Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,485,355	G→A	S47N (AGT→AAT)	unknown →	Type II/IV secretion system protein TadC, associated with Flp pilus assembly

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,485,355	0	G	A	94.4%	37.1 / ‑4.1	18	S47N (AGT→AAT)	unknown	Type II/IV secretion system protein TadC, associated with Flp pilus assembly
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (9/8);  total (9/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCTTTATTATGTTTTTGGCAGTGAACTTTTCGGTATGGGAATCATTTGGTGGTTGATGAGGAAGTCAACATGATGATTAAACTATTATTATCTTATGCGCTATTAACGATTTTTGGTATTATTGTATTGTTTGCCGCACTTTCAGCCAGAAAAAAATTCCAATATAGAAAGGAAGTTATTACTGGAGAAAGACCTAAGGATCAAGATAGTGACGAAGTAGCTAAAAATAAGAGCAAACAGCAAATTGAACTTGAACTATTACTAATTAATAATAATCCTATCTTAAAAGTACTCGGAATTATTGATAAAAATATAAAAGTAAAATTGTTGATCATGCTTTTGCTTTTTGGAGTTTACTATCTTTATTCATTTACTGATGAAACTACCGACAGTTCATCTCTGTTACTTGGCTTTCTAACTATATTAATAA  >  1/1485146‑1485576                                                                                                                                                                                                                  |                                                                                                                                                                                                                              tGCTTTATTATGTTTTTGGTAGTGAGCTTTTCGGTATGGGAATTATTTGGTGGTTGATGAGGAAGTCAACATGATAATTAAGCTATTACTGTCTTATGCATTATTAACCATTTTTGGTGTGTTTGTATTATTTTTGGCACTTTCAGCTAGAAGAAAATTCCAGCATAGGAAAGAAATTATTACTGGAGAAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAAttgaac                                                                                                                                                                                      <  1:460298/251‑1 (MQ=255)                 tggtaGTGAGCTTTTCGGTATGGGAATTATTTGGTGGTTGATGAGGAAGTCAACATGATAATTAAGCTATTACTGTCTTATGCATTATTAACCATTTTTGGTGTGTTTGTATTATTTTTGGCACTTTCAGCTAGAAGAAAATTCCAGCATAGGAAAGAAATTATTACTGGAGAAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTACtgat                                                                                                                                                                      <  1:343804/247‑4 (MQ=255)                                  gTATGGGAATTATTTGGTGGTTGATGAGGAAGTCAACATGATAATTAAGCTATTACTGTCTTATGCATTATTAACCATTTTTGGTGTGTTTGTATTATTTTTGGCACTTTCAGCTAGAAGAAAATTCCAGCATAGGAAAGAAATTATTACTGGAGAAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTAc                                                                                                                                                                          <  1:877369/230‑1 (MQ=255)                                      gggAATTATTTGGTGGTTGATGAGGAAGTCAACATGATAATTAAGCTATTACTGTCTTATGCATTATTAACCATTTTTGGTGTGTTTGTATTATTTTTGGCACTTTCAGCTAGAAGAAAATTCCAGCATAGGAAAGAAACTATTACTGGAGAAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTACTGATTAACAATAATcccgttttaaa                                                                                                                                                 >  1:889899/1‑242 (MQ=255)                                             aTTTGGTGGTTGATGAGGAAGTCAACATGATAATTAAGCTATTACTGTCTTATGCATTATTAACCATTTTTGGTGTGTTTGTATTATTTTTGGCACTTTCAGCTAGAAGAAAATTCCAGCATAGGAAAGAAATTATTACTGGAGAAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTACTGATtaacaat                                                                                                                                                               >  1:258979/1‑230 (MQ=255)                                                                     aCATGATAATTAAGCTATTACTGTCTTATGCATTATTAACCATTTTTGGTGTGTTTGTATTATTTTTGGCACTTTCAGCTAGAAGAAAATTCCAGCATAGGAAAGAAATTATTACTGGAGAAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTACTGATTAACAATAATcc                                                                                                                                                          >  1:318174/1‑211 (MQ=255)                                                                                 agcTATTACTGTCTTATGCATTATTAACCATTTTTGGTGTGTTTGTATTATTTTTGGCACTTTCAGCTAGAAGAAAATTCCAGCATAGGAAAGAAATTATTACTGGAGAAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTACTGATTAACAATAATCCCGTTTTAAAAATGCTTGGAATTATTGATAAAAATATAAAAGTAAAAtta                                                                                                         >  1:170225/3‑247 (MQ=255)                                                                                  gcTATTACTGTCTTATGCATTATTAACCATTTTTGGTGTGTTTGTATTATTTTTGGCACTTTCAGCTAGAAGAAAATTCCAGCATAGGAAAGAAATTATTACTGGAGAAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTACTGATtaacaat                                                                                                                                                               >  1:177660/2‑193 (MQ=255)                                                                                     attactgtCTTATGCATTATTAACCATTTTTGGTGTGTTTGTATTATTTTTGGCACTTTCAGCTAGAAGAAAATTCCAGCATAGGAAAGAAATTATTACTGGAGAAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTACTGATTAACAATAATCCCGTTTTAAAAATGCTTGGAATTATTGATAAAAATATAAAAGTAAAAttactgatta                                                                                                  >  1:741339/8‑243 (MQ=255)                                                                                           gtCTTATGCATTATTAACCATTTTTGGTGTGTTTGTATTATTTTTGGCACTTTCAGCTAGAAGAAAATTCCAGCATAGGAAAGAAATTATTACTGGAGAAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTACtgat                                                                                                                                                                      <  1:299930/176‑4 (MQ=255)                                                                                             cTTATGCATTATTAACCATTTTTGGTGTGTTTGTATTATTTTTGGCACTTTCAGCTAGAAGAAAATTCCAGCATAGGAAAGAAATTATTACTGGAGAAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTACTGATTAACAATAATCCCGTTTTAAAAATGCTTGGAATTATTGATAAAAATATAAAAGTAAAAttactgattatggtttta                                                                                          >  1:761644/1‑235 (MQ=255)                                                                                              ttatgcattATTAACCATTTTTGGTGTGTTTGTATTATTTTTGGCACTTTCAGCTAGAAGAAAATTCCAGCATAGGAAAGAAATTATTACTGGAGAAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTACTGATTAACAATAATCCCGTTTTAAAAATGCTTGGAATTATTGATAAAAATATAAAAGTAAAAttactgattatggttttac                                                                                         <  1:347992/243‑18 (MQ=255)                                                                                                                             gtattatttttggCACTTTCAGCTAGAAGAAAATTCCAGCATAGGAAAGAAATTATTACTGGAGAAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTACTGATTAACAATAATCCCGTTTTAAAAATGCTTGGAATTATTGATAAAAATATAAAAGTAAAAttac                                                                                                        >  1:738420/13‑203 (MQ=255)                                                                                                                                 tatttttggCACTTTCAGCTAGAAGAAAATTCCAGCATAGGAAAGAAATTATTACTGGAGAAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTACTGATTAACAATAATCCCGTTTTAAAAATGCTTGGAATTATTGATAAAAATATAAAAGTAAAATTACTGATTATGGTTTTACTTTGCGGGGTTTATTATCTTTATTCACTTATtgat                                                      <  1:806403/243‑1 (MQ=255)                                                                                                                                       tggCACTTTCAGCTAGAAGAAAATTCCAGCATAGGAAAGAAATTATTACTGGAGAAAGACCTAAGGATCAAAGTAGTGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTACTGATTAACAATAATCCCGTTTTAAAAATGCTTGGAATTATTGATAAAAATATAAAAGTAAAATTACTGATTATGGTTTTACTTTGCGGGGTTTATTATCTTTATTCACTTATTGATAAAACt                                                <  1:643794/249‑1 (MQ=255)                                                                                                                                                                   gcataggaaagaaattattaCTGGAGAAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTACTGATTAACAATAATCCCGTTTTAAAAATGCTTGGAATTATTg                                                                                                                                >  1:438670/15‑143 (MQ=255)                                                                                                                                                                          aaagaaattattaCTGGAGAAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTACTGATTAACAATAATCCCGTTTTAAAAATGCTTGGAATTATTGATAAAAATATAAAAGTAAAATTACTGATTATGGTTTTACTTTGCGGGGTTTATTATCTTTATTCACTTATTGATAAAACTACTGACAGCTCATCTCTGTTACTTGGCTTTCTAAc             <  1:282703/244‑1 (MQ=255)                                                                                                                                                                                          gagaAAGACCTAAGGATCAAAGTAATGATGAAATAGCCAAAGGTAAAAGCAAGCAGCAAATTGAACTTGAGCTGTTACTGATTAACAATAATCCCGTTTTAAAAATGCTTGGAATTATTGATAAAAATATAAAAGTAAAATTACTGATTATGGTTTTACTTTGCGGGGTTTATTATCTTTATTCACTTATTGATAAAACTACTGACAGCTCATCTCTGTTACTTGGCTTTCTAACTATATtaatag  <  1:611199/246‑2 (MQ=255)                                                                                                                                                                                                                  |                                                                                                                                                                                                                              TGCTTTATTATGTTTTTGGCAGTGAACTTTTCGGTATGGGAATCATTTGGTGGTTGATGAGGAAGTCAACATGATGATTAAACTATTATTATCTTATGCGCTATTAACGATTTTTGGTATTATTGTATTGTTTGCCGCACTTTCAGCCAGAAAAAAATTCCAATATAGAAAGGAAGTTATTACTGGAGAAAGACCTAAGGATCAAGATAGTGACGAAGTAGCTAAAAATAAGAGCAAACAGCAAATTGAACTTGAACTATTACTAATTAATAATAATCCTATCTTAAAAGTACTCGGAATTATTGATAAAAATATAAAAGTAAAATTGTTGATCATGCTTTTGCTTTTTGGAGTTTACTATCTTTATTCATTTACTGATGAAACTACCGACAGTTCATCTCTGTTACTTGGCTTTCTAACTATATTAATAA  >  1/1485146‑1485576

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑