Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	402,427	C→T	16.3%	G227G (GGC→GGT)	phoA →	alkaline phosphatase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	402,427	0	C	T	16.3%	43.7 / 3.1	25	G227G (GGC→GGT)	phoA	alkaline phosphatase
Reads supporting (aligned to +/- strand):  ref base C (13/8);  new base T (2/2);  total (15/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.83e-01

TGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTGCGTGAACAGGCACAGGCGCGTGGTTATCAGTTGGTGAGCGATGCTGCCTCACTGAATTCGGTGACGGAAGCGAATCAGCAA  >  NC_000913/402291‑402568                                                                                                                                         |                                                                                                                                              tggCACTTGTGTCCTCGCGCAAATGCTACGGTCCGAGCGCGACCCGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTggcggcggc                                                                                                                                         <  2:205914/143‑1 (MQ=255)      caTGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGTGGGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCaaa                                                                                                                                    <  1:217868/143‑1 (MQ=255)           gACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCCCTGGAAAACGGCGGAAAAGGATCGAGTACCGAACAGCTGCCTAACGCTCGGGCCGACGTTCCGCGTGGCGGCGGCGCAAAACCCt                                                                                                                               >  2:178184/1‑143 (MQ=255)           gACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGCTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCt                                                                                                                               >  2:261192/1‑143 (MQ=255)              gtCGCGCAAATGCTACGGTCCGGGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTg                                                                                                                            <  2:39235/142‑1 (MQ=255)              cTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAAGGCTCGTGCCGGCGGTACGCTTGGCGGCGGCGCaaaagacgttg                                                                                                                            >  2:541869/1‑136 (MQ=255)                 gcgcAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGTGGCGGCGCAACAACCTTTGCTg                                                                                                                         >  1:456776/1‑143 (MQ=255)                 gcgcAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTg                                                                                                                         >  1:435941/1‑143 (MQ=255)                 gcgcAAATGCTACGGTCCGAGCGCGACCAGCGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGTGGCGGCGCAAAAACCTTTGCTg                                                                                                                         >  1:161590/1‑143 (MQ=255)                   gcAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAACAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGaa                                                                                                                       >  2:524618/1‑143 (MQ=255)                     aaaTGCTACGGTCCGAGCGCGACGAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGGAAAGGCTCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAAc                                                                                                                     <  1:291642/143‑1 (MQ=255)                                               tGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTCCGCTTGGCGGCGGCGCAAAACCCTTTGCTGCACCGGCAACCGCCGGTACATGGCAGTGag                                                                                           >  1:197918/1‑142 (MQ=255)                                                        tCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTGc                                                                                  >  1:507579/1‑143 (MQ=255)                                                                       ggAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTGCGTGAacaggcacagg                                                                   >  1:405778/1‑143 (MQ=255)                                                                          aaaaGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTACGTGAACAGGCACAGgcgc                                                                >  1:13781/1‑143 (MQ=255)                                                                                  gAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTGCGTGAACAGGCACAGGCGCGTGGTGAt                                                        >  2:205681/1‑143 (MQ=255)                                                                                    aaaGGATCGAGTACCGACCAGCTGCTGAACGCTCTTGCCGACGTTACGCGTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTGCGTGAACAGGCACAGGCGCGTGGTTATCa                                                      <  1:12306/143‑1 (MQ=255)                                                                                          tCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGGGAATGGCAGGGAAAAACGCTGCGTGAACAGGCACAGGCGCGTGGTTATCAGTTggg                                                >  1:28412/1‑142 (MQ=255)                                                                                                 ccGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGTGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTGCGTGAACAGGCACAGGCGCGTGGTTATCAGTTGGTGAGCGAt                                         <  2:161590/143‑1 (MQ=255)                                                                                                 ccGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGTGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTGCGTGAACAGGCACAGGCGCGTGGTTATCAGTTGGTGAGCGAt                                         <  2:456776/143‑1 (MQ=255)                                                                                                             ttAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTGCGTGAACAGGCACAGGCGCGTGGTTATCAGTTGGTGAGCGATGCTGCCTCACTg                             >  1:54316/1‑143 (MQ=255)                                                                                                                         ccGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAACCGCTGCGTGAACAGGCACAGGCGCGTGGTTATCAGTTGGTGAGCGATGCTGCCTCACTGAATTCGGTGACg                 <  1:62993/143‑1 (MQ=255)                                                                                                                         ccGACGCTACGCGTGGCGGCGGCGCAGACACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTGCGTGAACAGGCACAGGCGCGTGGTTATCAGTTGGTGAGCGATGCTGCCTCACTGAATTCGGTGACg                 <  2:335005/143‑1 (MQ=255)                                                                                                                            aCGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGGATGGCAGGGAAAAACGCGGCGTGAACAGGCACAGGCGCGTGGTTGGCAGTTGGTGGGCGATGCTGCCGCACTGAAGTCGGTGACGGac              >  1:317125/1‑142 (MQ=255)                                                                                                                             cGTCACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTGCGCGAACAGGCACAGGCGCGTGGTTATCAGTTGGTGAGCGATGCCGCCTCACTGAATTCGGTGACGGAAg             <  2:435941/143‑1 (MQ=255)                                                                                                                                    cTTGGCGGCGGCGCAAAAACCTGTGCTGAAACGGCAACCGCGGGTGAATGGCAGGGAAAAACGCTGCGTGAACAGGCACAGGCGCGTGGTTATCAGTTGGTGAGCGATGCTGCCTCACTGAATTCGGTGACGGAAGCGAATCa      <  2:149347/143‑1 (MQ=255)                                                                                                                                        gcggcggcgCAAAAACCTTTGCTGAAACGGAAACCGCGGGAGAACGGCAGGGAAAAACGCTGCGTGAACAGGCACAGGCGCGTGGTTATCAGTTGGTGAGCGATGCTGCCTCACTGAATTCGGGGACGGAAGCGAATCAGCaa  >  2:98354/1‑143 (MQ=255)                                                                                                                                         |                                                                                                                                              TGGCACATGTGACCTCGCGCAAATGCTACGGTCCGAGCGCGACCAGTGAAAAATGTCCGGGTAACGCTCTGGAAAAAGGCGGAAAAGGATCGATTACCGAACAGCTGCTTAACGCTCGTGCCGACGTTACGCTTGGCGGCGGCGCAAAAACCTTTGCTGAAACGGCAACCGCTGGTGAATGGCAGGGAAAAACGCTGCGTGAACAGGCACAGGCGCGTGGTTATCAGTTGGTGAGCGATGCTGCCTCACTGAATTCGGTGACGGAAGCGAATCAGCAA  >  NC_000913/402291‑402568

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: ‑