Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,392,757	C→G	10.5%	intergenic (+99/‑135)	glyY → / → yjeV	tRNA‑Gly/uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,392,757	0	C	G	10.5%	194.2 / 10.7	57	intergenic (+99/‑135)	glyY/yjeV	tRNA‑Gly/uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base C (25/26);  new base G (3/3);  total (28/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.02e-01

GCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTATTTTTTTAACCTATTGATAGATAAGTTAAAAATTAAGATTCCGTTTTGTCGAGTCGATCACTTGACGATTTTATTCGTCTTGAATTGCAATGCGTTTTTATTTTTATTCACAAGCTGTGGATGAATCAGGCGTCACGCGGTAACCCTTTTTCAATCACCCGAACCAGACGCTG  >  NC_000913/4392495‑4392975                                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                           gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCt                                                                                                                                                                                                                >  2:197765/1‑275 (MQ=255)                                  aattcccggctCCCTCTCCAAAATTGGAAAGTGGTGTAAGGACAAGACCACCCAAGCGGGAATAGTGCAGTTGGTAGAGCCCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACATCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTTTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTa                                                                                                                                                                               <  4:536641/265‑1 (MQ=37)                                   aGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGGCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTa                                                                                                                                                                               <  2:530280/274‑1 (MQ=255)                                   aGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTa                                                                                                                                                                               <  2:82302/274‑1 (MQ=255)                                                                                                             agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAAt                                                                                                                                                                                   >  1:88849/1‑196 (MQ=255)                                                                                                                 cACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTa                                                                                                                                                                               <  3:88849/196‑1 (MQ=255)                                                                                                                                                       cGTTTCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGaa                                                                                                                                                                                                   <  6:624066/138‑1 (MQ=255)                                                                                                                                                       cGTTTCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGaa                                                                                                                                                                                                   >  5:624066/1‑138 (MQ=255)                                                                                                                                                          ttCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTaa                                                                                                                                                                                                             >  8:1105791/1‑125 (MQ=255)                                                                                                                                                          ttCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTaa                                                                                                                                                                                                             <  7:1105791/125‑1 (MQ=255)                                                                                                                                                                  ccAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAAt                                                                                                                                                                                                                  >  5:407028/1‑112 (MQ=255)                                                                                                                                                                  ccAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAAt                                                                                                                                                                                                                  <  6:407028/112‑1 (MQ=255)                                                                                                                                                                  ccAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGaa                                                                                                                                                                                                   <  7:423415/127‑1 (MQ=255)                                                                                                                                                                  ccAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGaa                                                                                                                                                                                                   >  8:423415/1‑127 (MQ=255)                                                                                                                                                                     aaTTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTaa                                                                                                                                                                                                             >  8:68785/1‑114 (MQ=255)                                                                                                                                                                     aaTTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTaa                                                                                                                                                                                                             <  7:68785/114‑1 (MQ=255)                                                                                                                                                                           tctctcAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATc                                                                                                                                                                                                                 >  8:832247/1‑104 (MQ=255)                                                                                                                                                                           tctctcAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATc                                                                                                                                                                                                                 <  7:832247/104‑1 (MQ=255)                                                                                                                                                                              ctcAATAAAATATCCACAGCGACGCGATGCGTTATTGCTTGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTGAGGCTg                                                                                                                                                                                                                      <  7:680215/96‑1 (MQ=255)                                                                                                                                                                              ctcAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTGAGGCTg                                                                                                                                                                                                                      >  8:680215/1‑96 (MQ=255)                                                                                                                                                                                  aTAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTGAGGCTGtg                                                                                                                                                                                                                    <  6:156764/94‑2 (MQ=255)                                                                                                                                                                                  aTAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTGAGGCTGtg                                                                                                                                                                                                                    >  5:156764/1‑93 (MQ=255)                                                                                                                                                                                  aTAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAg                                                                                                                                                                                                                          <  5:898456/88‑1 (MQ=255)                                                                                                                                                                                  aTAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAg                                                                                                                                                                                                                          >  6:898456/1‑88 (MQ=255)                                                                                                                                                                                    aaaaTATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAAc                                                                                                                                                                                                 <  8:293863/111‑1 (MQ=255)                                                                                                                                                                                    aaaaTATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAAc                                                                                                                                                                                                 >  7:293863/1‑111 (MQ=255)                                                                                                                                                                                    aaaaTATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGt                                                                                                                                                                                <  5:75217/128‑1 (MQ=255)                                                                                                                                                                                    aaaaTATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGt                                                                                                                                                                                >  6:75217/1‑128 (MQ=255)                                                                                                                                                                                           ccACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACgg                                                                                                                                                                                        >  2:126807/1‑113 (MQ=255)                                                                                                                                                                                               aGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGaa                                                                                                                                                                                    <  4:126806/113‑1 (MQ=255)                                                                                                                                                                                                 cGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTaa                                                                                                                                                                                                                   <  7:336904/80‑1 (MQ=255)                                                                                                                                                                                                 cGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTaa                                                                                                                                                                                                                   >  8:336904/1‑80 (MQ=255)                                                                                                                                                                                                    cgcgATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTAttt                                                                                                                                                                            >  2:553651/1‑116 (MQ=255)                                                                                                                                                                                                      cgATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTATTTTTTTAAc                                                                                                                                                                     >  8:208969/1‑121 (MQ=255)                                                                                                                                                                                                      cgATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTATTTTTTTAAc                                                                                                                                                                     <  7:208969/121‑1 (MQ=255)                                                                                                                                                                                                        aTGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTAttttttt                                                                                                                                                                        <  4:553650/116‑1 (MQ=255)                                                                                                                                                                                                               aTTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAACCAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTATTTTTTTAACCTATTGATAGATAAGTTAAAAATTAAGATTCCGTTTTGTCGAGTCGATCACTTGACGATTTTATTCGTCTTGAATTGCAATGCGTTTTTATTTTTATTCACAAGCTGTTGATGAATCAGGCGTCCCGCGGTAACCCTTTTTCAATCACCCGAACCAGACGCTg  >  2:76358/1‑275 (MQ=255)                                                                                                                                                                                                                    tGGTTTTTGTTGTCTCTGGCAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAAAAACTTCGCACGGTGAATAGTATTTTTTTAACCTAt                                                                                                                                                                 <  5:35765/111‑1 (MQ=255)                                                                                                                                                                                                                    tGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTATTTTTTTAACCTAt                                                                                                                                                                 >  6:35765/1‑111 (MQ=255)                                                                                                                                                                                                                     ggTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTGAGGCTg                                                                                                                                                                                                                      >  6:275001/1‑57 (MQ=255)                                                                                                                                                                                                                     ggTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTGAGGCTg                                                                                                                                                                                                                      <  5:275001/57‑1 (MQ=255)                                                                                                                                                                                                                                   ctGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTATTTTTTTAACCTATTgatagata                                                                                                                                                        <  5:334269/105‑1 (MQ=255)                                                                                                                                                                                                                                   ctGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTAAATTTCAAAGAAACTTCGCACGGTGAATAGTATTTTTTTAACCTATTgatagata                                                                                                                                                        >  6:334269/1‑105 (MQ=255)                                                                                                                                                                                                                                         aaCTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAAt                                                                                                                                                                                                                  <  7:564428/41‑1 (MQ=255)                                                                                                                                                                                                                                         aaCTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAAt                                                                                                                                                                                                                  >  8:564428/1‑41 (MQ=255)                                                                                                                                                                                                                                           ctctTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTATTTTTTTAACCTATTgatagata                                                                                                                                                        <  8:844811/97‑1 (MQ=255)                                                                                                                                                                                                                                           ctctTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTATTTTTTTAACCTATTgatagata                                                                                                                                                        >  7:844811/1‑97 (MQ=255)                                                                                                                                                                                                                                                     cAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTATTTTTTTAACCTATTGATAGATAAGTTAAAAATTAAGATTCCGtt                                                                                                                                  >  7:573020/1‑109 (MQ=255)                                                                                                                                                                                                                                                     cAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTATTTTTTTAACCTATTGATAGATAAGTTAAAAATTAAGATTCCGtt                                                                                                                                  <  8:573020/109‑1 (MQ=255)                                                                                                                                                                                                                                                                 caGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACg                                                                                                                                                                                         <  7:593117/42‑1 (MQ=255)                                                                                                                                                                                                                                                                 caGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACg                                                                                                                                                                                         >  8:593117/1‑42 (MQ=255)                                                                                                                                                                                                                                                                 caGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTATTTTTTTAACCt                                                                                                                                                                   >  6:864326/1‑64 (MQ=255)                                                                                                                                                                                                                                                                 caGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTATTTTTTTAACCt                                                                                                                                                                   <  5:864326/64‑1 (MQ=255)                                                                                                                                                                                                                                                                 caGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTATTTTTTTAACCTATTGATAGATAAGTTAAAAATTAAGATTCCGTTTTgtcgagtcga                                                                                                                      <  6:410387/109‑1 (MQ=255)                                                                                                                                                                                                                                                                 caGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTATTTTTTTAACCTATTGATAGATAAGTTAAAAATTAAGATTCCGTTTTgtcgagtcga                                                                                                                      >  5:410387/1‑109 (MQ=255)                                                                                                                                                                                                                                                                  aGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACgg                                                                                                                                                                                        >  2:495569/1‑42 (MQ=255)                                                                                                                                                                                                                                                                      tCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGaa                                                                                                                                                                                    <  4:495568/42‑1 (MQ=255)                                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                           GCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTCTTCTCTCAATAAAATATCCACAGCGACGCGATGCGTTATTGCTGGTTTTTGTTGTCTCTGACAAACTCTTGTAAACAGAGTTATCCACAGCCTCAGGCTGTAATCTTAATTTCAAAGAAACTTCGCACGGTGAATAGTATTTTTTTAACCTATTGATAGATAAGTTAAAAATTAAGATTCCGTTTTGTCGAGTCGATCACTTGACGATTTTATTCGTCTTGAATTGCAATGCGTTTTTATTTTTATTCACAAGCTGTGGATGAATCAGGCGTCACGCGGTAACCCTTTTTCAATCACCCGAACCAGACGCTG  >  NC_000913/4392495‑4392975

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑