Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	7,681	A→G	F93F (TTT→TTC)	yaaJ ←	putative transporter YaaJ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	7,681	0	A	G	93.8%	89.6 / ‑3.3	32	F93F (TTT→TTC)	yaaJ	putative transporter YaaJ
Reads supporting (aligned to +/- strand):  ref base A (0/2);  new base G (11/19);  total (11/21)
Fisher's exact test for biased strand distribution p-value = 5.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01

AGGGCGCGGGCAACGGCGTTCGCTTGAACTCCGCTGAAAATTATGCCATAGGCGATGAGCAAAAAGACGGCGAACAGAACGCCCATCCAGCGCATCCCCAGCCCGCGCGCCATATACCATGCCGGTCCGCCACGAAACTGCCCATTGACGTCACGTTCTTTATAAAGTTGTGCCAGAGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAA‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATAGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTACACAATGACTGAAATGAGGTTAAACCGCCTGGCTGTGGATGAATGCTATTTTT‑AAGACTTTTGCCAAACTGGCGGATGTAGCGAAACTGCACAAATCCGGTGCGAAAAGTGAACCAACAACCTGCGCCGAAGAGCAGGTAAATCATTACCGATCCCC  >  NC_000913/7451‑7922                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                     aGGGCGCGCGAAACGGCGTGCGTCTGAATTCTGCTGAAAATTAGGCCGTAGGCGATGAGAAAAAAGCCGGCAAACAGAACGCCCATCCAGCGCATCCCCAGCCCGCGCGCCATATATCATGCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCAcc                                                                                                                                                                                                                                 <  2:93977/251‑1 (MQ=255)         cgaaaCGGCGTTCGCCTGAATTCCGCTGAAAATTATGCCGTAGGCGATGAGCAAAAAGACGGCGAACAGACCGCCCATCCAGCGCATCCCCAGCCCGCGCGCCATATACCATGCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑Taa                                                                                                                                                                                                                        <  2:411608/248‑1 (MQ=255)                          gaattCCGCTGAAAATTATGCCGTAGGCGATGAGCAAAAAGACGGCGAACAGAACGCCCATCCAGCGCATCCCCAGCCCGCGCGCCATTTACCATGCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCCGCGCAACGCCg                                                                                                                                                                                                       >  1:381316/5‑251 (MQ=255)                           aattCCGCTGAAAATTATGCCGTAGGCGATGAGCAAAAAGACGGCGAACAGAACGCCCATCCAGCGCATCCCCAGCCCGCGCGCCATATACCATGCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGGCCGCGCAAcccccg                                                                                                                                                                                                      >  1:456193/4‑246 (MQ=255)                                    gAAAATTATGCCGTAGGCGATGAGCAAAAAGACGGCGAACAGAACGCCCATCCAGCGCATCCCCAGCCCGCGCGCCATATACCATGCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGTAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACcgg                                                                                                                                                                                                                               <  1:235609/218‑1 (MQ=255)                                    gAAAATTATGCCGTAGGCGATGAGCAAAAAGACGGCGAACAGAACGCCCATCCAGCGCATCCCCAGCCCGCGCGCCATATACCATGCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAAACCACATCCAG‑AAGACGGCTCCAGGTCCACcgg                                                                                                                                                                                                                               >  2:235609/1‑218 (MQ=255)                                     aaaaTTAGGCCGTAGGCGATGAGAAAAAAGACGCAGAACAGAACCCCCCTCCAGCGCATCCCCCGCCCGCGCCCCATATACCATGCCGGTCCGCCACGAAACGGCCCATTGGCATCACGTTCGTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCAGGTTGcc                                                                                                                                                                                            <  2:393739/251‑1 (MQ=255)                                               cgtAGGCGATGAGCAAAAAGACGGCGAACAGAACGCCCATCCAGCGCATCCCCAGCCCGCGCGCCATATACCATGCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGGGAAATTCCCAGGGCACCGCCGGCCAgttaccgtctcccacc                                                                                                                                                                                   >  1:244572/3‑236 (MQ=255)                                                    gCGATGAGCAAAAAGACGGCGAACAGAACGCCCATCCAGCGCATCCCCAGCCCGCGCGCCATATACCATGCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGAGCAACGCCAGCCAGGGTGCCGCAAcccccccggcc                                                                                                                                                                             >  1:347794/1‑243 (MQ=255)                                                     cGATGAGCAAAAAGACGGCGAACAGAACGCCCATCCAGCGCATCCCCAGCCCGCGCGCCATATACCATGCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑GAATTGCCAGCGCAACCCCGGCCAGGTGGCCGCTccccccccccgcc                                                                                                                                                                            >  2:310622/1‑242 (MQ=255)                                                              aaaaGACGGCGAACAGAACGCCCATCCAGCGCATCCCCAGCCCGCGCGCCATATACCATGCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAACGCCACCCCGGCCAGGCTGCCGCCACCCCcgcggcccccccaaccg                                                                                                                                                                   >  2:179556/1‑238 (MQ=255)                                                                aaGACGGCGAACAGAACGCCCATCCAGCGCATCCCCAGCCCGCGCGCCATATACCATGCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCCGCGCAACGCCGGCCAGGGTGCCGCTACCCCCGCGCGCCCCCAGACTggg                                                                                                                                                                 >  1:443645/1‑250 (MQ=255)                                                                    cGGCGAACAGAACGCCCATCCAGCGCATCCCCAGCCCGCGCGCCATATACCATGCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTacac                                                                                                                                                             <  1:92594/251‑1 (MQ=255)                                                                         aacaaaacccccccccAGCGCACCCCCAGCCCGCGCCCCATTTCCCATGCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTACACAATGa                                                                                                                                                        <  2:381316/237‑1 (MQ=255)                                                                               aCGCCCATCCAGCGCATCCCCAGCCCGCGCGCCATATACCATGCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCCGGTTGCCGCTACCCACGCGCGCCGCACGACTTGTCCACAAAGACTgga                                                                                                                                                   >  1:149829/1‑248 (MQ=255)                                                                                          gcgaaTCCCCAGCCCGCGCGCCATATCCCATGTCGGTCCGCCACGAAACTGCCCATTGACGTCACGTTCTTTATAAAGTTGTGCCAGAGAACATTCGGCAACCGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAA‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATAGCCAGCGCAACGCCGGCCAGGTTGACGCTACCCACGCGCGCCGCAAGACTGGTACACAATGACTGAAATGAGGTTAAAc                                                                                                                                       <  1:15719/247‑1 (MQ=255)                                                                                            ccaaccccCGCCCGCGCCCCAAATCCAATGCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTACACAATGACTGAAATGAGGTTAAACCg                                                                                                                                     <  2:119920/247‑1 (MQ=255)                                                                                               tCCCCAGCCCGCGCGCCATATACCATGCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCCGGGCAAAACCGGCCAGGGTGCCGCCACCCCCCCCCGCCGCCAGCCTGGTGCACAATGAAAGAAATGAGGGTAAACCCCCt                                                                                                                                  >  2:216041/1‑251 (MQ=255)                                                                                                   cagcccccccccaatatACCATGCCGGCCCCCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAACCTGGGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCCCATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTACACAATGACTGAAATGAGGTTAAACCGCCTGGCt                                                                                                                              <  1:128903/238‑1 (MQ=255)                                                                                                       ccgcccgcCATATCCCAGGCCGGCCCGCCACGAAACGGCCCATTGGCATCACGTTCTTTAAAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTACACAATGACTGAAATGAGGTTAAACCGCCTGGCTGTgg                                                                                                                          <  1:310622/251‑1 (MQ=255)                                                                                                                atatCCCATGCCGGTCCGCCACGAAACTGCCCATTGGCATCCCGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTACACAATGACTGAAATGAGGTTAAACCGCCTGGCTGTGGATGAATGCt                                                                                                                 <  1:245681/251‑1 (MQ=255)                                                                                                                aaatcccaggCCGGTCCGCCACGAAACTGCCCATTGGCATCACGTTCTTTATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGCCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTACACAATGACt                                                                                                                                                      <  1:325746/205‑1 (MQ=255)                                                                                                                                                                ttATAAAGCTGTGCGAGGGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCAGGGTGCCGCTACCCCCGCGCGCCGCAAGACTGGTGCACAAAGACTGAAATGAGGTTAAACCGCCTGGGTGTGGGGGGAGGCTATTTTTTAATA‑TTTTTCCAAACTGGCGGGTGTAgggcaaaccgcaaa                                                                 >  2:238255/1‑237 (MQ=255)                                                                                                                                                                                gggaACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTACACAATGACTGAAATGAGGTTAAACCGCCTGGCTGTGGATGAATGCTATTTTT‑AAGACTTTTGCCAAACTGGCGGATGTAGCGAAACTGCACAAATCCGGTGCGAAAAGTg                                                <  1:95815/249‑1 (MQ=255)                                                                                                                                                                                            caaccGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGTCCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTACACAATGACTGAAATGAGGTTAAACCGCCTGGCTGTGGATGAATGCTATTTTT‑AAGACTTTTGCCAAACTGGCGGATGTAGCGAAACTGCACAAATCCGGTGCGAAAAGTGAACCAACAACCt                                    <  1:456696/247‑1 (MQ=255)                                                                                                                                                                                            cAAACGAGGCCGCCATGCCTATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGCCCACCGGCGG‑TAATGGCCAGCTCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTACACAATGACTGAAATGAGGTTAAACCGCCTGGCTGTGGATGAATGCTATTTTT‑AAGACTTTTGCCAAACTGGCGGATGTAGCGAAACTGCACAAATCCGGTGCGAAAAGTGAACCAACAACCt                                    <  1:123262/251‑1 (MQ=255)                                                                                                                                                                                                      cGCCATGCCGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTACACAATGACTGAAATGAGGTTAAACCGCCTGGCTGTGGATGAATGCTATTTTT‑AAGACTTTTGCCAAACTGGCGGATGTAGCGAAACTGCACAAATCCGGTGCGAAAAGTGAACCAACAACCTGCGCCGAaga                          <  1:142317/251‑1 (MQ=255)                                                                                                                                                                                                              cGATAAACGCGGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTACACAATGAc                                                                                                                                                       <  1:76755/119‑1 (MQ=255)                                                                                                                                                                                                                  aaaCGCGGACACCCACA‑CCAAGAAGACGGCTCCATGCCCACCGGCGG‑TAATTGCCACCGCAACGCCGGCCAGGTTGCCGCTACCCCCGCGCGCCGCAAGACTGGTACACAATGACTGAAATGAGGTTAAACCGCCTGGCTGTGGATGAATGCTATTTTT‑AAGACTTTTGCCAAACTGGCGGATGTAGCGAAACTGCACAAATCCGGTGCGAAAAGTGAACCAACAACCTGCGCCGAAGAGCAGGTAAATCa              <  2:456193/251‑1 (MQ=255)                                                                                                                                                                                                                     cgcgGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTAcaca                                                                                                                                                            <  1:215910/107‑1 (MQ=255)                                                                                                                                                                                                                      gcgGCAACCCACATCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTACACAATGACTGAAATGAGGTTAAACCGCCTGGCTGTGGATGAATGCTATTTTT‑AAGACTTTTGCCAAACTGGCGGATGTAGCGAAACTGCACAAATCCGGTGCGAAAAGTGAACCAACAACCTGCGCCGAAGAGCAGGTAAATCATTAc          <  1:238255/251‑1 (MQ=255)                                                                                                                                                                                                                              ccccaTCCAG‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATTGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTACACAATGACTGAAATGAGGTTAAACCGCCTGGCTGTGGATGAATGCTATTTTT‑AAGACTTTTGCCAAACTGGCGGATGTAGCGAAACTGCACAAATCCGGTGCGAAAAGTGAACCAACAACCTGCGCCGAAGAGCAGGTAAATCATTACCGATcccc  <  1:362665/248‑1 (MQ=255)                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                     AGGGCGCGGGCAACGGCGTTCGCTTGAACTCCGCTGAAAATTATGCCATAGGCGATGAGCAAAAAGACGGCGAACAGAACGCCCATCCAGCGCATCCCCAGCCCGCGCGCCATATACCATGCCGGTCCGCCACGAAACTGCCCATTGACGTCACGTTCTTTATAAAGTTGTGCCAGAGAACATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAA‑AAGACGGCTCCAGGTCCACCGGCGG‑TAATAGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTACACAATGACTGAAATGAGGTTAAACCGCCTGGCTGTGGATGAATGCTATTTTT‑AAGACTTTTGCCAAACTGGCGGATGTAGCGAAACTGCACAAATCCGGTGCGAAAAGTGAACCAACAACCTGCGCCGAAGAGCAGGTAAATCATTACCGATCCCC  >  NC_000913/7451‑7922

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑