Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,674,576	T→A	10.0%	intergenic (+201/‑210)	yhjD → / → yhjE	putative transporter YhjD/putative transporter YhjE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,674,576	0	T	A	10.0%	127.1 / 5.1	40	intergenic (+201/‑210)	yhjD/yhjE	putative transporter YhjD/putative transporter YhjE
Reads supporting (aligned to +/- strand):  ref base T (17/19);  new base A (2/2);  total (19/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.38e-01

AAACGCCTTATCCGGCATACGATTTTATTCGGCCTGGCTCCCCGTAGGCCGGATAAGATGCGCCAGCATCGCATCCGGCTATAATGCGCACATAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACTTTTGCTGTGCGTAATATGGCTATTCGTTAGCCAAAAAATAAGAAAAGATTATGCAAGCAACAGCCACAACACTCGACC  >  NC_000913/3674395‑3674813                                                                                                                                                                                       |                                                                                                                                                                                                                                              aaaCGCCTTATCCGGCATACGATTTTATTCGGCCTGGCTCCCCGTAGGCCGGATAAGATGCGCCAGCATCGCATCCGGCTATAATGCGCACATAACCTCTTGGAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGc                                                                                                                                                     <  1:260434/272‑1 (MQ=255)         tATCCGGCATACGATTTTATTCGGCCTGGCTCCCCGTAGGCCGGATAAGATGCGCCAGCATCGCATCCGGCTATAATGCGCACATAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTACCCACTATTTATAAAATTATGTGAAGCATTTAATAGAAAAAAAATCACAGGCCAAAACAt                                                                                                                                             >  2:59586/1‑272 (MQ=255)          ttCCGGCATACGATTTTATTCGGCCTGGCTCCCCGTAGGCCGGATAAGATGCGCCAGCATCGCATCCGGCTATAATGCGCACATAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACAtt                                                                                                                                            <  1:59586/271‑1 (MQ=255)             cGGCATACGATTTTATTCGGCCTGGCTCCCCGTAGGCCGGATAAGATGCGCCAGCATCGCATCCGGCTATAATGCGCACATAACCTCTTGAAACTCGTCCACAGAGCCTCTTCAGCCATCTATTTGGGAGCACACACTTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAAcctgtcc                                                                                                                                         >  1:200631/1‑266 (MQ=255)                                             tAGGCCGGATAAGATGCGCCAGCATCGCATCCGGCTATAATGCGCACATAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAAACCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGcc                                                                                                                                                    <  1:80393/229‑1 (MQ=255)                                             tAGGCCGGATAAGATGCGCCAGCATCGCATCCGGCTATAATGCGCACATAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAAACCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGcc                                                                                                                                                    >  2:80403/1‑229 (MQ=255)                                             tAGGCCGGATAAGATGCGCCAGCATCGCATCCGGCTATAATGCGCACATAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAAACCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGcc                                                                                                                                                    >  2:80393/1‑229 (MQ=255)                                             tAGGCCGGATAAGATGCGCCAGCATCGCATCCGGCTATAATGCGCACATAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAAACCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGcc                                                                                                                                                    <  1:80403/229‑1 (MQ=255)                                               ggCCGGATAAGATGCGCCAGCATCGCATCCGGCTATAATGCGCACATAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGAtt                                                                                                      <  1:135535/273‑1 (MQ=255)                                                                 aGCATCGCATCCGGCTATAATGCGCACATAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAAt                                                                                                                                                            >  1:256918/1‑201 (MQ=255)                                                                 aGCATCGCATCCGGCTATAATGCGCACATAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAAt                                                                                                                                                            <  2:256918/201‑1 (MQ=255)                                                                        catcCGGCTATAATTCGCACATAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAACAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACtttt                                                                             <  1:264860/273‑1 (MQ=255)                                                                             ggCTATAATGCGCACATAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACt                                                                                                                                                        <  1:296411/193‑1 (MQ=255)                                                                             ggCTATAATGCGCACATAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACt                                                                                                                                                        >  2:296411/1‑193 (MQ=255)                                                                                          acaTAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACTTTTGCTGTGCGTAATATGGCt                                                           >  1:146868/1‑273 (MQ=255)                                                                                            aTAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCCAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACttt                                                                              <  1:48336/252‑1 (MQ=255)                                                                                            aTAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTcc                                                                                                            >  1:137010/1‑222 (MQ=255)                                                                                            aTAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTcc                                                                                                            <  2:137010/222‑1 (MQ=255)                                                                                            aTAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACttt                                                                              >  2:48336/1‑252 (MQ=255)                                                                                               aCCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACAtt                                                                                                                                            <  1:187560/187‑1 (MQ=255)                                                                                               aCCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACAtt                                                                                                                                            >  2:187560/1‑187 (MQ=255)                                                                                                       aaaCTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGaaa                                                                                       <  1:39696/232‑1 (MQ=255)                                                                                                       aaaCTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGaaa                                                                                       >  2:39696/1‑232 (MQ=255)                                                                                                         aCTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACtt                                                                               >  2:200655/1‑238 (MQ=255)                                                                                                         aCTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACtt                                                                               <  1:200655/238‑1 (MQ=255)                                                                                                         aCTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACTTTTGCt                                                                          >  2:172699/1‑243 (MQ=255)                                                                                                         aCTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACTTTTGCt                                                                          <  1:172699/243‑1 (MQ=255)                                                                                                            cGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGaaaaa                                                                                                                                                             <  2:17254/157‑1 (MQ=255)                                                                                                            cGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGaaaaa                                                                                                                                                             >  1:17254/1‑157 (MQ=255)                                                                                                                              aGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATc                                                                                                                                                           <  1:220330/141‑1 (MQ=255)                                                                                                                              aGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATc                                                                                                                                                           >  2:220330/1‑141 (MQ=255)                                                                                                                                                    tttttttttCCAACTTCCTACCCCCTGCATTTAATTCCAGTTTGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACTTTTGCTGTGCGTAATATGGCTATTCGTTAGCCAAAAAATAAGAAAAGATTATGCAAGCAACAGCCACAACACTCGAcc  <  2:146868/266‑1 (MQ=255)                                                                                                                                                     aTTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTaa                                                                                                                                                 <  2:149218/128‑1 (MQ=255)                                                                                                                                                     aTTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTaa                                                                                                                                                 >  1:149218/1‑128 (MQ=255)                                                                                                                                                                               cATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACTTTTGCTGTGCGTAATATGGCTATTCGTTAGCCAAAAAATAAGAAAAGATTATgcaa                        <  2:39602/224‑1 (MQ=255)                                                                                                                                                                               cATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACTTTTGCTGTGCGTAATATGGCTATTCGTTAGCCAAAAAATAAGAAAAGATTATgcaa                        >  1:39602/1‑224 (MQ=255)                                                                                                                                                                                atatAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTaa                                                                                                                                                 >  1:227627/1‑102 (MQ=255)                                                                                                                                                                                atatAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTaa                                                                                                                                                 <  2:227627/102‑1 (MQ=255)                                                                                                                                                                                atatAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACTTTTGCTGTGCGt                                                                    <  1:64871/179‑1 (MQ=255)                                                                                                                                                                                atatAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACTTTTGCTGTGCGt                                                                    >  2:64871/1‑179 (MQ=255)                                                                                                                                                                                       tCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACTTTTGCt                                                                          >  1:152344/1‑166 (MQ=255)                                                                                                                                                                                       tCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACTTTTGCt                                                                          <  2:152344/166‑1 (MQ=255)                                                                                                                                                                                       |                                                                                                                                                                                                                                              AAACGCCTTATCCGGCATACGATTTTATTCGGCCTGGCTCCCCGTAGGCCGGATAAGATGCGCCAGCATCGCATCCGGCTATAATGCGCACATAACCTCTTGAAACTCGTCCCCAGAGCCTCTTCAGCCATCTATTTGGGAGCAAACAATTTCATTCCAAC‑TCATAACCCCAGCATATAAATCCAGTTGGTAACTTTTATTTAACCTGAAACCAGTTTTATCCACTATTTATAAAATTATGTGAAGCATTTCATAGAAGAAAAATCACTGGCCTAAACATTATCCCCTTTTTGCCTGATTTTTGACCATTTCCGCGATTTGTTACACATTGAAATATCACTTTTGCTGTGCGTAATATGGCTATTCGTTAGCCAAAAAATAAGAAAAGATTATGCAAGCAACAGCCACAACACTCGACC  >  NC_000913/3674395‑3674813

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑