Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,446,362	Δ1 bp	17.8%	intergenic (+156/+16)	ydbL → / ← feaR	DUF1318 family protein/transcriptional activator for tynA and feaB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,446,362	0	A	.	17.8%	199.4 / 41.5	73	intergenic (+156/+16)	ydbL/feaR	DUF1318 family protein/transcriptional activator for tynA and feaB
Reads supporting (aligned to +/- strand):  ref base A (33/26);  new base . (4/9);  total (37/36)
Fisher's exact test for biased strand distribution p-value = 1.31e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.41e-01

CTGAAACAAGGTGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCGTTGAAAAATGACTCTGGTCAGAAAA  >  NC_000913/1446263‑1446461                                                                                                     |                                                                                                    cTGAAAAAAGGTGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACa                                                                                                     <  2:953898/100‑1 (MQ=255)   gAAACAAGGTGAATATTCAAAAACTCCTGTCAAATTGTCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATg                                                                                                   <  1:2027285/100‑1 (MQ=255)     aaCAAGGTGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCa                                                                                                 >  2:1785140/1‑100 (MQ=255)     aaCAAGGTGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCa                                                                                                 >  2:922505/1‑100 (MQ=255)       cAAGGTGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAAc                                                                                               <  2:2753743/100‑1 (MQ=255)       cAAGGTGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAAc                                                                                               >  1:2572524/1‑100 (MQ=255)        aaGGTGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCATGTAC‑TGCAACg                                                                                              <  2:1603042/100‑1 (MQ=38)        aaGGTGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCATGTAC‑TGCAACg                                                                                              <  2:2277678/100‑1 (MQ=38)          ggTGAATATTCAAAAGCTCCTGTCAAATTGCTTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCATGTAC‑TGCAACGcc                                                                                            <  1:1917818/100‑1 (MQ=37)          ggTGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCATGTAC‑TGCAACGcc                                                                                            <  1:2564331/100‑1 (MQ=38)          ggTGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCATGTAC‑TGCAACGcc                                                                                            <  2:2694362/100‑1 (MQ=38)          ggTGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGcc                                                                                            <  2:117315/100‑1 (MQ=255)          ggTGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGcc                                                                                            <  2:361971/100‑1 (MQ=255)           gTGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCa                                                                                           >  2:185081/1‑100 (MQ=255)            tGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCaa                                                                                          >  2:1390188/1‑100 (MQ=255)            tGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCaa                                                                                          >  1:1662210/1‑100 (MQ=255)            tGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCACTGAAAAATGTATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCATGTAC‑TGCAACGCCa                                                                                           <  1:173473/99‑1 (MQ=37)             gAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCATGTAC‑TGCAACg                                                                                              <  1:1682610/95‑1 (MQ=38)             gAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCATGTAC‑TGCAACGCCAAt                                                                                         <  2:1851342/100‑1 (MQ=38)             gAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAAt                                                                                         >  2:2904175/1‑100 (MQ=255)             gAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATAGCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCaa                                                                                          >  1:526720/1‑99 (MQ=255)              aaTATTCAAAAACTCCTGTCAAATTGCCTTTTGCTCTGAAAAATGCGTAGTCAAATATCTGTTTTAACTAACTGGCGTTGCA‑GTACATGCAACGCCAAtt                                                                                        <  1:1814719/100‑1 (MQ=255)                tatTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAGCGCCAAtt                                                                                        <  1:2731238/98‑1 (MQ=255)                tatTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAAttag                                                                                      <  2:2205902/100‑1 (MQ=255)                    cAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCATGTAC‑TGCAACGCCAAttagttaa                                                                                  <  1:1541325/100‑2 (MQ=37)                    cAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAAttagttag                                                                                  <  1:2243792/100‑1 (MQ=255)                     aaaaaCTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGc                                                                                 <  2:1367331/100‑1 (MQ=255)                     aaaaaCTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGc                                                                                 >  2:562967/1‑100 (MQ=255)                      aaaaCTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCg                                                                                >  2:2246868/1‑100 (MQ=255)                      aaaaCTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCg                                                                                <  1:1978022/100‑1 (MQ=255)                       aaaCTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCgg                                                                               <  1:324848/100‑1 (MQ=255)                        aaCTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGa                                                                              >  1:2407928/1‑100 (MQ=255)                             cTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTa                                                                         >  2:2093847/1‑100 (MQ=255)                              tGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTAc                                                                        >  2:2361102/1‑100 (MQ=255)                                 cAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGTAATTTACGTc                                                                     <  1:185079/100‑1 (MQ=255)                                  aaaTTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCg                                                                    >  1:525365/1‑100 (MQ=255)                                     ttGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATa                                                                 >  2:2412275/1‑100 (MQ=255)                                       gCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACt                                                               <  2:2828365/100‑1 (MQ=255)                                       gCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACt                                                               >  1:2026719/1‑100 (MQ=255)                                        ccTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTc                                                              >  2:640595/1‑100 (MQ=255)                                         cTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCg                                                             <  2:2395481/100‑1 (MQ=255)                                              gCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTgg                                                        >  2:1948044/1‑100 (MQ=255)                                                 cTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACACCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGt                                                     >  1:1248037/1‑100 (MQ=255)                                                  tGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTc                                                    >  1:1597636/1‑100 (MQ=255)                                                         tGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCaa                                             <  2:2155260/100‑1 (MQ=255)                                                           cATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAg                                           <  1:775445/100‑1 (MQ=255)                                                           cATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAg                                           >  2:2491881/1‑100 (MQ=255)                                                           cATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAg                                           >  2:2109204/1‑100 (MQ=255)                                                             tAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCg                                         >  2:1288874/1‑100 (MQ=255)                                                               gTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGtt                                       >  2:2788139/1‑100 (MQ=255)                                                               gTCAAATATCTGTGTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGtt                                       >  2:1954284/1‑100 (MQ=255)                                                                 cAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGc                                     <  1:1472969/100‑1 (MQ=255)                                                                 cAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGc                                     <  2:1077401/100‑1 (MQ=255)                                                                  aaaTATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTGCGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCt                                    >  2:1030722/1‑100 (MQ=255)                                                                     tatCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTaa                                 <  1:1558416/100‑1 (MQ=255)                                                                     tatCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTaa                                 <  1:2412264/100‑1 (MQ=255)                                                                     tatCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTaa                                 <  1:1697865/100‑1 (MQ=255)                                                                      atCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTaa                                 >  2:1579189/1‑99 (MQ=255)                                                                           cgctAACTAATTGGCGTTGCATGTAC‑TGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCg                           >  1:350311/4‑100 (MQ=25)                                                                            tttAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCg                           <  2:578343/99‑1 (MQ=255)                                                                            tttAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCGt                          <  1:386247/100‑1 (MQ=255)                                                                             ttAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCGtt                         <  2:2890823/100‑1 (MQ=255)                                                                                   aaTTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCGTTGaaaaa                   >  2:2183686/1‑100 (MQ=255)                                                                                     ttGGCGTTGCA‑GTACATGCACCGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCGTTGAAAAATg                 >  1:93168/1‑100 (MQ=255)                                                                                       ggCGTTGCATGTAC‑TGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCGTTGAAAAATGAc               >  1:2225602/1‑100 (MQ=38)                                                                                       ggCGTTGCATGTAC‑TGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCGTTGAAAAATGAc               >  2:2312941/1‑100 (MQ=38)                                                                                       ggCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCGTTGAAAAATGAc               <  1:1402589/100‑1 (MQ=255)                                                                                       ggCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCGTTGAAAAATGAc               >  2:995163/1‑100 (MQ=255)                                                                                        gCGTTGCATGTAC‑TGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCGTTGAAAAATGAct              >  2:772329/1‑100 (MQ=38)                                                                                        gCGTCGCA‑GTACCTCCTACGCCACTCAGTTAGCGGAATTTATGTCGATCCTCGCCTGGCGTCATGCCAAAGCGTTTCTTAAATACCGTTGAAAAATGAc               <  1:325356/99‑1 (MQ=255)                                                                                               a‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCGTTGAAAAATGACTCTGGTCa       >  2:326101/1‑100 (MQ=255)                                                                                               a‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCGTTGAAAAATGACTCTGGTCa       >  1:1726932/1‑100 (MQ=255)                                                                                                 gTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCGTTGAAAAATGACTCTGGTCAg      <  2:963065/100‑1 (MQ=255)                                                                                                   aCATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCGTTGAAAAATGACTCTGGTCAGaa    >  1:1113332/1‑100 (MQ=255)                                                                                                     aTGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCGTTGAAAAATGACTCTGGTCAGaaaa  >  1:1267704/1‑100 (MQ=255)                                                                                                     |                                                                                                    CTGAAACAAGGTGAATATTCAAAAACTCCTGTCAAATTGCCTTTTGCCCTGAAAAATGCATAGTCAAATATCTGTTTTAACTAATTGGCGTTGCA‑GTACATGCAACGCCAATTAGTTAGCGGAATTTACGTCGATACTCGCCTGGCGTCATCCCAAAGCGTTGCTTAAATACCGTTGAAAAATGACTCTGGTCAGAAAA  >  NC_000913/1446263‑1446461

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑