Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,320,875	T→C	20.9%	I186T (ATT→ACT)	proP →	proline/glycine betaine transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,320,875	0	T	C	20.9%	31.6 / 3.8	19	I186T (ATT→ACT)	proP	proline/glycine betaine transporter
Reads supporting (aligned to +/- strand):  ref base T (7/8);  new base C (2/2);  total (9/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.66e-01

TTATGTCGATCAGTACGTTCTGTATTGGCTTAATACCGTCCTACGACACGATTGGTATTTGGGCACCGATTCTGCTGTTGATCTGTAAGATGGCACAAGGTTTCTCGGTCGGCGGTGAATATACCGGGGCGTCGATATTTGTTGCGGAATACTCCCCTGACCGTAAACGTGGCTTTATGGGCAGCTGGCTGGACTTCGGTTCTATTGCCGGGTTTGTGCTGGGTGCGGGCGTGGTGGTGTTAATTTCGACCATTGTCGGCGAAGCGAACTTCCTCGATTGGGGCTGGCGTATTCCGTTCTTTATCGCTCTGCCGTTAGGGATTATCGGGCTTTACCTGCGCCATGCGCTGGAAGAGACTCCGGCGTTCCAGCAGCATGTCGATAAACTGGAACAGGGCGACCGTGAAGGTTTGCAGGATGGCCCGAAAGTCTCGTTTAAAGAGATTGCCACTAAATACTGGCGCAGCCTGTTGACATGTAT‑TGGTCTGGTAATTGCCACCAACGTGAC  >  CP009273/4320632‑4321139                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                                          ttATGTCGATCAGTACGTTCTGTATTGGCTTAATACCGTCCTACGACACGATTGGTATTTGGGCACCGATTCTGCTGTTGATCTGTAAGANGGCACAAGGTTTCTCGGTCGGCGGTGAATATACCGGGGCGTCGATATTTGTTGCGGAATACTCCCCTGACCGTAAACGTGGCTTTATGGGCAGCTGGCTGGACTTCGGTTCTATTGCCGGGTTTGTGCTGGGTGCGGGCGTGGTGGTGTTAATTTCGACCATTGTCCGCGAAGCGAACTTCCt                                                                                                                                                                                                                                             <  1:297136/274‑1 (MQ=255)                                       tCCTACGACACGATTGGTATTTGGGCACCGATTCTGCTGTTGATCTGTAAGATGGCACAAGGTTTCTCGGTCGGCGGTGAATATACCGGGGCGTCGATATTTGTTGCGGAATACTCCCCTGACCGTAAACGTGGCTTTATGGGCAGCTGGCTGGACTTCGGTTCTATTGCCGGGTTTGTGCTGGGTGCGGGCGTGGTGGTGTTAATTTCGACCATTGTCGGCGAAGCGAACTTCCGTGATTGGGGCTGGCGTATTCTGGTCTTTATCGCTCTGcc                                                                                                                                                                                                      >  1:333599/1‑275 (MQ=255)                                                                                              cacaAGGTTTCTCGGTCGGCGGTGAATATACCGGGGCGTCGATATTTGTTGCGGAATACTCCCCTGACCGTAAACGTGGCTTTATGGGCAGCTGGCTGGACTTCGGTTCTATTGCCGGGTTTGTGCTGGGTGCGGGCGTGGTGGTGTTAACTTCGACCATTGTCGGCGAAGCGAACTTCCTCGATTGGGGCTGGCGTAGTACGTTCTTTATCGCTCTGCCGTTAGTGATTATCGGGCTATACTTGCGCCATGCGCTGGAGAAGACACCGGCggta                                                                                                                                               >  1:108199/1‑272 (MQ=255)                                                                                                         tcggttggCGGTGAATATACCGGGGCGTCGATATTTGTTGCGGAATCTTCCCCTGACCGTAAACGTGGCTTTATGGGCAGCTGGCTGGACTTCGGTTCTATTGCCGGGTTTGTGCTGGGTGCGGGCGTGGTGGTGTTAATTTCGACCATTGTCGGCGAAGCGAACTTCCTCGATTGGGGCTGGCGTATTCCGTTCTTTATCGCTCTGCCGTTAGGGATTATCGGGCTTTACCTGCGCCATGCGCTGGAAGAGACTCCGGCGTTGCAGCAGCATg                                                                                                                                     <  1:387391/274‑1 (MQ=255)                                                                                                                                                              tGACCGTAAACGTGGCTTTATGGGCAGCTGGCTGGACTTCGGTTCTATTGCCGGGTTTGTGCTGGGTGCGGGCGTGGTGGTGTTAATTTCGACCATTGTCGGCGAAGCGAACTTCCTCGATTGGGGCTGGCGTATTCCGTTCTTTAt                                                                                                                                                                                                               >  2:392230/1‑147 (MQ=255)                                                                                                                                                              tGACCGTAAACGTGGCTTTATGGGCAGCTGGCTGAACTTCGGTTCTATTGCCGGGTTTGTGCTGGGTGCGGGCGTGGTGGTGTTAATTTCGACCATTGTCGGCGAAGCGAACTTCCTCGATTGGGGCTGGCGTATTCCGTTCTTTATCGCTCTGCCGTTAGGGATTATCGAGCTTTACCTGCGNCATGCGCTNGAAGAGACTCCGGCGTTCCAGCAGCATGTCGATAAACTGGAACAGGGCGACCGTGAAGGTTTGCAGGATGGCCCGAAAGtct                                                                               >  1:267057/1‑275 (MQ=255)                                                                                                                                                                aCCGTAAACGTGGCTTTATGGGCAGCTGGCTGGACTTCGGTTCTATTGCCGGGTTTGTGCTGGGTGCGGGCGTGGTGGTGTTAATTTCGACCATTGTCGGCGAAGCGAACTTCCTCGATTGGGGCTGGCGTATTCCGTTCTTTATCGCTCTGCCGTTAGGGATTATCGGGCTTTACCTGCGCCATGCGCTGGAAGAGACTCCGGCGTTCCAGCAGCATGTCGATAAACTGGAACAGGGCGACCGTGAAGGTTTGCAGGATGGCCCGAAAGtcac                                                                              >  1:155668/1‑272 (MQ=255)                                                                                                                                                                  cGTAAACGTGGCTTTATGGGCAGCTGGCTGGACTTCGGTTCTATTGCCGGGTTTGTGCTGGGTGCGGGCGTGGTGGTGTTAATTTCGACCATTGTCGGCGAAGCGAACTTCCTCGATTGGGGCTGGCGTATTCCGTTCTTTATCGct                                                                                                                                                                                                           <  1:392236/147‑1 (MQ=255)                                                                                                                                                                       gacaggCTTTATGGGCAGCTGGCTGGACTTCGGTTCTATTGCCGGGTTTGTGCTGGGTGCGGGCGTGGTGGTGTTAATTTCGACCATCGTCGGCGAAGCGAACTTCCTCGATTGGGGCTGGCGTATTCCGTTCTTTATCGCTCTGCCGTTAGGGATTATCGGGCTTTACCTGCGCCATGCGCTGGAAGAGACTCCGGCGTTCCAGCAGCATGTCGATAAACTGGAACAGGGCGACCGTGAAGGTTTGCAGGATGGCCCGAAAGTCTCGTTTaaa                                                                       <  1:336373/270‑1 (MQ=255)                                                                                                                                                                                       aGCTGGCTGGACTTCGGTTCTATTGCCGGGTTTGTGCTGGGTGCGGGCGTGGTGGTGTTAATTTCGACCATCGTCGGCGAAGCGAACTTCCTCGATTGGGGCTGGCGTATTCCGTTCTTTATCGCTCTGCCGTTAGGGATTATCGGGCTTTACCTGCGCCATGCGCTGGCAGAGACTCCGGCGTTCCAGCAGCATGTCGATAACCTGGAACAGGGCGACCGTGAAGGGTTGCAGGATGGCCCGGAAGTCCCGTTTAAAGAAATTTcccccttttt                                                      >  2:336367/1‑267 (MQ=255)                                                                                                                                                                                             cggtaCTTGNGTTCTATTGCCGGGGTTGTGCTGGGTGCGGGCGTGGTTGTGTTAATTTCGACCATTGTCGGCGAAGCGAACTTCCTCGATTGGGGCTGGCGTATTCCGTTCTTTATCGCTCTGCCGTTAGGGATTATCGGGCTTTACCTGCGCCATGCGCTGGAAGAGACTCCGGCGTTCCAGCAGCATGTCGATAAACTGGAACAGGGCGACCGTGAAGGTTTGCAGGATGGCCCGAAAGTCTCGTTTAAAGAGATTGCCACTAAATACTGgcg                                                <  2:155663/271‑1 (MQ=255)                                                                                                                                                                                             agggATTTGGGTTTTTTTGCCTGGTTTGTGCTGGGTTCGGGGGTGGTGTTGTTAATTTCGACCATTGTCGGCGAAGCGAACTCCCTCGATTGGGGCTGGCGTATTCCGTTCTTTATCGCTCTGCCGTTAGGGATTAGCGGGCTTTCCCTGCGCCATGCGCTGGAAGAGACTCCGGCGTTCCAGCAGCATGTCGTTAAACTGGAACAGGGCGACCGTGAAGGTTTGCAGGATGGCCCGAAAGTCTCGTTTAAAGAGATTGCCACTAAATACTGgcg                                                <  2:333593/273‑1 (MQ=255)                                                                                                                                                                                              ttcaCTTCGGTTCGATTGCCGGGTTTGTCCTGGGGGCGGGCGTGGTGGTGTTAACGTCGACCTTTGTCTGCGAAGTGAACTTCCTCGATTTGTGCTGGCGTATGCCGTTCTTGATCGCTCTGCCGTTAGCGATTATCGGGCTTTACCTGCGCCATGCGCTGGAAGAGACTCCGGCGTTCCAGCAGCATGTCGATAAACTGGAACAGGGCGACCGTGAAGGTTTGCAGGATGGCCCGAAAGTCTCGTTTAAAGAGATTGCCACTAAATTCTGgcg                                                <  2:108195/271‑1 (MQ=255)                                                                                                                                                                                                       gTTCTATTGCCGGGTTTGTGCTGGGTGCGGGCGTGGTGGTGTTAACTTCGACCATTGTCGGCGAAGCGAACTTCCTCGATTGGGGCTGGCg                                                                                                                                                                                                                              >  1:148813/1‑91 (MQ=255)                                                                                                                                                                                                           tATTGCCGGGTTTGTGCTGGGTGCGGGCGTGGTGGTGTTAACTTCGACCATTGTCGGCGAAGCGAACTTCCTCGATTGGGGCTGGCGTAtt                                                                                                                                                                                                                          <  2:148808/91‑1 (MQ=255)                                                                                                                                                                                                                  gggTTTGTGCTGGGTGCGGGCGTGGTGGTGTTAATTTCGACCATTGTCGGCGAAGCGAACTTCCTCGATTGGGGCTGGCGTATTCCGTTCTTTATCGCTCTGCCGTTAGGGATTATCGGGCTTTACCTgcgc                                                                                                                                                                          >  1:68209/1‑132 (MQ=255)                                                                                                                                                                                                                      ttGTGCTGGGTGCGGGCGTGGTGGTGTTAATTTCGACCATTGTCGGCGAAGCGAACTTCCTCGATTGGGGCTGGCGTATTCCGTTCTTTATCGCTCTGCCGTTAGGGATTATCGGGCTTTACCTGCGCCATg                                                                                                                                                                      <  2:68206/132‑1 (MQ=255)                                                                                                                                                                                                                               gtgcgtgcGCGGTGGCGTTAATTTCGACCATTGTCGGCGAAGCGAACTTCCTCGATTGGGGCTGGCGTATTACGTCCTTTATCGCTCTGCCGTTCGGGATTATCTGGCGTCACCTGCGCCATGCGCTGGAAGAGACTCCGGCGTTCCAGCAGCATGTCGATAAACTGGAACAGGGCGACCGCTAAGTCTTCCAGGATGGCCCGAAAGTCTAGATTAAAGAGAAGACCCATAAATACTGGCGCAGCCAGATTACATTTATGTGGT‑TGGTCATTGcc             >  2:140402/1‑275 (MQ=255)                                                                                                                                                                                                                                          ggggtgTTAATTTCGACTATTGTCTGNGAAGCGAACTGTCGCGTTTGGGGCTGGCGTATTCCGTTCTTTATCGCTCTGCCGTTAGGGATTATCGGGCTTTACCTGCGCCATGCGCTGGAAGAGACTCCGGCGTGCCAGCAGCATGTCGATAAACTGGAACAGGGCGACCGTGAAGGTTTGCAGGATGGCCCGAAAGTCTCGTTTAAAGAGATTGCCACTAAATACTGGCGCAGCCTGTTGACATGTAT‑TGGTCTGGTAATTGCCACCAACGTGAc  <  2:267052/273‑1 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                                          TTATGTCGATCAGTACGTTCTGTATTGGCTTAATACCGTCCTACGACACGATTGGTATTTGGGCACCGATTCTGCTGTTGATCTGTAAGATGGCACAAGGTTTCTCGGTCGGCGGTGAATATACCGGGGCGTCGATATTTGTTGCGGAATACTCCCCTGACCGTAAACGTGGCTTTATGGGCAGCTGGCTGGACTTCGGTTCTATTGCCGGGTTTGTGCTGGGTGCGGGCGTGGTGGTGTTAATTTCGACCATTGTCGGCGAAGCGAACTTCCTCGATTGGGGCTGGCGTATTCCGTTCTTTATCGCTCTGCCGTTAGGGATTATCGGGCTTTACCTGCGCCATGCGCTGGAAGAGACTCCGGCGTTCCAGCAGCATGTCGATAAACTGGAACAGGGCGACCGTGAAGGTTTGCAGGATGGCCCGAAAGTCTCGTTTAAAGAGATTGCCACTAAATACTGGCGCAGCCTGTTGACATGTAT‑TGGTCTGGTAATTGCCACCAACGTGAC  >  CP009273/4320632‑4321139

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑