Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	696,470	C→T	noncoding (35/75 nt)	glnX ←	tRNA‑Gln

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	696,470	0	C	T	93.3%	111.0 / ‑4.0	47	noncoding (35/75 nt)	glnX	tRNA‑Gln
Reads supporting (aligned to +/- strand):  ref base C (3/0);  new base T (18/24);  total (23/24)
Fisher's exact test for biased strand distribution p-value = 9.37e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTG  >  NC_000913/696335‑696605                                                                                                                                        |                                                                                                                                        cATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGCTTCGAACCTCGGAATGCCGGAATTAGAATcc                                                                                                                                  >  2:168832/1‑143 (MQ=255)     cGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATGGAATGAACGAAGAAAAGCAAAAAGCACGCGGAAGCGAGCTTTTTTAAGGTGGATGTGGTACGAGGATTCGAACCTCCGAATCGCGGAATCAGGATCCggat                                                                                                                              >  2:376786/1‑141 (MQ=255)      gACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGc                                                                                                                             >  1:886139/1‑143 (MQ=255)       aCATCGAAGGCTAAGACGTGTCAACATCGCATGCGACATTGAATGAACGCAGAAAAGCAAAAAGCGCGGCGAAGCGAGCTTGTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGcc                                                                                                                            <  1:530853/143‑1 (MQ=37)         aTTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTTGGAATGGCGAAAGAAGAACCCGGTCCCtt                                                                                                                          >  1:1002861/1‑143 (MQ=38)          gtGAAGGATAAGACGTGTCAACATCGCAGTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTa                                                                                                                         <  2:962955/142‑1 (MQ=255)           tGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGCGTACGAGGATCCGAGCCTCGGCATGCCGGAATCAGAATCCGGTGCCTTAc                                                                                                                        >  1:15661/1‑143 (MQ=255)                gATAAGACGTGTCAACATCGCATTCGACCTTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGCGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACATCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCtt                                                                                                                   >  1:802159/1‑143 (MQ=255)                gATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGACGGAATTAGAATCAGGTGACTTACCGCtt                                                                                                                   >  2:496754/1‑143 (MQ=255)                  tAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTgg                                                                                                                 <  1:56992/143‑1 (MQ=255)                     gACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCCTGGCgc                                                                                                              >  2:733217/1‑142 (MQ=255)                          gtCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTAc                                                                                                                        >  1:1040133/1‑128 (MQ=255)                          gtCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTAc                                                                                                                        <  2:1040133/128‑1 (MQ=255)                             aaCATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCAGAGCGGAACCGCCTGGCGAtgggccag                                                                                                      >  2:203989/1‑136 (MQ=37)                              aCATCGCATTCAACATATAATCAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAAc                                                                                                     >  2:135719/1‑143 (MQ=255)                                 tCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCACCTgg                                                                                                  >  1:463312/1‑143 (MQ=255)                                  cGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTggg                                                                                                 >  1:672309/1‑143 (MQ=255)                                       tCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCAc                                                                                            <  1:764519/143‑1 (MQ=255)                                            aTTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGCATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACGTACa                                                                                       >  2:981845/1‑143 (MQ=255)                                             ttGAATGAACGCAGAAGTGCAAGAATCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACaa                                                                                      <  2:418286/143‑1 (MQ=21)                                              tgaatgaaCGCAGAAAAGCAAAAATCTCGCCGAAGCGATCCTTTTGAATGTGGCTGGGGTCAGGGGATGCTTACCGCTTGATACGCGATTTCCACTCCTTTGCCTTACCGCGTGGCGATACCCCAACTGGGTGCACTTACAAg                                                                                     <  1:496754/143‑1 (MQ=255)                                                aatgaaCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGt                                                                                   >  1:59252/1‑143 (MQ=255)                                                         gcacaggCACAACGCTAGCCGAAGCGAGCTCTTTAAATGTGTCTGGGCTACGAGGATTCGCACCTCGGACTGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCtt                                                                          <  2:123946/137‑1 (MQ=21)                                                         ataaaaGCAAAATGCTCGCCGTATCGAGCTTTTTTAATGTGGCTGTGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCtt                                                                          <  2:134489/141‑1 (MQ=25)                                                         aGAAAAGCAAAAAGCCAGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCtt                                                                          <  1:2362/143‑1 (MQ=255)                                                           aaaaGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTGCGAGGATCCGAACCTCGGAATGCCGGAATTAGAATCCGGTGAATTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAAGTAAGCGTCttta                                                                        >  1:475736/1‑141 (MQ=25)                                                              aGCACAAGGGTCGGCGAAGCGGGCTGTTGTAAGGTGGGTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATa                                                                     <  1:903055/143‑1 (MQ=18)                                                                  aaaaGATCGTCGTCGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAAtt                                                                 <  2:310566/143‑1 (MQ=21)                                                                   caaGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACAGGGTGCACTTACAAGGTGAGCGCATTGAACAAAtaa                                                                >  2:1021583/2‑141 (MQ=21)                                                                    aaGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTgg                                                               <  1:740979/143‑1 (MQ=255)                                                                          cccGTAGGGATCTTTTTTAATGTTGCTTGTGTACGAGTATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTgggg                                                         <  2:369866/142‑1 (MQ=25)                                                                               aGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGACTACGGTCCCGCACCTCTTGGCGATGCCCTGACCTTGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGa                                                    <  1:247353/143‑1 (MQ=25)                                                                                    gCTTCTTTAAGCTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTGGAATCCGGTGCCTTACCGCTTTGCTATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGAtt                                               <  1:163848/143‑1 (MQ=25)                                                                                            aaTGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATGAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATACATTGGCAGGGCTACGAGGATTCGCCCCTc                                       >  1:412542/1‑143 (MQ=21)                                                                                                    ggcggTACGAGGATGTGAACCCCGGAAGGCCGAAATTAGAATCCGGTGCCTTACCGCTTGGCGATACGCCAACTGGGTGCACGTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGcc                               <  2:25719/140‑1 (MQ=37)                                                                                                     ggggTACGAGGATTCTCACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCg                              <  2:301347/143‑1 (MQ=255)                                                                                                             aGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTACGCGTCTTGAATAAATTGGCTTGGGTACGAGGCTTCGAACCCCGGAATGCCGGCATCAgc                      >  1:406900/1‑142 (MQ=25)                                                                                                                aTTCGAACCACGAAATGCCTGAATTAGAATCCAGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACCAGGTAAGCGTCTTGACTAAATCGGCTGGGGGACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATc                   <  1:203989/143‑1 (MQ=37)                                                                                                                   cGAACCTCGGAATGCCTGAATTAGAACCCAGTGCCTTACCGCTTGTCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTCGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCgg                <  1:625228/143‑1 (MQ=38)                                                                                                                   cGAACCCTGGAATGACGGAATTAGAATCCGGGGCCATAGCGCATGGTGATACCCCCGCTGGAAACACTGACAAGGTAAGCGTCTTGAAGAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCgg                <  1:396394/143‑1 (MQ=21)                                                                                                                    gagcggcGGAACGCCGGAATTAGGGTGGGGTGGCTGACCGCGTGGCGATGACCCAACTGGGTGCACGTACAAGGTAAGCGGCTTGAATAAAGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGt               <  2:586049/137‑1 (MQ=18)                                                                                                                    ccgccctggAATGCCCGCATTAGTATCCGGCGCCTTCCCGCTTGGCGGTACGCCAACTGGCTGCACTCACAAGGTAAGCGTCTTTAATAATTTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGt               <  2:889835/136‑1 (MQ=21)                                                                                                                     aaCCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGCTTCGAACCTCGGAATGCCGGAATCAGAATCCGGTg              >  1:83685/1‑143 (MQ=255)                                                                                                                           ggAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGCCTTGAATAAATTGGCTGGGGTACGAGGCTTCGAACCTCGGCCTGCCGGCATCAGAATCCGGTGGATTAc        >  1:497859/1‑143 (MQ=37)                                                                                                                                 ccGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGAt                                                <  2:410479/97‑1 (MQ=255)                                                                                                                                 ccGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGAt                                                >  1:410479/1‑97 (MQ=255)                                                                                                                                 ccGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAGCCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTg  >  1:136101/1‑143 (MQ=255)                                                                                                                                        |                                                                                                                                        CATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTG  >  NC_000913/696335‑696605

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑