Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,392,261	(A)8→9	intergenic (+112/‑99)	orn → / → glyV	oligoribonuclease/tRNA‑Gly

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,392,253	1	.	A	76.5%	25.2 / ‑1.0	17	intergenic (+104/‑107)	orn/glyV	oligoribonuclease/tRNA‑Gly
Reads supporting (aligned to +/- strand):  ref base . (0/4);  new base A (1/12);  total (1/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.68e-02

CGGAGCTGGAAGCCTACTTCCACTACCGTTATCTCGATGTCAGCACCCTGAAAGAGCTGGCGCGCCGCTGGAAGCCGGAAATTCTGGATGGTTTTACCAAGCAGGGGACGCATCAGGCGATGGATGATATCCGTGAATCGGTGGCGGAGCTGGCTTACTACCGCGAGCA‑TTTTATCAAGCTGTAAAA‑TTTTTCCTGGTCACGTAAGCGCCGGAATCCACTTGCGGCGGCGTGATTTTGACGCTAAATTGAACGTCTTGCTGATAATTTCAGCACTTGAG‑AT‑AAAAACGC‑‑‑‑‑‑‑‑AAAAAAAACTTTTTT‑‑GGGGGGTT‑GCAGAGGG‑AAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAG‑AAATGCGAAAATTACGAAAGCAAAATTAAGTAGTACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTG‑AAAAGTGCTGCAAAGCA  >  NC_000913/4391965‑4392459                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                            cGGAGCTGGAAGCCTACTTCCACTACCG‑TATCTCGATGTCAGCACCCTGAAAGAGCTGGCGCG‑CGCTGGAAGCCGG‑AATTCTGGATGGTTTTACCAAGCAGGGGACGCATCAGGCGATGGATGATATCCGTGAATCGGTGGCGGAGCTGGCTTACTACCGCGAGCA‑TTTTATCAAGCTGTAAAA‑TTTTTCCTGGTCACGTAAGCGCCGGAATCCACTTGCGGCGGCGTGATTTTGACGCTAAATTGAACGTCTTGCTGATAATTTCAGCACTTGAG‑ATAAAAAACGCAA‑‑‑‑‑‑AAAAAAAACTTTTTT‑‑tgggggggttg                                                                                                                                                                                          <  1:1582425/315‑6 (MQ=255)                                         cAGCACCCTGAAAGAGCTGGCGCGCCGCTGGAAGCCGGAAATTCTGGATGGTTTTACCAAGCAGGGGACGCATCAGGCGATGGATGATATCCGTGAATCGGTGGCGGAGCTGGCTTACTACCGCGAGCA‑TTTTATCAAGCTGTAAAA‑TTTTTCCTGGTCACGTAAGCGCCGGAATCCACTTGCGGCGGCGTGATTTTGACGCTAAATTGAACGTCTTGCTGATAATTTCAGCACTTGAG‑AT‑AAAAACGCA‑‑‑‑‑‑‑AAAAAAAACTTTTTT‑‑GGGGGGTT‑GCAGAGGG‑AAAGATTTCTCGTATAATGCGCCTCCCGt                                                                                                                                                      <  1:1582433/310‑1 (MQ=255)                                                                    cTGGAAGCCGG‑AATTCTGGATGGTTTTACCAAGCAGGGGACGCATCAGGCGATGGATGATATCCGTGAATCGGTGGCGGAGCTGGCTTACTACCGCGAGCA‑TTTTATCAAGCTGTAAAA‑‑TTTTCCTGGTCACGTAAGCGCCGGAATCCACTTGCGGCGGCGTGATTTTGACGCT‑AATTGAACGTCTTGCTGATAATTTCAGCACTTGAG‑AT‑AAAAACGCA‑‑‑‑‑‑‑AAAAAAAACTTTTTT‑‑GGGGGGTT‑GCAGAGGG‑AAAGATTTCTCGtat                                                                                                                                                                    <  1:1582437/266‑1 (MQ=255)                                                                                    cTGGATGGTTTTACCAAGCAGGGGACGCATCAGGCGATGGATGATATCCGTGAATCGGTGGCGGAGCTGGCTTACTACCGCGAGCATTTTTATCAAGCTGTAAAATTTTTTCCTGGTCACGTAAGCGCCGGAATCCACTTGCGGCGGCGTGATTTTGACGCTAAATTGAACGTCTTGCTGATAATTTCAGCACTTGAG‑AT‑AAAAACGCA‑‑‑‑‑‑‑AAAAAAAACTTTTTT‑‑GGGGGGTTGGCAGAGGG‑AAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAG‑AAATGCGAAAATTACg                                                                                                                           >  1:1582443/1‑296 (MQ=255)                                                                                     tGGATGGTTTTACCAAGCAGGGGACGCATCAGGCGATGGATGATATCCGTGAATCGGTGGCGGAGCTGGCTTACTACCGCGAGCA‑TTTTATCAAGCTGTAAAA‑TTTTTCCTGGTCACGTAAGCGCCGGAATCCACTTGCGGCGGCGTGATTTTGACGCTAAATTGAACGTCTTGCTGATAATTTCAGCACTTGAG‑ATAAAAAACGCAA‑‑‑‑‑‑AAAAAAAACTTTTTTTGGGGGGGTT‑GCAGAGGGAAAAGAttt                                                                                                                                                                           <  1:1582440/250‑1 (MQ=255)                                                                                                         gggACGCATCAGGCGATGGATGATATCCGTGAATCGGTGGCGGAGCTGGCTTACTACCGCGAGCA‑TTTTATCAAGCTGTAAAA‑TTTTTCCTGGTCACGTAAGCGCCGGAATCCACTTGCGGCGGCGTGATTTTGACGCTAAATTGAACGTCTTGCTGATAATTTCAGCACTTGAG‑AT‑AAAAACGCA‑‑‑‑‑‑‑AAAAAAAACTTTTTT‑‑GGGGGGTT‑GCAGAGGG‑AAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAG‑AAATGCGAAAATTACGAAAGCAAAAtt                                                                                                                <  1:1582441/283‑1 (MQ=255)                                                                                                                                    cGTGAATCGGTGGCGGAGCTGGCTTACTACCGCGAGCA‑TTTTATCAAGCTGTAAAA‑TTTTTCCTGGTCACGTAAGCGCCGGAATCCACTTGCGGCGGCGTGATTTTGACGCTAAATTGAACGTCTTGCTGATAATTTCAGCACTTGAG‑AT‑AAAAACGCA‑‑‑‑‑‑‑AAAAAAAACTTTTTT‑‑GGGGGGTT‑GCAGAGGG‑AAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAG‑AAATGCGAAAATTACGAAAGCAAAATTAAGTAGTACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCa                                                                  <  1:1582445/302‑1 (MQ=255)                                                                                                                                            ggTGGCGGAGCTGGCTTACTACCGCGAGCA‑TTTTATCAAGCTGTAAAA‑TTTTTCCTGGTCACGTAAGCGCCGGAATCCACTTGCGGCGGCGTGATTTTGACGCTAAATTGAACGTCTTGCTGATAATTTCAGCACTTGAG‑AT‑AAAAACGCAA‑‑‑‑‑‑AAAAAAAACTTTTTTG‑GGGGGGTT‑GCAGAGGG‑AAAGATTTCTCGta                                                                                                                                                                     <  1:1582446/198‑1 (MQ=255)                                                                                                                                                   gAGCTGGCTTACTACCGCGAGCA‑TTTTATCAAGCTGTAAAA‑TTTTTCCTGGTCACGTAAGCGCCGGAATCCACTTGCGGCGGCGTGATTTTGACGCTAAATTGAACGTCTTGCTGATAATTTCAGCACTTGAG‑AT‑AAAAACGCA‑‑‑‑‑‑‑AAAAAAAACTTTTTT‑‑GGGGGGTT‑GCAGAGGG‑AAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAG‑AAATGCGAAAATTACGAAAGCAAAATTAag                                                                                                             <  1:1582447/244‑1 (MQ=255)                                                                                                                                                   gAGCTGGCTTACTACCGCGAGCA‑TTTTATCAAGCTGTAAAA‑‑TTTTCCTGGTCACGTAAGCGCCGGAATCCACTTGCGGCGGCGTGATTTTGACGCTAAATTGAACGTCTTGCTGATAATTTCAGCACTTGAG‑AT‑AAAAACGCA‑‑‑‑‑‑‑AAAAAAAACTTTTTT‑‑GGGGGGTT‑GCAGAGGG‑AAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAG‑AAATGCGAAAATTACGAAAGCAAAATTAAGTAGTACGCGGGAATAGCTCAGTTGGt                                                                                   <  1:1582448/269‑1 (MQ=255)                                                                                                                                                                acCGCGAGCA‑TTTTATCAAGCTGTAAAA‑TTTTTCCTGGTCACGTAAGCGCCGGAATCCACTTGCGGCGGCGTGATTTTGACGCTAAATTGAACGTCTTGCTGATAATTTCAGCACTTGAG‑AT‑AAAAACGCA‑‑‑‑‑‑‑AAAAAAAACTTTTTT‑‑GGGGGGTT‑GCAGAGGG‑AAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAG‑AAATGCGAAAATTACGAAAGCAAAATTAAGTAGTACGCGGGAATAGCTCAGTTGGTa                                                                                  <  1:1582449/258‑1 (MQ=255)                                                                                                                                                                                               ttttCCTGGTCACGTAAGCGCCGGAATCCACTTGCGGCGGCGTGATTTTGACGCTAAATTGAACGTCTTGCTGATAATTTCAGCACTTGAG‑AT‑AAAAACGC‑‑‑‑‑‑‑‑AAAAAAAACTTTTTT‑‑GGGGGGTT‑GCAGAGGG‑AAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAGAAAATGCGAAAATTACGAAAGCAAAATTAAGTAGTACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTG‑aaaa               <  1:1582450/295‑1 (MQ=255)                                                                                                                                                                                                                   ccGGAATCCACTTGCGGC‑GCGTGATTTTGACGCTAAATTGAACGTCTTGCTGATAATTTCAGCACTTGAG‑ATAAAAAACGCAAAAAAAAAAAAAAAACTTTTTT‑‑GGGGGGTT‑GCAGAGGG‑AAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAG‑AAATGCGAAAATTACGAAAGCAAAATTAAGTAGTACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAAAGTGCTGCAAAGca  <  1:1582451/296‑1 (MQ=37)                                                                                                                                                                                                                                                                tCTTGCTGATAATTTCAGCACTTGAG‑AT‑AAAAACGC‑‑‑‑‑‑‑‑AAAAAAAACTTTTTT‑‑GGGGGGTT‑GCAGAGGG‑AAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAg                                                                                                                                            <  1:1582455/106‑1 (MQ=255)                                                                                                                                                                                                                                                                  ttGCTGATAATTTCAGCACTTGAG‑AT‑AAAAACGC‑‑‑‑‑‑‑‑AAAAACAAAACTTTT‑‑GGGGGGTT‑GCAGAGGG‑AAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAG‑AAATGCGAAAATTAc                                                                                                                            <  1:653849/119‑1 (MQ=255)                                                                                                                                                                                                                                                                    gCTGATAATTTCAGCACTTGAG‑AT‑AAAAACGCAAAA‑‑‑‑AAAAAAAACTTTTTT‑‑GGGGGGTT‑GCAGAGGG‑AAAGATTTCTCGTATAATGCGCCTCCCGTAac                                                                                                                                                   <  1:1582456/99‑1 (MQ=255)                                                                                                                                                                                                                                                                            tttCAGCACTTGAGAAT‑AAAAACGC‑‑‑‑‑‑‑‑‑AAAAAAACTTTTTT‑‑GGGGGGTT‑GCAGAGGG‑AAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAg                                                                                                                                            <  1:1582459/94‑1 (MQ=255)                                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                            CGGAGCTGGAAGCCTACTTCCACTACCGTTATCTCGATGTCAGCACCCTGAAAGAGCTGGCGCGCCGCTGGAAGCCGGAAATTCTGGATGGTTTTACCAAGCAGGGGACGCATCAGGCGATGGATGATATCCGTGAATCGGTGGCGGAGCTGGCTTACTACCGCGAGCA‑TTTTATCAAGCTGTAAAA‑TTTTTCCTGGTCACGTAAGCGCCGGAATCCACTTGCGGCGGCGTGATTTTGACGCTAAATTGAACGTCTTGCTGATAATTTCAGCACTTGAG‑AT‑AAAAACGC‑‑‑‑‑‑‑‑AAAAAAAACTTTTTT‑‑GGGGGGTT‑GCAGAGGG‑AAAGATTTCTCGTATAATGCGCCTCCCGTAACGACGCAG‑AAATGCGAAAATTACGAAAGCAAAATTAAGTAGTACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTG‑AAAAGTGCTGCAAAGCA  >  NC_000913/4391965‑4392459

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑