Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,254,980	A→G	62.3%	F325L (TTT→CTT)	ycgV ←	putative adhesin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,254,980	0	A	G	62.3%	49.7 / 57.4	61	F325L (TTT→CTT)	ycgV	putative adhesin
Reads supporting (aligned to +/- strand):  ref base A (9/14);  new base G (22/16);  total (31/30)
Fisher's exact test for biased strand distribution p-value = 1.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.36e-01

TATTTTGCATGTTGACAACAGCCGTTGCCGTCTGGGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGATAGTGGTTGTACCACCACGA  >  NC_000913/1254884‑1255074                                                                                                 |                                                                                               tATTTTTCATGTTGACAACAGCCGTTACCGTATATGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGTGCTGCCGTGCCAGTAAAAtt                                                                                             <  2:479081/100‑1 (MQ=255) tATTTTGCATGTTGACAACAGCCGTTGCCGTCTGGGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGAtt                                                                                             <  1:1134783/100‑1 (MQ=255)     ttGTATGTTGATAACAGCCGTTGCCGTCTGGGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAgattgatt                                                                                         <  1:123251/100‑1 (MQ=255)          tGTTGACAACAGCCGTTGCCGTCTGGGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATcgc                                                                                    >  2:1963335/1‑100 (MQ=255)            ttGACAACAGCCGTTGCCGTCTGGGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGt                                                                                  >  1:2187651/1‑100 (MQ=255)             tGACAACAGCCGTTGCCGTCTGGGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTc                                                                                 <  2:714836/100‑1 (MQ=255)              gACAACATCCGTTGCCGTATGGGCCGAGGCAACATAAGAACCGCCGTAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTc                                                                                 >  2:1155896/1‑99 (MQ=255)                 aacaGCCGTTGCCGTCTGGGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGaa                                                                             <  1:1676842/100‑1 (MQ=255)                    aGCCGTTGCCGTCTGGGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCa                                                                          >  2:35858/1‑100 (MQ=255)                     gCCGTTGCCGTCTGGGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCAc                                                                         >  2:1469616/1‑100 (MQ=255)                      ccGTTGCCGTCTGGGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACt                                                                        >  2:1397008/1‑100 (MQ=255)                        gTTGCCGTCTGGGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCTAGTAAGATTGATTATCGCGTCTGAACCACTgg                                                                      <  1:2278210/100‑1 (MQ=255)                        gTTGCCGTCTGGGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTgg                                                                      <  2:2173121/100‑1 (MQ=255)                          tGCCGTCTGTGCCGAGTCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGt                                                                     <  2:1484147/99‑1 (MQ=255)                             cGTCTGGGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACg                                                                 <  2:139981/100‑1 (MQ=255)                                cTGGGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAgg                                                              >  1:206286/1‑100 (MQ=255)                                 tGGGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAgg                                                              <  1:1277537/99‑1 (MQ=255)                                  gggCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGcc                                                            >  2:2232771/1‑100 (MQ=255)                                  gggCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAgg                                                              >  2:2262435/1‑98 (MQ=255)                                   ggCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCa                                                           >  2:1946615/1‑100 (MQ=255)                                         ggCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGccc                                                     <  2:2310487/100‑1 (MQ=255)                                         ggCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGccc                                                     >  1:114629/1‑100 (MQ=255)                                           cACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTCCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGccc                                                     >  2:2229944/1‑98 (MQ=255)                                             ccATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTgcg                                                 >  2:236590/1‑100 (MQ=255)                                                 aaGAACTGTCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGga                                             <  1:974465/100‑1 (MQ=255)                                                  aGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGgaa                                            >  2:1097536/1‑100 (MQ=255)                                                  aGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGgaa                                            >  2:1071073/1‑100 (MQ=255)                                                  aGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGgaa                                            <  2:1595288/100‑1 (MQ=255)                                                   gAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGACTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGgaag                                           <  1:1082499/100‑1 (MQ=255)                                                    aaCCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCATCGCCCTGCGCGgaag                                           <  2:1026199/99‑1 (MQ=255)                                                       cgccgGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAat                                       <  1:2404635/100‑1 (MQ=255)                                                        gccgGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAata                                      >  1:409988/1‑100 (MQ=255)                                                         ccgGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAatat                                     >  1:407996/1‑100 (MQ=255)                                                             aaaaGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGc                                  <  2:703929/99‑1 (MQ=255)                                                              aaaGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTa                                <  1:1806877/100‑1 (MQ=255)                                                               aaGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTAt                               <  1:535929/100‑1 (MQ=255)                                                                aGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATc                              <  1:1729586/100‑1 (MQ=255)                                                                     cTGTTTCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGc                           <  2:1759917/98‑1 (MQ=255)                                                                     cTGTTTCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCAc                         >  2:606916/1‑100 (MQ=255)                                                                      tGTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCAcc                        >  1:2104336/1‑100 (MQ=255)                                                                       gTTTCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCg                       >  1:1435341/1‑100 (MQ=255)                                                                       gTTTCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCg                       >  2:480453/1‑100 (MQ=255)                                                                        tttCGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGa                      >  1:1923194/1‑100 (MQ=255)                                                                         ttCGTTGGGCTACCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGGCCTGCGCGGAAGAAATATGGCTATCTGCACCGAt                     >  2:1258055/1‑100 (MQ=255)                                                                         ttCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGAt                     <  2:561977/100‑1 (MQ=255)                                                                          tCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGATa                    <  1:480456/100‑1 (MQ=255)                                                                           cGTTGCGCTGCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATAGCTATCTGCACCGaaa                    >  1:1225734/1‑97 (MQ=255)                                                                           cGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGATAg                   <  1:865102/100‑1 (MQ=255)                                                                           cGTTGCGCTGCCGTGCAAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGATAg                   >  2:2126171/1‑100 (MQ=255)                                                                              tGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGATAGTgg                <  1:898936/100‑1 (MQ=255)                                                                                cgcTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGATAGTGGtt              >  2:1149291/1‑100 (MQ=255)                                                                                   tGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGATAGTGGTTGTa           <  1:2181744/100‑1 (MQ=255)                                                                                    gCCGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGATAGTGGTTGTac          >  2:1644198/1‑100 (MQ=255)                                                                                    gCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGATAGTGGTTGTac          <  2:1655706/100‑1 (MQ=255)                                                                                     ccGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGATAGTGGTTGTacc         <  1:2395905/100‑1 (MQ=255)                                                                                      cGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGATAGTGGTTGTacca        <  2:1263499/100‑1 (MQ=255)                                                                                      cGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGATAGTGGTTGTacca        >  1:1006371/1‑100 (MQ=255)                                                                                      cGTGCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGATAGTGGTTGTacca        <  2:8418/100‑1 (MQ=255)                                                                                         gCCAGTAAGATTGATTATCGCGTCTTAACCACTGGTGACGAGGCCACCGCCATGCGCGGAAGAAATATGGCTATCTGCACCGATAGAGGTTGTacc         <  2:407141/96‑1 (MQ=255)                                                                                         gCCAGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGATAGTGGTTGTAccacca     >  1:353340/1‑100 (MQ=255)                                                                                            aGTAAGATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGATAGTGGTTGTACCACCACGa  >  1:1152941/1‑100 (MQ=255)                                                                                            aGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACTGCCCTGCGTGGAAGAAATATGGCTATCTGCACCGATAGTGGTTGTACTACCACGa  >  2:1552852/1‑100 (MQ=255)                                                                                                 |                                                                                               TATTTTGCATGTTGACAACAGCCGTTGCCGTCTGGGCCGAGGCACCATAAGAACCGCCGGAAAAGATGCTGTTTCGTTGCGCTGCCGTGCCAGTAAAATTGATTATCGCGTCTGAACCACTGGTGACGAGGCCACCGCCCTGCGCGGAAGAAATATGGCTATCTGCACCGATAGTGGTTGTACCACCACGA  >  NC_000913/1254884‑1255074

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑