Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	225,246	2 bp→CA	coding (78‑79/375 nt)	unknown ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	225,246	0	T	C	80.0%	15.9 / 0.5	15	K27E (AAA→GAA)	unknown	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (1/2);  new base C (7/5);  total (8/7)
Fisher's exact test for biased strand distribution p-value = 5.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.75e-01
*	1	225,247	0	C	A	80.0%	18.5 / 1.9	15	A26A (GCG→GCT)	unknown	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (1/2);  new base A (7/5);  total (8/7)
Fisher's exact test for biased strand distribution p-value = 5.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

CCAACTCCTTTAGGTAAGCAATCTGTGCACGTGCTAATGCCAGCTCTCGTTGCAGCTTTTTAAACGCTTTTGGGGAAAAGTCTGTTTGTTCCGGGATTTCAATCGCTTTCTTTTTCATCTTTGGCTTCACTATTTTAGGGCGTTGAGGGTTTATATAAGGGGATTTTACGCCATTAAGCCCTCTTTCACGAAATGCTTTTAGCCAATAAATGACGAGCGCGTGGGAGATTTTATGAAGTTTCGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAGTTTTTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCGGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATACGCGGACCGCCGCCGCCAAGTGGGGCCGGGTGATCGGAGTGGTTATCGCCACCAGCGTGGATCATGAGGGAG  >  1/225006‑225488                                                                                                                                                                                                                                                 ||                                                                                                                                                                                                                                                  ccAACTCCTTTAGGTAAGCAATCTGTGCACGTGCTAATGCCAGCTCTCGTTGCAGCTTTTTAAACGCTTTTGGGGAAAAGTCTGTTTGTTCCGGGATTTCAATCGCTTTCTTTTTCATCTTTGGCTTCACTATTTTAGGGCGTTGAGGGTTTATATAAGGGGATTTTACGCCATTAAGCCCTCTTTCACGAAATGCTTTTAGCCAATAAATGACGAGCGAATGGGAGATTTTATGAAGTTTCGcc                                                                                                                                                                                                                                                >  1:477617/1‑245 (MQ=255)                                                                   cTTTTGGGGAAAAGTCTGTTTGTTCCGGGATTTCAATCGCTTTCTTTTTCATCTTTGGCTTCACTATTTTAGGGCGTTGAGGGTTTATATAAGGGGATTTTACGCCATTAAGCCCTCTTTCACGAAATGCTTTTAGCCAATAAATGACGAGCGAATGGGAGATTTTATGAAGTTTCGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAGTTTTTAAACGAAATTGGTAAGAGTAAGAc                                                                                                                                                                        <  1:897128/251‑1 (MQ=18)                                                                                                                                                                  gATTTTACGCCATTAAGCCCTCTTTCACGAAAGGCTTTT‑‑CCAATAAATGACTTGAGAACGAGAAATCTGATGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATAcg                                                                        <  1:624914/250‑1 (MQ=255)                                                                                                                                                                   aTTTTACGCCATTAAGCCCTCTTTCACGAAAGGCTTTT‑‑CCAATAAATGACTTGAGAACGAGAAATCTGATGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATAcgcg                                                                      >  1:661990/1‑251 (MQ=11)                                                                                                                                                                    ttttACGCCATTAAGCCCTCTTTCACGAAAGGCTTTT‑‑CCAATAAATGACTTGAGAACGAGAAATCTGATGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATAcg                                                                        <  1:226559/248‑1 (MQ=255)                                                                                                                                                                             aTTAAGCCCTCTTTCACGAAAGGCTTTT‑‑CCAATAAATGACTTGAGAACGAGAAATCTGATGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATAcgc                                                                       >  1:303672/1‑240 (MQ=11)                                                                                                                                                                             aTTAAGCCCTCTTTCACGAAAGGCTTTT‑‑CCAATAAATGACTTGAGAACGAGAAATCTGATGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATACGCGGAccgccgc                                                             >  1:675978/1‑250 (MQ=11)                                                                                                                                                                                                                      cttgagaacgagaaatctgaTGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATACGCGGACCGCCGCCGCCAAGTGGGGCCGGGTGATCGGAGTGGTTATCGccac                      >  1:105708/20‑250 (MQ=18)                                                                                                                                                                                                                              cgagaaatctgaTGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATACGCGGACCGCCGCCGCCAAGTGGGGCCGGGTGATCGGAGTGGTTATCGCCACCAGCGTGGa             >  1:443709/12‑251 (MQ=21)                                                                                                                                                                                                                                agaaatctgaTGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATACGCGGACCGCCGCCGCCAAGTGGGGCCGGGTGATCGGAGTGGTTATCGCCACCAGCGTGGAt            <  1:846594/241‑1 (MQ=21)                                                                                                                                                                                                                                   gaTTTTATGAAGTTTCGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAGTTTTTTAACGAAATTGATAag                                                                                                                                                                                <  1:94868/83‑1 (MQ=25)                                                                                                                                                                                                                                      ctgaTGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATACGCGGACCGCCGCCGCCAAGTGGGGCCGGGTGATCGGAGTGGTTATCGCCACCAGCGTGGATCATGAgg     >  1:134948/4‑251 (MQ=255)                                                                                                                                                                                                                                       tgaTGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATACGCGGACCGCCGCCGCCAAGTGGGGCCGGGTGATCGGAGTGGTTATCGCCACCAGCGTGGATCATGAggg    <  1:555863/249‑1 (MQ=255)                                                                                                                                                                                                                                        gaTGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATACGCGGACCGCCGCCGCCAAGTGGGGCCGGGTGATCGGAGTGGTTATCGcc                        >  1:737475/2‑230 (MQ=255)                                                                                                                                                                                                                                         aTGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTGGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATACGCGGACCGCCGCCGCCAAGTGGGGCCGGGTGATCGGAGTGGTTATCGCCACCAGCGTGGATCATGAGGGAg  <  1:514412/251‑1 (MQ=255)                                                                                                                                                                                                                                                 ||                                                                                                                                                                                                                                                  CCAACTCCTTTAGGTAAGCAATCTGTGCACGTGCTAATGCCAGCTCTCGTTGCAGCTTTTTAAACGCTTTTGGGGAAAAGTCTGTTTGTTCCGGGATTTCAATCGCTTTCTTTTTCATCTTTGGCTTCACTATTTTAGGGCGTTGAGGGTTTATATAAGGGGATTTTACGCCATTAAGCCCTCTTTCACGAAATGCTTTTAGCCAATAAATGACGAGCGCGTGGGAGATTTTATGAAGTTTCGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAGTTTTTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCGGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATACGCGGACCGCCGCCGCCAAGTGGGGCCGGGTGATCGGAGTGGTTATCGCCACCAGCGTGGATCATGAGGGAG  >  1/225006‑225488

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑