Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,512,223	G→T	16.8%	T563T (ACC→ACA)	yjhG ←	putative dehydratase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,512,223	0	G	T	16.8%	55.8 / 3.6	24	T563T (ACC→ACA)	yjhG	putative dehydratase
Reads supporting (aligned to +/- strand):  ref base G (9/11);  new base T (2/2);  total (11/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.49e-01

CTCACGGCCTGAAGCATTGCCCATAGCCGGGTATCATCTGGCAATTCAGGATCGGGAAGTAAATCCTGATGGCTGGGTCTGGCATTTAATATTGCAGTTGCCTCCTCCTGTGAAGGTAATTGTTCATCGCTACGGGTTCCGAGGAAATTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCGGTGCGTAATTTACCGATGGGGCCTCCGGCCAGCGCTTCTGGCCCCACATGGCCGATGCACGCGCCAGTAGAAACGCCCGAGAAACGTGCATCGGTGATTAACGAAACATGCTTACCGTATGACAGATGCTTCAGGGCACTGGTAACCTGGTAGGTTTCTTCCATCCCTGTACCTGAAGGTCCAACGCCAATAATGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGAT  >  CP009273/4512023‑4512485                                                                                                                                                                                                         |                                                                                                                                                                                                                                                                       cTCACGGCCTGAAGCATTGCCCATAGCCAGGTATCATCTGGCAATTCAGGATCGGGAAGTAAATCCTGATGGCTGGGTCTGGCATTTAATATTGCAGTTGCCTCCTCCTGTGAAGGTAATTGTTCATCGCTACGGGTTCCGAGGAAATTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTANTTTCAATTAAATCCCCGGTGCGTAATTTACCGATGGGGCCTCCGGCCAGCGCTTCTGGCCCCACATGGCCGCTGCACGCGCCAGTAGaaa                                                                                                                                                                                               >  1:303927/1‑274 (MQ=255)                 ttGCCCATAGCCGGGTATCATCTGGCAATTCAGGAACGGGAAGTAAATCCTGATGGCTGGGTCTGGCATTTAATATTGCAGGTGCCTCCTCCTGTGAAGGTAATTGTTCATCGCTACGGGTTCCGAGGAAATTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCGGTACGTAATTTACCGATGGGGCCTCAGGCCAGCGCTTCTGGCCCCACGTGGCCCATCCACGGCGCAGTAGAACCGCCCGTGaaaagaggc                                                                                                                                                                              >  2:73136/1‑269 (MQ=255)                                  tcatcTGGCAATTCAGGATCGGGAAGTAAATCCTGATGGCTGGGTCTGGCATTTAATATTGCAGTTGCCTCCTCCTGTGAAGGTAATTGTTCATCGCTACGGGTTCCGAGGAAATTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCGGt                                                                                                                                                                                                                                                                      <  1:348961/170‑1 (MQ=255)                                       tGGCAATTCAGGATCGGGAAGTAAATCCTGATGGCTGGGTCTGGCATTTAATATTGCAGTTGCCTCCTCCTGTGAAGGTAATTGTTCAGCTCTACGGGTTCCGAGGAAATTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCGGTGCGTAATTTACCGATGGGGCCTCCGGCCAGCGCTTCTGGCCCCACATGGCCGATGCACGCGCCAGTAGAAACGCCCGAGAAACGTGCATCGGTGATTAACGAAACATGCt                                                                                                                                                        <  1:73139/275‑1 (MQ=255)                                         gCAATTCAGGATCGGGAAGTAAATCCTGATGGCTGGGTCTGGCATTTAATATTGCAGTTGCCTCCTCCTGTGAAGGTAATTGTTCATCGCTACGGGTTCCGAGGAAATTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCGGTGCGTAATTTACCg                                                                                                                                                                                                                                                         >  1:74297/1‑176 (MQ=255)                                             ttCAGGCTCAGGAAGTACATCCTGATGGGTGGGTCTGGCATTTATTATTGCAGTTGCCTCCTCCTGTGAAGGTAATTGTTCATCGCTACGTGTTCCGAGGAAATTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCGGTGCGTAATTTACCGATgg                                                                                                                                                                                                                                                     <  2:74294/176‑1 (MQ=255)                                                                                           atTGCAGTTGCCTCCTCCTGTGAAGGTAATTGGTCATCGCTACGGGTTACGAGGAAATTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAAGTAAATCCCCGGTGCGTAATTTACCGATGGGGCCTCCGGCCAGCGCTTCTGGCCCCACATGGCCGATGCACGCGCCAGTAGAAACGCCCGAGAAACGTGCATCGGTGATTAACGAAACATGCTTACCGTATGACAGATGCTTCAGGGCACTGGTAACCTGGTAGGTTTCTTCCa                                                                                                     <  1:54138/274‑1 (MQ=255)                                                                                                              gtgAAGGTATTTGTTCATCGCTACGGGTTACGAGGAAATTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCGGTGCATAATTTACCGATGGGGCCTCCGGCCAGCGCTTCTGGCCCCACATGGCCGATGCACGCGCCAGTAGAAACGCCCGAGAAACGTGCATCGGTGATTAACGAAACATGCTTACCGTATGACAGATGCTTCAGGGCACTGGTAACCTGGTAGGTTTCTTCCATCCCTGTACCTGAAGGTcc                                                                                  <  1:209305/274‑1 (MQ=255)                                                                                                               tgAAGGTAATTGTTCATCGCTACGGGTTCCGAGGAAATTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCTGTGCGTAATTTACCg                                                                                                                                                                                                                                                         >  2:523/1‑106 (MQ=255)                                                                                                                   ggTAATTGTTCATCGCTACGGGTTCCGAGGAAATTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCTGTGCGTAATTTACCGATgg                                                                                                                                                                                                                                                     <  1:523/106‑1 (MQ=255)                                                                                                                    gTAATTGTTCATCGCTACGGGTTCCGAGGAAATTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCGGTGCGTAATTTACCGATGGGGCCTCCGGCCAGCGCTTCTGGccc                                                                                                                                                                                                                            >  2:150631/1‑130 (MQ=255)                                                                                                                    gTAATTGTTCATCGCTACGGGTTCCGAGGAAATTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCGGTGCGTAATTTACCGATGGGGCCTCCGGCCAGCGCTTCTGGCCCCACATGGCCGATGCACGCGCCAGTAGAAACGCCCGAGAAACGAGCATCGGTGATTAACGAAAAATGCTTACCGTATGACAGATGCTTAAGGGCACTGGTAACCTGGTAGGTTTCTTCCATCCCTGTACCTGAAGGTCCAACGACa                                                                           >  1:71626/1‑275 (MQ=255)                                                                                                                        ttGTTCATCGCTACGGGTTCCGAGGAAATTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCGGTGCGTAATTTACCGATGGGGCCTCCGGCCAGCGCTTCTGGCCCcaca                                                                                                                                                                                                                        <  1:150636/130‑1 (MQ=255)                                                                                                                              aTCGCTACGGGTTCCGAGGAAATTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCGGTGCGTAATTTACCGATGGGGCCTCCGGCCAGCGCTTCTGGCCCCACATGGCCGATGCACGCGCCAGTAGAAACGCCCGAGAAACGTGCATCGGTGATTAACGAAACa                                                                                                                                                            >  2:385819/1‑184 (MQ=255)                                                                                                                                  cTACGGGTTCCGAGGAAATTGACTTCGCCGTGAAGCTCGCGACCATCAATTTTAATTTCAATTAAATCCCCGGTGCGTAATTTACCGATGGGGCCTCCGGCCAGCGCTTCTGGCCCCACATGGCCGATGCACGCGCCAGTAGAAACGCCCGAGAAACGTGCATCGGTGATTAACGAAACATGCt                                                                                                                                                        <  1:385825/184‑1 (MQ=255)                                                                                                                                             gAGGAAGTTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCgg                                                                                                                                                                                                                                                                       >  2:53346/1‑62 (MQ=255)                                                                                                                                                 aagttGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCGGTGCg                                                                                                                                                                                                                                                                   <  1:53349/59‑1 (MQ=255)                                                                                                                                                           cGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCGGTGCGTAATTTACCGATGGGGCCTCCGGCCAGCGCTTCTGGCCCCACATGGCCGATGCACGCGCCAGTAGAAACGCCCGAGAAACGTGCATCGGTGATTAACGAAACa                                                                                                                                                            >  1:176731/1‑155 (MQ=255)                                                                                                                                                                     cTCGCGACAATCAATTTTAATTTCAATTAAATCCCCTGTGCg                                                                                                                                                                                                                                                                   >  1:375010/1‑42 (MQ=255)                                                                                                                                                                         cgACAATCAATTTTAATTTCAATTAAATCCCCTGTGCGTAAt                                                                                                                                                                                                                                                               <  2:375004/42‑1 (MQ=255)                                                                                                                                                                                           tCAATTAAATCCCCGGTGCGTAATTTACCGATGGGGCCTCCGGCCAGCGCTTCTGGCCCCACATGGCCGATGCACGCGCCAGTAGAAACGCCCGAGAAACGTGCATCGGTGATTAACGAAACATGCt                                                                                                                                                        >  2:115474/1‑127 (MQ=255)                                                                                                                                                                                               ttagtaccccGTTGCGTAATTGCCCGATGGGGCCTCCGGCCAGCGCTTCTGGCCCCACATGGCCGATGCACGAGCCAGTAGAAACGCCCGAGAAACGTGCATCGGTGATTAACGAAACATGCTTACCGTATGACAGATGCTTCAGGGCACTGGTAACCTGGTAGGTTTCTTCCATCCCTGTACCTGAAGGTCCAACGCCAATAATGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGAt  <  2:71623/267‑1 (MQ=255)                                                                                                                                                                                               ttAAATCCCCGGTGCGTAATTTACCGATGGGGCCTCCGGCCAGCGCTTCTGGCCCCACATGGCCGATGCACGCGCCAGTAGAAACGCCCGAGAAACGTGCATCGGTGATTAACGAAACATGCTTAcc                                                                                                                                                    <  1:115478/127‑1 (MQ=255)                                                                                                                                                                                                   aTCCCCGGTGCGTAATTTACCGATGGGGCCTCCGGCCAGCGCTTCTGGc                                                                                                                                                                                                                              >  2:36727/1‑49 (MQ=255)                                                                                                                                                                                                       ccGGTGCGTAATTTACCGATGGGGCCTCCGGCCAGCGCTTCTGGCCCca                                                                                                                                                                                                                          <  1:36728/49‑1 (MQ=255)                                                                                                                                                                                                         |                                                                                                                                                                                                                                                                       CTCACGGCCTGAAGCATTGCCCATAGCCGGGTATCATCTGGCAATTCAGGATCGGGAAGTAAATCCTGATGGCTGGGTCTGGCATTTAATATTGCAGTTGCCTCCTCCTGTGAAGGTAATTGTTCATCGCTACGGGTTCCGAGGAAATTGACTTCGCCGTGAAGCTCGCGACAATCAATTTTAATTTCAATTAAATCCCCGGTGCGTAATTTACCGATGGGGCCTCCGGCCAGCGCTTCTGGCCCCACATGGCCGATGCACGCGCCAGTAGAAACGCCCGAGAAACGTGCATCGGTGATTAACGAAACATGCTTACCGTATGACAGATGCTTCAGGGCACTGGTAACCTGGTAGGTTTCTTCCATCCCTGTACCTGAAGGTCCAACGCCAATAATGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGAT  >  CP009273/4512023‑4512485

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑