Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,476,605	G→A	S390N (AGC→AAC)	yjgL →	protein YjgL

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,476,605	0	G	A	90.5%	45.1 / ‑0.8	21	S390N (AGC→AAC)	yjgL	protein YjgL
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base A (8/11);  total (9/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.40e-01

ACTTGAAGAAATAGATAAGCTCTACGCATTAAATGATCACGGAATTGATAATGACAAAGTAGGTAACAATGAAATTAATGACATCAAAGTTAACCTGTCTCATATTCTTATTGATTCCTTAGATGATGCAAAGGTTAACCTTACACCGGTCATCGATTCGATTCTGGAGACTTTTTCAAAATCCCCATATATTAATGATGTAAGAATACTGGATTGGTGTTTTAATAAAAGCATGCAATATTTTGATGATACTAAAAAGATAAAGCATGCATGCTCCGTAATAAATCATATTAATCTTCGCAGCGATCAGTCTAAAATAGCTGAGACATTATTTTTCAATCTCGATAAAGAACCCTATAAAAATAGCCCTGAATTACAGGGGTTGATTTGGAATAAGTTGGTTGTATATGTCAATGAATTTAACTTAAGTAATCGAGAAAAAACAAATTTAATACAAAGGCTATTTGATAA  >  NC_000913/4476375‑4476845                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                 aCTTGAAGAAATAGATAAGCTCTACGCATTAAATGATCACGGAATTGATAATTACAAAGTAGGTAACAATGAAATTAATGACATCAAAGTTAACCTGTCTCATATTCTTATTGATTCCTTAGATGATGCAAAGGTTAACCTTACACCGGTCATCGATTCGATTCTGGAGACTTTTTCAAAATCTCCATATATTAATGATGTAAGAATACTGGATTGGTGTTTTAATAAAAACATGCAATATTTTgatgat                                                                                                                                                                                                                               <  2:170807/250‑1 (MQ=255)    tGAAGAAATAGATAAGCTCTACGCATTAAATGATCACGGAATTGATAATGACAAAGTAGGTAACAATGAAATTAATGACATCAAAGTTAACCTGTCTCATATTCTTATTGATTCCTTAGATGATGCAAAGGTTAACCTTACACCGGTCATCGATTCGATTCTGGAGACTTTTTCAAAATCCCCATATATTAATGATGTAAGAATACTGGATTGGTGTTTTAATAAAAACATGCAATATTTTGATGATACt                                                                                                                                                                                                                            <  2:208457/250‑1 (MQ=255)                  aGCTCTACGCATTAAATGATCACGGAATTGATAATGACAAAGTAGGTAACAATGAAATTAATGACATCAAAGTTAACCTGTCTCATATTCTTATTGATTCCTTAGATGATGCAAAGGTTAACCTTACACCGGTCATCGATTCGATTCTGGAGACTTTTTCAAAATCCCCATATATTAATGATGTAAGCATACTGGATTGGTGTTTTAATAAAAACATGCAATATTTTGATGATACTACAAAAATAAAgcat                                                                                                                                                                                                             >  2:604001/1‑251 (MQ=255)                                       ccGGAATTGATAATGACAAAGTAGGTAACAATGAAATTAATGACAACAAAGTTAACCTGTCTCATATTCTTATTGATTCCTTAGATGATGCATAGGTTACCCTTACACCTGTCATCGATTCGATTCTGGAGACTTTTTCAAAAGCCTCATATATTAATGATGTAAGAATACTGGATTGGTGCTGTAATAAAAACATGCAATATTTTGATGATACTAAAAAGATAAAGCAGGCATGCTCCGTAATAAATCat                                                                                                                                                                                        <  2:138044/250‑1 (MQ=255)                                                 tAATGACAAAGTAGGTAACAATGAAATTAATGACATCAAAGTTAACCTGTCTCATATTCTTATTGATTCCTTAGATGATGCAAAGGTTAACCTTACACCGGTCATCGATTCGATTCTGGAGACTTTTTCAAAATCCCCATATATTAATGATGTAAGAATACTGGATTGGTGTTTTAATAAAAGCATGCAATATTTTGATGATACTAAAAAGATAAAGCATGCATGCTCCGTAATAAATCATATTAATCTTc                                                                                                                                                                              >  2:339266/1‑251 (MQ=255)                                                     gACAAAGTAGGTAACAATGAAATTAATGACATCAAAGTTAACCTGTCTCATATTCTTATTGATTCCTTAGATGATGCAAAGGTTAACCTTACACCGGTCATCGATTCGATTCTGGAGACTTTTTCAAAATCCCCATATATTAATGATGTAAGAATACTGGATTGGTGTTTTAATAAAAACATGCAATATTTTGATGATACTAAAAAGATAAAGCATGCATGCTCCGTAATAAATCATATTACTCTTCGc                                                                                                                                                                            >  1:588531/1‑249 (MQ=255)                                                         aaGTAGGTAACAATGAAATTAATGACATCAAAGTTAACCTGTCTCATATTCTTATTGATTCCTTAGATGATGCAAAGGTTAACCTTACACCGGTCATCGATTCGATTCTGGAGACTTTTTCAAAATCCCCATATATTAATGATGTAAGAATACTGGATTGGTGTTTTAATAAAAACATGCAATATTTTGATGATACTAAAAAGATAAAGCATGCATGCTCCGTAATAAATCATATTAATCTTCGCAGCGAt                                                                                                                                                                      <  1:604001/251‑1 (MQ=255)                                                                   cAATGAAATTAATGACATCAAAGTTAACCTGTCTCATATTCTTATTGATTCCTTAGATGATGCAAAGGTTAACCTTACACCGGTCATCGATTCGATTCTGGAGACTTTTTCAAAATCCCCATATATTAATGATGTAAGAATACTGGATTGGTGTTTTAATAAAAACATGCAATATTTTGATGATACTAAAAAGATAAAGCATGCATGCTCCGTAATAAATCATATTAATCTTCGCAGCGATCAGTCTaaa                                                                                                                                                             >  1:145576/1‑250 (MQ=255)                                                                    aaTGAAATTAATGACATCAAAGTTAACCTGTCTCATATTCTTATTGATTCCTTAGATGATGCAAAGGTTAACCTTACACCGGTCATCGATTCGATTCTGGAGACTTTTTCAAAATCCCCATATATTAATGATGTAAGAATACTGGATTGGTGTTTTAATAAAAACATGCAATATTTTGATGATACTAAAAAGATAAAGCATGCATGCTCCGTAATAAATCATATTAATCTTCGCAGCGATCAGTCTAAAAt                                                                                                                                                           >  1:644270/1‑251 (MQ=255)                                                                                     cAAAGTTAACCTGTCTCATATTCTTATTGATTCCTTAGATGATGCAAAGGTTAACCTTACACCGGTCATCGATTCGATTCTGGAGACTTTTTCAAAATCCCCATATATTAATGATGTAAGAATACTGGATTGGTGTTTTAATAAAAACATGCAATATTTTGATGATACTAAAAAGATAAAGCATGCATGCTCCGTAATAAATCATATTAATCTTCGCAGCGATCAGTCTAAAATAGCTGAGACATTAttt                                                                                                                                           <  1:157114/250‑1 (MQ=255)                                                                                                              aTTGATTCCTTAGATGATGCAAAGGTTAACCTTACACCGGTCATCGATTCGATTCTGGAGACTTTTTCAAAATCCCCATATATTAATGATGTAAGAATACTGGATTGGTGTTTTAATAAAAACATGCAATATTTTGATGATACTAAAAAGATAAAGCATGCATGCTCCGTAATAAATCATATTAATCTTCGCAGCGATCAGTCTAAAATAGCTGAGACATTATTTTTCAATCTCGATAAAGAACCCtata                                                                                                                  >  1:498236/1‑250 (MQ=255)                                                                                                                                     ggTTAACCTTACATCGGTCATCGATTCGATTCTGGAGACTTTTTCAAAATCCCCATATATTAATGATGTAAGAATACTGGATTGGGGTTTTAATAAAAACATGCAATATTTTGATGATTCTAAAAAGATAAAGCATGCATGCTCCGTAATAAATCATATGAATCTTCGCAGCGATCAGTCTAAAATAGCTGAGACATTATTTTTCAAGCTCGATACAGAACCCTATAAAAATAGCCCTGAATTACAGGGGt                                                                                          <  2:88304/251‑1 (MQ=255)                                                                                                                                        tatccTTACACCGGTCATCGATTCGATTCTGGAGACTTTTTCAAAATCCCCATATATTAATGATGTAAGAATACTGGATTGGTGTTTTAATAAAAACATGCAATATTTTGATGATACTAAAAAGATAAAGCATGCATGCTTCGTAATAAATCATATTAATCTTCGCAGCGATCAGTCTAAAATAGCTGAGACATTATTTTTCAATCTCGATAAAGAACCCTATAAAAATAGCCCTGAATTACAGGGGTTg                                                                                        <  2:604629/247‑1 (MQ=255)                                                                                                                                                                  ttcTGGAGACTTTTTCAAAATCCCCATATATTAATGATGTAAGAATACTGGATTGGTGTTTTAATAAAAACATGCAATATTTTGATGATACTAAAAAGATAAAGCATGCATGCTCCGTAATAAATCATATTAATCTTCGCAGCGATCAGTCTAAAATAGCTGAGACATTATTTTTCAATCTCGATAAAGAACCCTATAAAAATa                                                                                                            >  1:665520/1‑204 (MQ=255)                                                                                                                                                                  ttcTGGAGACTTTTTCAAAATCCCCATATATTAATGATGTAAGAATACTGGATTGGTGTTTTAATAAAAACATGCAATATTTTGATGATACTAAAAAGATAAAGCATGCATGCTCCGTAATAAATCATATTAATCTTCGCAGCGATCAGTCTAAAATAGCTGAGACATTATTTTTCAATCTCGAGAAAGAACCCTATAAAAATa                                                                                                            <  2:665520/204‑1 (MQ=255)                                                                                                                                                                       gagaCTTTTTCACAATCCCCATATATTAATGATGTACGAATACTGGATTGTTGTTTTAATAAGAACATGCAATATTTTGATGATACTAAAAAGAAAAAGCATGCATGCTCCGTAATAAATCATATTAATCTTCGCAGCGATCAGTCTAAAATAGCTGCGCCATTATTTTTCAATCTCGATAAGGAACCCTATAAAAATAGCCTTGAATTACAGGGGTTGGTTTGGAATAAGTTGGTTGTATATTTCag                                                           >  2:217044/1‑247 (MQ=255)                                                                                                                                                                              tttCAAAATCCCCATATATTAATGATGTAAGAATACTGGATTGGTGTTTTAATAAAAACATGCAATATTTTGATGATACTAAAAAGATAAAGCATGCATGCTCCGTAATAAATCATATTAATCTTCGCAGCGATCAGTCTAAAATAGCTGAGACATTATTTTTCAATCTCGATAAAGAACCCTATAAAAATAGCCCTGAATTACAGGGGTTGATTTGGAATAAGTTGGTTGTATATGTCAATGAATTTAAc                                                 >  1:93955/1‑251 (MQ=255)                                                                                                                                                                                             atatTAATGATGTAAGAATACTGGATTGGTGTTTTAATAAAAGCATGCAATATTTTGATGATACTAAAAAGATAAAGCATGCATGCTCCGTAATAAATCATATTAATCTTCGCAGCGATCAGTCTAAAATAGCTGAGACATTATTTTTCAATCTCGATAAAGAACCCTATAAAAATAGCCCTGAATTACAGGGGTTGATTTGGAATAAGTTGGTTGTATATGTCAATGAATTTAACTTAAGTAATCGAGaa                                  <  1:339266/251‑1 (MQ=255)                                                                                                                                                                                                          aaGAATACTGGAATGGTGTTTTAATAAAAACATGCAATATTTTGATGATACTAAAAAGATAAAGCATGCATGCTCCGTAATAAATCATATTAATCTTCGCAGCGATCAGTCTAAAATAGCTGAGACATTATTTTTCAATCTCGATAAAGAACCCTATAAAAATAGCCCTGAATTACAGGGGTTGATTTGGAATAAGTTGGTTGTATATGTCAATGAATTTAACTTAAGTAATCGAGAAAAAACAAATTTaa                     <  2:644270/251‑1 (MQ=255)                                                                                                                                                                                                                              ttAATAAAAACATGTAATATTTTGATGATAATAAAAAGATAAAGCAAGCATGCATCGTAAGAAAACATATTAATCTTCGCAACGATCAGGCTAAAATAGCTGAGACATTATTTTGCAATCTCGATAAAGAATCCTATAAAAATAGCCCTTAATTACAGTGGTTGATTTGGAATAAGTTGGTTGTATATGTCAATGACTTTATCTTAAGTAATCGAGAAAAAACAAATTTAATACAAAGGCTATTTTATaa  <  2:49419/250‑1 (MQ=255)                                                                                                                                                                                                                              ttAATAAAAACATGCAATATTTAGATGATACTAAAAAGATAAATCATGCATGCTCCTTAATAACTCATATTAATCTTCGCAGCGATCAGTCTAAAATATCTTAGACATTATTTTTCAATCTCTATAAATAACCCTATAAAAATAGCCCTGAATTACATTGGTTTATTTGGAATAAGTTGTTTGTATATGTCAATGAATTTAACTTAAGTAATCGAGAAAAATCAAATTTAATACAAAGGCTATTTGATaa  <  1:615377/250‑1 (MQ=255)                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                 ACTTGAAGAAATAGATAAGCTCTACGCATTAAATGATCACGGAATTGATAATGACAAAGTAGGTAACAATGAAATTAATGACATCAAAGTTAACCTGTCTCATATTCTTATTGATTCCTTAGATGATGCAAAGGTTAACCTTACACCGGTCATCGATTCGATTCTGGAGACTTTTTCAAAATCCCCATATATTAATGATGTAAGAATACTGGATTGGTGTTTTAATAAAAGCATGCAATATTTTGATGATACTAAAAAGATAAAGCATGCATGCTCCGTAATAAATCATATTAATCTTCGCAGCGATCAGTCTAAAATAGCTGAGACATTATTTTTCAATCTCGATAAAGAACCCTATAAAAATAGCCCTGAATTACAGGGGTTGATTTGGAATAAGTTGGTTGTATATGTCAATGAATTTAACTTAAGTAATCGAGAAAAAACAAATTTAATACAAAGGCTATTTGATAA  >  NC_000913/4476375‑4476845

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑