Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,503,143	T→A	10.1%	intergenic (+18/+75)	ydcL → / ← insP	lipoprotein/pseudogene, IS609 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,503,143	0	T	A	10.1%	125.5 / 3.5	39	intergenic (+18/+75)	ydcL/insP	lipoprotein/pseudogene, IS609 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related
Reads supporting (aligned to +/- strand):  ref base T (22/13);  new base A (2/2);  total (24/15)
Fisher's exact test for biased strand distribution p-value = 6.31e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

TCAAAGTCGTTCGTCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTGGCA  >  NC_000913/1502995‑1503290                                                                                                                                                     |                                                                                                                                                    tCAAAGTCGTTCGTCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGt                                                                                                                                                     <  3:115913/149‑1 (MQ=255)  cAAAGTCGTTCGTCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGtt                                                                                                                                                    <  3:240463/149‑1 (MQ=255)      gTCGTTCGTCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGtt                                                                                                                                                    >  4:18594/1‑145 (MQ=255)      gTCGTTCGTCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGtt                                                                                                                                                    <  3:18594/145‑1 (MQ=255)              tCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCttt                                                                                                                                        >  2:457577/1‑149 (MQ=255)               cAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCtttt                                                                                                                                       <  4:283354/149‑1 (MQ=255)                   gCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATc                                                                                                                                   >  4:510418/1‑149 (MQ=255)                               aCCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTa                                                                                                                       >  1:784750/1‑149 (MQ=255)                                  tGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTaaaa                                                                                                                    <  3:312029/149‑1 (MQ=255)                                   gAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAAc                                                                                                                   <  3:510418/149‑1 (MQ=255)                                    aaTAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAAcc                                                                                                                  <  2:784750/149‑1 (MQ=255)                                                  gCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGc                                                                                                    >  2:607850/1‑149 (MQ=255)                                                     aaTGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCggg                                                                                                 <  1:457577/149‑1 (MQ=255)                                                           tttCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCttttt                                                                                                                                      <  3:768189/106‑1 (MQ=255)                                                           tttCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTGCCAGACGCGCCATCGTTAGATGGCGCttttt                                                                                                                                      >  4:768189/1‑106 (MQ=255)                                                               gAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCTAACGATGgcgc                                                                                                                                           <  2:191962/97‑1 (MQ=255)                                                               gAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCTAACGATGgcgc                                                                                                                                           >  1:191962/1‑97 (MQ=255)                                                               gAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCTAACGATGgcgc                                                                                                                                           <  2:735818/97‑1 (MQ=255)                                                               gAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCTAACGATGgcgc                                                                                                                                           >  1:735818/1‑97 (MQ=255)                                                               gAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGgc                                                                                       >  4:61219/1‑149 (MQ=255)                                                                     atTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGtt                                                                                 >  2:512296/1‑149 (MQ=255)                                                                          aCAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCa                                                                            >  1:55945/1‑149 (MQ=255)                                                                           cAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCAc                                                                           <  3:61219/149‑1 (MQ=255)                                                                               ttATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGt                                                                                                                        <  2:291151/100‑1 (MQ=255)                                                                               ttATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGt                                                                                                                        >  1:291151/1‑100 (MQ=255)                                                                                               gACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCtgtt                                                       >  2:791336/1‑149 (MQ=255)                                                                                                     tGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTgttgtt                                                    >  2:278820/1‑146 (MQ=255)                                                                                                     tGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTgttgtt                                                    <  1:278820/146‑1 (MQ=255)                                                                                                      gCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAAt                                                <  1:607850/149‑1 (MQ=255)                                                                                                               tttGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCg                                       >  2:53038/1‑149 (MQ=255)                                                                                                                          cAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCTTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCtgtt                                                       >  4:754068/1‑122 (MQ=255)                                                                                                                          cAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCTTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCtgtt                                                       <  3:754068/122‑1 (MQ=255)                                                                                                                             aaaGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGTGGATGACGGATATTg                         <  1:512296/149‑1 (MQ=255)                                                                                                                                  agtTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCa                    >  3:403906/1‑149 (MQ=255)                                                                                                                                   gtTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGAc                                 <  1:738647/135‑1 (MQ=255)                                                                                                                                   gtTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGAc                                 >  2:738647/1‑135 (MQ=255)                                                                                                                                    ttCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCAcc                  >  4:632223/1‑149 (MQ=255)                                                                                                                                    ttCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCAcc                  >  2:635816/1‑149 (MQ=255)                                                                                                                                                  tCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTgg    >  4:172232/1‑149 (MQ=255)                                                                                                                                                    gTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTGGCa  >  4:390327/1‑149 (MQ=255)                                                                                                                                                    gTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTGGCa  >  2:505908/1‑149 (MQ=255)                                                                                                                                                    gTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTGGCa  >  2:503023/1‑149 (MQ=255)                                                                                                                                                    gTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTGGCa  >  1:581268/1‑149 (MQ=255)                                                                                                                                                     ttAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTcc                                                                             >  2:194924/1‑73 (MQ=255)                                                                                                                                                     ttAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTcc                                                                             <  1:194924/73‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                    TCAAAGTCGTTCGTCAGGGCGAAGGTAAAGACCTGAATAACGAAAGTACGCCAATGGCTTTCGAAAATATTAAACAAGTTATTGATGACATGGCGACCGATGCCACCATGTTTGACGTTAACAAAAAGTAGTTCCAGACGCGCCATCGTTAGATGGCGCTTTTTATCCGGTGCGCCGTAAAACCCCATCCTTCAGGGCGGGGATATAAGGCGCGGTTTTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTGGCA  >  NC_000913/1502995‑1503290

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑