Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,111,727	2 bp→TT	coding (865‑866/2544 nt)	opgH →	osmoregulated periplasmic glucans biosynthesis protein H

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,111,727	0	C	T	90.5%	46.6 / ‑1.1	22	P289M (CCG→TTG)	opgH	osmoregulated periplasmic glucans biosynthesis protein H
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base T (12/7);  total (13/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.44e-01
*	NC_000913	1,111,728	0	C	T	90.9%	47.2 / ‑0.8	22	P289M (CCG→TTG)	opgH	osmoregulated periplasmic glucans biosynthesis protein H
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base T (12/8);  total (13/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.41e-01

GGGCTTCCTGCAACTGCTTATTGGTCGCGATAAATACAGTATATCTGCGTCAACAGTTGGCGATGAACCATTAAACCCGGAGCATCGCACGGCGTTGATCATGCCTATCTGTAACGAAGACGTGAACCGTGTTTTTGCTGGCCTGCGTGCAACGTGGGAATCAGTAAAAGCCACCGGGAATGCCAAACACTTTGATGTCTACATTCTTAGTGACAGTTATAACCCGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCGGTGGCGAAGGTCAGATTTTCTATCGCCGCCGCCGTCGCCGCGTGAAGCGTAAAAGCGGTAATATCGATGACTTCTGCCGTCGCTGGGGCAGCCAGTACAGCTACATGGTGGTGCTGGATGCTGACTCGGTAATGACCGGTGATTGTTTGTGCGGGCTGGTGCGCCTGATGGAAGCCAAC  >  NC_000913/1111504‑1111960                                                                                                                                                                                                                                ||                                                                                                                                                                                                                                         gggCTTGCTGCAACTGGTTATTTGTCGGGAAAAATTCAGGATACCTGCGGCACCAGTGGGCGATGAACCATTAAACCCGGAGCATCGCACGGCGTTGATCATGCCGATCTGTAACGAAGACGTGAACCGTGTTTTTGCTGGCCTGCGTGCAACGTGGGAATCAGTAAAAGCCACCGGTAATGCCAAACTCTTTGATGTCTACATTCTTAGTGACAGTTATAACTTGGATATCTGCGTCGCAGAGCAAAAAg                                                                                                                                                                                                                <  2:79974/251‑1 (MQ=255)                    aTTGGTCGCGATAAATACAGTATATCTGCGTCAACAGTTGGCGATGAACCATTAAACCCGGAGCATCGCACGGCGTTGATCATGCCTATCTGTAACGAAGACGTGAACCGTGTTTTTGCTGGCCTGCGTGCAACGTGGGAATCAGTAAAAGCCACCGGGAATGCCAAACACTTTGATGTCTACATTCTTAGTGACAGTTATAACTTGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGc                                                                                                                                                                                             >  1:52083/1‑251 (MQ=255)                          cgcgATAAATACAGTATATCTTCGTCAACCGTTGACGATGAACCCTTAAACCCGGAGCATCGCACGGCGTTGATCAAGCCTATCTGTAACGAAGACGTGAACAGTGTTTTTGCTGGCCTGCGTGCAACGTGGGACTCAGTAAAAGCCACCGGGACTGCCAAACCCTACGATGTATACATTCTTAGCGACAGTTATAACTTGGATATCTCCGTCGCAGACCCAAAGGCCTGGCAGGAGCTTATCgtttgacg                                                                                                                                                                                       >  2:279206/1‑244 (MQ=255)                            cgATAAATACAGTATATCTGCGTCAACAGTTGGCGATGAACCATTAAACCCGGAGCTTCGCACGGCGTTGATCATGCCTATCTGTAACGAAGACGTGAACCGTGTTTTTGCTGGCCTGCGTGCAACGTGGGAATCAGTAAAAGCCACCGGGAATGCCAAACACTTTGATGTCTACATTCTTAGTGACAGTTATAACTTGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCg                                                                                                                                                                                     >  1:31434/1‑251 (MQ=255)                                aaaTACAGTATATCTGCGTCAACAGTTGGCGATGAACCATTAAACCCGGAGCATCGCACGGCGTTGATCATGCCTATCTGTAACGAAGACGTGAACCGTGTTTTTGCTGGCCTGCGTGCAACGTGGGAATCAGTAAAAGCCACCGGGAATGCCAAACACTTTGGTGTCTACATTCTTAGTGACAGTTATAACTTGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCGGTg                                                                                                                                                                                  <  1:29494/250‑1 (MQ=255)                                     cAGTATATCTGCGTCAACAGTTGGCGATGAACCATTAAACCCGGAGCATCGCACGGCGTTGATCATGCCTATCTGTAACGAAGACGTGAACCGTGTTTTTGCTGGCCTGCGTGCAACGTGGGAATCAGTAAAAGCCACCGGGAATGCCAAACACTTTGATGTCTACATTCTTAGTGACAGTTATAACTTGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCGGTGGCGa                                                                                                                                                                              >  1:41659/1‑249 (MQ=255)                                                     aCAGGTGGCGATGAATAATTAATGCCGGAGCATCGCACGGCGTTGAACATGCCGATCTGCAGCGAAGACGTGAACCGTTTTGTTGCTGGCCTGCGTGCAACGTGTGAATCAGTAAAAGCCACCGGGAATGCCAAACACTTTGATGTCTACATTCTTAGTGACAGTTATATCTTGGATATCTGCGTTGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCGGTGGCGAAGGTCAGATTTTCTAt                                                                                                                                                              <  2:241626/249‑1 (MQ=255)                                                             cGATGAACCATTAAACCCGGAGCATCGCACGGCGTTGATCATGCCTATCTGTAACGAAGACGTGAACCGTGTTTTTGCTGGCCTGCGTGCAACGTGGGAATCAGTAAAAGCCACAGGGAATGCCAAACACTTTGATGTCTACATTCTTAGTGACAGTTATAACTTGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCGGTGGCGAAGGTCAGATTTTCTATCgccgccgcc                                                                                                                                                    >  1:284976/1‑251 (MQ=255)                                                                 gAACCATTAAACCCGGTGCATCGCACGGCGTTTATCATGCCCATCTGTAACTAAGACGTGAACCGTGTTTTTGCTGGCCTGCGTGCAACGTGGGAATCAGTAAAAGCCACCGGGAATGCCAAACACTTTGATGTCTACATTCTTAGTGACAGTTATAACTTGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCGGTGGCGAAGGTCAGATTTTCTATCGCCGCCGCCGTcg                                                                                                                                                <  2:92598/251‑1 (MQ=255)                                                                     cATTAAACCCGGAGCATCGCACGGCGTTGATCATGCCTATCTGTAACGAAGACGTGAACCGTGTTTTTGCTGGCCTGCGTGCAACGTGGGAATCAGTAAAAGCCACCGGGAATGCCAAACACTTTGATGTCTACATTCTTAGTGACAGTTATAACTTGGATATCTGCGTCGCAGAGCAAAAAGCCTGGTTGGAGCTTATCGCTGAAGTCGGTGGCGCAGGTCAGATTTTCTATCGCCGCCGCCGTcgccgc                                                                                                                                            >  2:185383/1‑251 (MQ=255)                                                                                gAGCATCGCACGGCGTTGATCATGCCTATCTGTAACGAAGACGAGAACCGTGTTTTTGCTGGCCTGCGTGCAACGTGGGAATCAGTAAAAGCCACCGGGAATGCCAAACACTTTGATGTCTACATTCTTAGTGACAGTTATAACTTGGATATCTGCTTCGCAGAGCAAAAAGCCTGGCTGGAGCTTATCGATGAAGACGGTGGAGCAGGTCAGATTTTCTATCGCCGCCGCCGTctccgagagtagaggt                                                                                                                                  >  2:265206/1‑239 (MQ=255)                                                                                                              tGTAACGAAGACGTGAACCGTGTTTTTGCTGGCCTGCGTGCAACGTGGGAATCAGTAAAAGCCACCGGGAATGCCAAACACTTTGATGTCTACATTCTTAGTGACAGTTATAACCCGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCGGTGGCGAAGGTCAGATTTTCTATCGCCGCCGCCGTCGCCGCGTGAAGCGTAAAAGCGGTAATATCGATGACTTCTGCCGTCg                                                                                                   >  1:157207/1‑251 (MQ=255)                                                                                                                          gTGAACCGTGTTTTTGCTGGCCTGCGTGCAACGTGGGAATCAGTAAAAGCCACCGGGAATGCCAAACACTTTGATGTCTACATTCTTAGTGACAGTTATAACTTGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCGGTGGCGAAGGTCAGATTTTCTATCGCCGCCGCCGTCGCCGCGTGAAGCGTAAAAGCGGTAATATCGATGACTTCTGCCGTCGCTGGGGCAGCCa                                                                                       <  1:185383/251‑1 (MQ=255)                                                                                                                              aCCGTGTTTTTGCTGGCCTGCGTGCAACGTGGGAATCAGTAAAAGCCACCGGGAATGCCAAACACTTTGATGTCTACATTCTTAGTGACAGTTATAACTTGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCGGTGGCGAAGGTCAGATTTTCTATCGCCGCCGCCGTCGCCGCGTGAAGCGTAAAAGCGGTAATATc                                                                                                                    >  1:175964/1‑218 (MQ=255)                                                                                                                              aCCGTGGTTTTGCTGGCCTGCGTGCAACGTGGGAATCAGTAAAAGCCACCGGGAATGCCAAACACTTTGATGTCTACATTCTTAGTGACATTTATAACTTGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCGGTGGCGAAGGTCAGATTTTCTATCGCCGCCGCCGTCGCCGCGTGAAGCGTAAAAGCGGTAATATc                                                                                                                    <  2:175964/218‑1 (MQ=255)                                                                                                                                            ggcttGCGTGCAAAGGGGGAATCAGTAAAAGCCACCTGGAATGCCAAACACTTTGAGGTCTACATTCTTAGGGACAGTTATAACGTGGATATCTGTGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGGGGGTGGCGAAGTGCAGATTGTCTATCGCCGCCGCCGTCGCCGCGGGAAGCGGAAAAGCGGTAATATCGATGACTTCGGCCGTCGCTGGGGCAGCGAGTACAGCTACATggtggt                                                                     <  2:44522/247‑1 (MQ=255)                                                                                                                                                                                     tGCCAAACACTTTGATGTCAACATTCTTAGTGACAGTTATAACTTGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCGGTGGCGAAGGTCAGATTTTCTATCGCCGCCGCCGTCGCCGCGTGACGCGTAAAAGCGGTAATATCGATGACTTCTGCCGTCGCTGGGGCAGCCAGTACAGCTACATGGTGGTGCTGGATGCTGACTCGGTAATGACCGGTGATTGTTTGTGCg                            >  1:89474/1‑251 (MQ=255)                                                                                                                                                                                       ccAAACACTTTGATGTCTACATTCTTAGTGACAGTTATAACTTGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCGGTGGCGAAGGTCAGATTTTCTATCGCCGCCGCCGTCGCCGCGTGAAGCGTAAAAGCGGTAATATCGATGACTTCTGCCGTCGCTGGGGCAGCCAGTACAGCTACATGGTGGTGCTGGATGCTGACTCGGTAATGACCGGTGATTGTTTGTGCggg                          >  1:59279/1‑251 (MQ=255)                                                                                                                                                                                                 tGATGTCTACATTCTTAGTGACAGTTATAACTTGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCGGTGGCGAAGGTCAGATTTTCTATCGCCGCCGCCGTCGCCGCGTGAAGAGAAAAAGCGGTAATATCGATGACTTCTGCCTTCGCTGGGGCAGCCAGTACAGCTACATGGTGGGTCTGGATGCAGCCTCGGTAATGACCGGGGATTGTTTGGGCGGGCTGGtccccc                >  2:82062/1‑246 (MQ=255)                                                                                                                                                                                                    tGTCTACATTCTTAGTGACAGTTATAACTTGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCGGTGGCGAAGGTCAGATTTTCTATCGCCGCCGCCGTCGCCGCGTGAAGCGTAAAAGCGGTAATATCGATGACTTCTGCCGTCGCTGGGGCAGCCAGTACAGCTACATGGTGGTGCTGGATGCTGACTCGGTAATGACCGGTGATTGTTTGTGCGGGCTGGTGCGCCTg              >  1:111910/1‑250 (MQ=255)                                                                                                                                                                                                     gTCTACATTCTTAGTGACAGTTATAACTTGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCGGTGGCGAAGGTCAGATTTTCTATCGCCGCCGCCGTCGCCGCGTGAAGCGTAAAAGCGGTAATATCGATGACTTCTGCCGTCGCTGGGGCAGCCAGTACAGCTACATGGTGGTGCTGGATGCTGACTCGGTAATGACCGGTGATTGTTTGTGCGGGCTGGTGCGCCTGAt            <  1:168342/251‑1 (MQ=255)                                                                                                                                                                                                                tAGTGACAGTTATAACCCGGATATCTGCGTCGCAGAGTAAAAAGCCTGGATGGAGCTTATCGGTGAAGTCGGTGGCGAAGGTCAGATTTTCTATCGCCGCTGCCGTCGCCGCGTGAAGCGTAAAAGCGGTAATATCGATGACTTCTGCCGTCGCTGGGGCAGCCAGTACAGCTACATGGTGGTGCTGGATGCTGACTCGGTAATGACCGGTGATTGTTCGTGCGGGCTGGTGCGCCTGATGGAAGCCAAc  <  1:129790/250‑1 (MQ=255)                                                                                                                                                                                                                                ||                                                                                                                                                                                                                                         GGGCTTCCTGCAACTGCTTATTGGTCGCGATAAATACAGTATATCTGCGTCAACAGTTGGCGATGAACCATTAAACCCGGAGCATCGCACGGCGTTGATCATGCCTATCTGTAACGAAGACGTGAACCGTGTTTTTGCTGGCCTGCGTGCAACGTGGGAATCAGTAAAAGCCACCGGGAATGCCAAACACTTTGATGTCTACATTCTTAGTGACAGTTATAACCCGGATATCTGCGTCGCAGAGCAAAAAGCCTGGATGGAGCTTATCGCTGAAGTCGGTGGCGAAGGTCAGATTTTCTATCGCCGCCGCCGTCGCCGCGTGAAGCGTAAAAGCGGTAATATCGATGACTTCTGCCGTCGCTGGGGCAGCCAGTACAGCTACATGGTGGTGCTGGATGCTGACTCGGTAATGACCGGTGATTGTTTGTGCGGGCTGGTGCGCCTGATGGAAGCCAAC  >  NC_000913/1111504‑1111960

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑