Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,125,322	G→A	S2F (TCC→TTC)	mdtH ←	multidrug efflux pump MdtH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,125,322	0	G	A	96.8%	78.9 / NA	31	S2F (TCC→TTC)	mdtH	multidrug efflux pump MdtH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (15/15);  minor base C (1/0);  total (16/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01

GGTCGGCAATTGCACCGCCGAAAATACCCAGACCTTGCTGAATAAATTGGCGTAGACCGAGAGCAATACCGACCATGACGGCGGCCCAGCCCATTTGATCAACGAAGCGGATAGAGATCAGCGGGAAGACAACAAAGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGGACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTCCCATCACTTCGGGGACAATATTTTTTTATCAAAACGTCGCTTTGATAGAGAGTTTTTATCAAATATGTGAATAATGCAGAAAATGGCATTTTGGACTTTTCACAGGGTCTGGTTGCGCAGGTATAGTAATACTTACAGCGTATTAAAGACGTTACGGG  >  NC_000913/1125113‑1125545                                                                                                                                                                                                                  |                                                                                                                                                                                                                                ggTCGGCAATTGCACCGCCGAAAATACCCAGACCTTGCTGAATAAATTGGCGTAGACCGAGAGCAATACCGACCATGACGGCGGCCCAGCCCATTTGATCAACGAAGCGGATAGAGATCAGCGGGAAGACAACAAAGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTc                                                                                                                                                                                           >  1:284173/1‑248 (MQ=255)     gnaanNTGCANCGCCGAAAATACCCAGACCTTGCTNAATAAATTGGCGTAGACCGAGAGCAATACCGNCNATGACGGCGGCCCAGCCCATTTGATCAACGAAGCGGATAGAGATCAGCNGGAATACAACNAAGNNCCCCNGNANGACCAGCATATGATCGATGAGCAGGAAATNTTTACCCAGGTTCCTCGCCTGCGNNACNNNGANNATTTc                                                                                                                                                                                                                          <  2:378557/210‑1 (MQ=255)     ggCAATTGCACCGCAGAAAATACCCCGACCTTGCTGAATAAATTGGCGTAGACCGAGCGCACTACCGACCATGACGGCAGCACAGCCCATTTGATCAACCAAGCGGATAGAGATCAGCGGGCAGACAACAAAGAACCCCAGCACGACCAGAATATTATCGATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTc                                                                                                                                                                                                                          >  1:378557/1‑213 (MQ=255)            gCACCGCCGAAAATACCCAGACCTTGCTGAATAAATTGGCGTAGACCGAGAGCAATACCGACCATGACGGCGGCCCAGCCCATTTGATCAACGAAGCGGATAGAGATCAGCGGGACGACAACAAAGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATATTTACCAAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGCAATAAAAGAt                                                                                                                                                                                                     >  1:295305/1‑227 (MQ=255)               ccgccgCAAATACCCAGACCTTGCTGAATAAATTGGCGTAGACCGAGAGCAATACCGACCATGACGGCGGCCCAGCCCATTTGATCAACGAAGCGGATAGAGATCAGCGGGAAGACAACAAGGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTCTTCTGCATTGCCGCt                                                                                                                                                                          >  1:144807/1‑251 (MQ=255)                    gcaaaTACCCAGACCTTGCTGACTAAATTGGCGTGAACCGAGAGAAATACCGACCATGACGGCGGACCAGCCCCTTTGGTCAACGAAGAGGATAGCGATCAGAGGGAAGACAACACAGATCCCAAGCCCGACCAGCATATTATCGCTGGTCAGGCACTTTTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGAc                                                                                                                                                                     >  1:439588/3‑251 (MQ=255)                                                 ggCGTAGACCGAGAGCAATACCGACCAGGACGGCGGCCCAGCCCATTTGATCAACGAAGCGGATAGAGATCAGCGGGAAGACAACAAAGAACCCCAGCACGACCAGCATATTATCGATTAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTCCCATCACTTCgg                                                                                                                                                    <  1:343402/239‑1 (MQ=255)                                                       gACCGAGAGCAATACCGACCATGACGGCGGCCCAGCCCATTTGATCAACGAAGCGGATAGAGATCAGCGGGAAGACAACAAAGAACCCCAGCACTACCAGCATATTATCGATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTc                                                                                                                                                                >  1:6600/1‑221 (MQ=255)                                                                             ggcggcggCCCAGCCCATTTGATCAAAGAAGCGGATAGCGAACAGCGGGCAGACAACAAAGAACCCACGCACGACCCGCATATTATCGATGAGAAGGCAATATTTAACCCGGTTCCTCGCCTGCGACACGCGGAACATTTc                                                                                                                                                                                                                          >  1:473912/3‑141 (MQ=255)                                                                                 gcggcCCAGCCCATTTGATCAACGAAGCGGATAGAGATCAGCGGGAAGACAACAAAGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTCCCATCACTTCGGGGACAATATTTTTTTATCAAAACGTCGCTTTGATAGAGAGttt                                                                                                         <  1:213123/250‑1 (MQ=255)                                                                                     cccagcccaTTTGATCAACGAAGCGGATAGAGATCAGCGGGAAGACAACAAAGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATGCTTCATTGCCGCTAAGACTTTTCCCAtn                                                                                                                                                           <  1:150182/196‑2 (MQ=255)                                                                                                 gATCAACGAAGCGGATAGAGATCAGCGGGAAGACAACAAAGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCgg                                                                                                                                                                                                                 <  1:460130/130‑1 (MQ=255)                                                                                                      aCGAAGCGGATAGAGATCAGCGGGAAGACAACAAAGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGc                                                                                                                                                                                   <  1:9301/155‑1 (MQ=255)                                                                                                            cGGATAGAGATCAGCGGGAAGACAACAAAGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATATTTGCCCAGGTTCCTCGCCTGCGACACGCGGAACAGTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCATCATTGCCGCTAAGACTTTTCCCATCACTTCGGGGACAATATTTTTTTATCAAAACGTCGCTTTg                                                                                                                    <  1:273015/212‑1 (MQ=255)                                                                                                                         ncGGGAAGACAACAAAGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTCCCATCACTTCGGGGACAATATTTTTTTATCAAAACGTCGCTTTGATAGAGAGTTTTTATCAAATATGTGAATAATGCAGAAAATGGCATTTTGGAc                                                                >  1:93103/2‑251 (MQ=255)                                                                                                                         gCGGGAACACAACAAAGAACCCCCGCACGACCAGCATATGATCGATGAGCAGGAAATATTTACCCAGGTTCCGCGCCTGCGACACGCGGAACAGTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCTCCAATACTTTTCCCATCACTTCGGGGACAATAGACTTGTAGCAAAACGTCGCGTTGACAGAGAGTTTTGATCAAATATGTGAATAATGCAGAAAATGGCATTTTGGAc                                                                <  1:383467/251‑1 (MQ=255)                                                                                                                            ggAAGACAACAAAGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCATCCCGGGAAATCAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTCCCATCCCTTCGGGGACAATATTTTTTTATCAAAACGTCGCTTTGATAGAGAGttt                                                                                                         >  1:240989/1‑207 (MQ=255)                                                                                                                             naaGACAACAAAGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTCCCATCACTTCGGGGACAATATTTTTTTATCAAAACGTCGCTTTGATAGAGAGTTTTTATCAAATATGTGAATAATGCAGAAAATGGCATTTTGGACtttt                                                            >  1:103552/2‑251 (MQ=255)                                                                                                                                 acaacaAAGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTCCCATCACTTCGGGGACAATATTTTTTTATCAAAACGTCGCTTTGATAGAGAGTTTTTATCAAATATGTGAATAATGCAGAAAATGGCATTTTGGACTTTTcacn                                                        <  1:301774/251‑2 (MQ=255)                                                                                                                                    ncaaAGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTCCCATCACTTCGGGGACAATATTTTTTTATCAAAACGTCGCTTTGATAGAGAGTTTTTATCAAATATGTGAATAATACAGAAAATgg                                                                          >  1:147945/2‑230 (MQ=255)                                                                                                                                      aaaGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATTTTTACCCAGGTTCCTCGACTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTcc                                                                                                                                                               >  1:450643/1‑143 (MQ=255)                                                                                                                                                                    gATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCAACGAGCGGCACATTTACCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTCCCATCACTTCGGGGACAATATTTTTTTATCAAAACGTCGCTTTGATAGAGAGttttt                                                                                                       >  1:335306/1‑169 (MQ=255)                                                                                                                                                                          cAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTCCCATc                                                                                                                                                           >  1:422732/1‑111 (MQ=255)                                                                                                                                                                                  atTTACCCAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCAGTGCCGCTAAGACTTTTCCCATCACTTCGGGGACAATATTTTTTTATCAAAACGTCGCTTTGATAGAGAGTTTTTATCAAATATGTGAATAATGCAGAAAATGGCATTTTGGGCTTTGCACAGGGTCTGGTTGCGCAGGTATAGTAATACTTACAGCGTATTAAAGACGt        <  1:267848/250‑1 (MQ=255)                                                                                                                                                                                    ttACCCNNGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTc                                                                                                                                                                <  2:6600/96‑1 (MQ=255)                                                                                                                                                                                       cccAGGTTCCTCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTCCCATCACTTCGGGGACAATATTTTTTTATCAAAACGTCGCTTTGATAGAGAGTTTTTATCAAATATGTGAATAATGCAGAAAATGGCATTTTGGACTTTTCACAGGGTCTGGTTGCGCAGGTATAGTAATACTTACAGCGTATTAAAGACGTTACggg  >  1:116096/1‑251 (MQ=255)                                                                                                                                                                                               ccTCGCCTGCGACACGCGGAACATTCCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATGCTGCATTGCCGCTAAGACTTTTCCCATCACTTCGGGGACAATAttttttt                                                                                                                                     <  1:430371/112‑1 (MQ=255)                                                                                                                                                                                                ntCGCCTGAGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTCCCATCACTTCGGGGACAATATTTTTTTATCAAAACGTCGCTTTGATAGAGAGTTTTTATCAAATATGTGAATAATGCAGAAAATGGCATTTTGGAc                                                                >  1:405715/2‑180 (MQ=255)                                                                                                                                                                                                 tCGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATGGCCGCTAAGACTTTTCCCATCACTTCGGGGACAATATTTTTTTATCAAAACGTCGCTTTGATAGAGAGTTTTTATCAAATATGTGAATAATGCAGAAAATGGCATTTTg                                                                   <  1:255753/176‑1 (MQ=255)                                                                                                                                                                                                  cGCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTCCCATCACTTCGGGGACAATATTTTTTTATCAAAACGTCGCTTTGATagagag                                                                                                            <  1:141222/134‑1 (MQ=255)                                                                                                                                                                                                   gCCTGCGACACGCGGAACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGc                                                                                                                                                                           <  1:143862/70‑1 (MQ=255)                                                                                                                                                                                                                  |                                                                                                                                                                                                                                GGTCGGCAATTGCACCGCCGAAAATACCCAGACCTTGCTGAATAAATTGGCGTAGACCGAGAGCAATACCGACCATGACGGCGGCCCAGCCCATTTGATCAACGAAGCGGATAGAGATCAGCGGGAAGACAACAAAGAACCCCAGCACGACCAGCATATTATCGATGAGCAGGAAATATTTACCCAGGTTCCTCGCCTGCGACACGCGGGACATTTCCCCTCCCGGGAAATAAAAGATGAGCACTTTCTATTCTGCATTGCCGCTAAGACTTTTCCCATCACTTCGGGGACAATATTTTTTTATCAAAACGTCGCTTTGATAGAGAGTTTTTATCAAATATGTGAATAATGCAGAAAATGGCATTTTGGACTTTTCACAGGGTCTGGTTGCGCAGGTATAGTAATACTTACAGCGTATTAAAGACGTTACGGG  >  NC_000913/1125113‑1125545

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑