                                                                                    ggAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTAGCGTATCGTGC‑GCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATc                                                                                                                                                >  1:262021/1‑251 (MQ=255)                                                                                                         aaTCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTTAAAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTAGCGTATCGTGC‑GCTGCGTGACCAGTTGAATTCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAACCGTTGGATCTGCCAAAAGAGCTGGCAGAAc                                                                                                                           <  1:184688/251‑1 (MQ=255)                                                                                                             tGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGC‑GCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGc                                                                                                                       >  1:166399/1‑251 (MQ=255)                                                                                                                     gAAAGAGCTGGGTTATGCAGACGTGGGTGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTAGCGTATCGTGC‑GCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGAttt                                                                                                                 <  1:63037/249‑1 (MQ=255)                                                                                                                       aaGAGATGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAACAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTAGCGTATCGTGC‑GCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGGGTAACGTTGGATCTGCCAAAAGAGCTGGAAGAACGTGCTGATTTAccc                                                                                                             >  1:104402/1‑251 (MQ=255)                                                                                                                                   atgcagcagtgtctggtgacaCCATGCAACATAAAATGCGTGAGTTAACAGAACTGGGCTACACATCGAAGGCGCACGATTCCGCAGCATATCGTGC‑GCTGCGTGACCAGTTGAATCCAGGCGCATATGGCTTGCTCCTCGGCACC‑GCGCAGCAGGCGATATTTACAGAGAGCGTGGAAACGCTTCCCGGTGTATCGTTGGATGTGCCAAACGACCTGGCAGAACGTGCTGATTTACCCTTGCtttacaat                                                                                                 >  2:32161/21‑246 (MQ=255)                                                                                                                                            gggtgtatgaAACCACGCAACAGACAATGCGTGAGCTCAAAGACCTGGCATACACCACAGAGCCGCCCGCTGCTGTAGCGTATCGTGC‑GCTGCGTGACAAGTTGAAATTAGGCGCATATGGCGTGTTCCTCGTCCCC‑GCTCATCCGGCGAAATATAAAGAGAGCGTGTAAGCGAGTCTCGGTGAAACGTTGGAGCTGCCAAAAGAGCTGGCAGAACGTGCTGATGTTCCCTTTCTGTCACATAATCCGccc                                                                                        <  2:295107/245‑1 (MQ=255)                                                                                                                                                  atgaAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTAGCGTATCGTGC‑GCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATCTGCccgccggt                                                                                  >  1:331417/1‑249 (MQ=255)                                                                                                                                                                 aGACAATGCGTGAGATAAAAGAACTGGGCTACACCTCGGAGCCGCACGCTGCCGTAGCGTATCGTGC‑GCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATCTGCCCGCCGATTTTGCtgcgttgcgt                                                                   >  1:303320/1‑251 (MQ=255)                                                                                                                                                                   aCAATGTGTGATTTAAAATAACAGGGCTACACCTCGGAGCCTCGCTCTGCCTTAGTGTGTCGTTC‑GCTGCGTGACTAGTTGAATCCAGGCGAATAGGGCTTGTTCCTCGGCACC‑TCGCATCCGGCTAAATGTAAAGAGAGCGTGGAATCGATTCTCGGTGAAACTTTGGATCTGCAAAAAGAGCTGGCAGAACGTGCTTTTTTCCCCTTGTTTTCACATAATCTGCCCGCCGATTTTGCTGCGTTGCGTa                                                                  <  1:215049/250‑1 (MQ=255)                                                                                                                                                                     aaTGCGTGAGGAAAAAGAACTGGGCTAAACCGCGGAGCGGCACGCTGCCGTAGCGTATCGGGG‑GATGGGGGACGAGTTGAATCCAGGCGAATAGGGCGTGTTCCTGGGCACG‑GGGCAAACGGAGAAATTTAAAGAGAGCGGGGAAGCGATTCGCGGGGAAACGTGGAATATGCAAAAAGAGAGGGCAGAACGGGCTGATTTCCCCTTCCTTTCACATAATCTGCCCGCCGATTTTGCTGCGTTGCGTAAAt                                                               <  1:68793/251‑1 (MQ=255)                                                                                                                                                                                 aaaaGAACTGGGCTACGCCTCGGAGCCGCACGCGGCCGTAGCGTTTCGTGC‑GCTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGAAGAACGTGGTGATTTACCCTTGCTTTCACATAATCTGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAatc                                                   <  1:34778/251‑1 (MQ=255)                                                                                                                                                                                     aaaCTGGGCTACTCTTGGGAGCCGCAGGCTGCGGTAGCGTTTC‑TGCCGCTGCGTCACCAGTTGACTCCAGGCGAATAGGGCTTGTTCCTCGGCCCC‑GCGCAGCCGGAAAAATTAAAAGAAAGTGTGGAAGCGATTCTCGGTGAAACGTTGGATCTCCCAAAAGAGCTGGCAGAACGTGCTGATTTCCCCTTTCTTTCACATAATCTGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAAtcatca                                               <  1:307314/250‑1 (MQ=255)                                                                                                                                                                                          gggCTACACCCCGGATCAGCACGGTGCCGTAGCGTACCGTGC‑GCTGCGTAACCAGTTGAAACCAGGCGAATATGGCTTGTTCCCCGGCACC‑GCGCTTCCGGCGAAATTAAAAGATAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGATCTGGCAGACCGGGCTAATTTACCCTTGCTTTCACATAATCTGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATTATGAATCATCAGTaa                                           <  1:338652/250‑1 (MQ=255)                                                                                                                                                                                                    ccGGAGCCGCACGCTGCTGTGGCGTATCGTGC‑GTTGCTGGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATCTGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCAt                                <  1:370674/250‑1 (MQ=255)                                                                                                                                                                                                                             aTCGTGC‑GTTGCGTGACCAGTTGAACCCAGGCAAATATGGCTTGTTCCTCGGCCCC‑GCCAACCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAATCGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTAATTTCCCTTTGCTTTAACAAAATCTGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCt        <  1:186860/250‑1 (MQ=255)                                                                                                                                                                                                                                  gc‑gcTGCGTGACCAGTTGAACTCAGGCGAATATGGTTTGTTCCTCGGCACC‑GCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATGATCTGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATg  <  1:274134/251‑1 (MQ=255)                                                                                                                                                                                                                                   gctcTGCGTGACCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATCGGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATg  <  1:64307/248‑1 (MQ=255)                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                 GACGGTCAGTGGTCACCCAAAGCGACTCAGGCGACGTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGC‑GCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC‑GCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATCTGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATG  >  NC_000913/4586‑5061

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑