Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,116,551	G→A	21.0%	intergenic (‑91/+14)	cpsG ← / ← cpsB	phosphomannomutase/mannose‑1‑phosphate guanyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,116,551	0	G	A	21.0%	44.0 / 6.1	23	intergenic (‑91/+14)	cpsG/cpsB	phosphomannomutase/mannose‑1‑phosphate guanyltransferase
Reads supporting (aligned to +/- strand):  ref base G (9/9);  new base A (3/2);  total (12/11)
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

TCGCCAGCGCCAGTTTTAAGGTTTCGCTGGTGAGGCGGACATCACCGCCTAACACAATGGTTTTCGGTTTGAGAAATTCGCCATAGGCGCGACCAATGCGCCAGGCGATATCTTCATTCAGTTCTTCGCCTAATTTCCCGCGAATATCATAGGCTTTAAAGCAGGTTAATTTTTTCATATCGTTACCCTTTTTCAGGCAATAGTTGGCCCTGACCGAAGCGGCCAATTTTATTTTTGTCGTTATTTACACCGCGGTTTCGCATTCATTGCCTGATGCGACGTTTACACCCGTCCGTAGCGATCCGCGAAACGCACCACATCATCCTCTTCGAGATAAGAGCCGGAGCGCACTTCAATTAAATCGAGCGGAATTTTCCCCGGGTTTTCCAGGCAATGCGTCGCCCCCAGCGGAATATAAATGGACTCGTTTTCACCAAGCAGTTTGATATCACCATCAATGGTGACTTTTGCCGTTCCCGCGACAACCACCCAGTGTTCCGCGCGGTGATGGTGCATCTGTACCGAC  >  CP009273/2116283‑2116808                                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                                                  tCGCCAGCGCCAGTTTTAAGGTTTCGCTGGTGAGGCGGACATCACCGCCTAACACAATGGTTTTCGGTTTGAGAAATTCGCCATAGGCGCGACCAATGCGCCAGGCGATATCTTCATTCAGTTCTTCGCCTAATTTCCCCCGAATATCATAGNCTTTAAAGCAGGTTAATTTTTTCATATCGTTACCCTTTTTCAGGCAATAGTTGGCCCTGACCGAAGCGGCCAATTTTATTTTTGTCGTTATTTACACCGCGGTTTTGCATTCATTACCt                                                                                                                                                                                                                                                                >  1:476943/1‑272 (MQ=255)                                        cATCACCGGCTAACACCATGGTCTGCGGTTTGAGAAATTCGCCATAGGCGCGACCAATGCGCCAGGCGATAACGTAGAGCAGTTCTTAGTCTAATTTCCCGCGAATATCATAGGCTTAAAAGCAGGTTAATGTGTTCAGACCGTTACCCTGTATCAGGCAATAGTTCGCACTGACAGCAGCGGCCAATTTTATTGTTGTCGTAATTAACCCCGCGGATTCTCATTCATTGCCTGCTGCAACGTTTACACGCGTCCGAGGAGATCCGCGAAACGca                                                                                                                                                                                                                      >  2:189507/1‑275 (MQ=255)                                                               ttCGGTTTGAGAAATTCGCCATAGGCGCGACCAATGCGCCAGGCGATATCTTCATTCAGTTCTTCGCCTAATTTCCCGCGAATATCATAGGCTTTAAAGCAGGTTAATTTTTTCATATCGTTACCCTTTTTCAGGCAATAGTTGGCCCTGACCGAAGCGGCCAATTTTATTTTTGTCGTTATTTACACCGCGGTTTCGCATTCATTACCTGa                                                                                                                                                                                                                                                              >  1:117270/1‑212 (MQ=255)                                                                   gTTTGAGAAATTCGCCATAGGCGCGACCAATGCGCCAGGCGATATCTTCATTCAGTTCTTCGCCTAATTTCCCGCGAATATCATAGGCTTTAAAGCAGGTTAATTTTTTCATATCGTTACCCTTTTTCAGGCAATAGTTGGCCCTGACCGAAGCGGCCAATTTTATTTTTGTCGTTATTTACACCGCGGTTTCGCATTCATTACCTGATGCg                                                                                                                                                                                                                                                          <  2:117270/212‑1 (MQ=255)                                                                                            aCCAATGCGCCAGGCGATATCTTCATTCAGTTCTTCGCCTAATTTCCAGCGAGTATCATAGGCTTTAAAGCAGGTTAATTTTTTCATATCGTTACCCTTTTTCAGGCAATAGTTGGCCCTGACCGAAGCGGCCAATTTTATTTTTGTCGTTATTTACACCGCGGTTTCGCATTTATTGCATGATGCGACGTTTACACCCGTCCGTAGCGATCCGCGAAACGCACCACATCATCCTCTTCGAGATAAGAGCAGGAGCGCACTTAAATTCAATAGac                                                                                                                                                                  >  1:191507/1‑274 (MQ=255)                                                                                                                  tcattcaGTTCTTCGCCTAATTTCCCGCGAATATCATAGGCTTTAAAGCAGGTTAATTTTTTCATATCGTTACCCTTTTTCAGGCAATAGTTGGCCCTGACCGAAGCGGCCAATTTTATTTTTGTCGTTATTTACACCGCGGTTTCGCATTCATTGCCTGa                                                                                                                                                                                                                                                              >  2:527598/1‑161 (MQ=255)                                                                                                                      tcaGTTCTTCGCCTAATTTCCCGCGAATATCATAGGCTTTAAAGCAGGTTAATTTTTTCATATCGTTACCCTTTTTCAGGCAATAGTTGGCCCTGACCGAAGCGGCCAATTTTATTTTTGTCGTTATTTACACCGCGGTTTCGCATTCATTGCCTGATGCg                                                                                                                                                                                                                                                          <  1:527606/161‑1 (MQ=255)                                                                                                                                                             tAAAGCAGGTTAATTTTTTCATATCGTTACCCTTTTTCAGGCAATAGTTGGCCCTGACCGAAGCGGCCAATTTTATTTTTGTCGTTATTTACACCGCGGTTTCGCATTCATTGCCTGATGCGACGTTTACACCCGTCCGTAGCGATCCGCGAAACGCACCACATCATCCTCTTCGAGATAAGAGCCGGAGCGCACTTCAATTAAATCGAGCGGAATTTTCCCCGGGTTTTCCAGGCAATGAGTCGCCCCCAGCGGAATATAAATGGACTCGtttt                                                                                                 >  1:354767/1‑275 (MQ=255)                                                                                                                                                                           tttttCATATCGTTAACCTTTTTCAGGCAATAGTTGGCCCTGACCGAAGCGGCCAATTTTATTTTTGTCGTTATTTACACCGCGGTTTCGCATTCATTGCCTGATGCGACGTTTACACCCGTCCGTAGCGATCCGCGAAACGCACCACATCATCCTCTTCGAGATAAGAGCCGGAGCGCACTTCAATTAAATCGAGCGGAATTTTCCCCGGGTTTTCCAGGCAATGCGTCGCCCCCAGCGGAATATAAATGGACTCGTTTTCACCAAGCAGTTTg                                                                                   <  1:148139/275‑1 (MQ=255)                                                                                                                                                                                                       taTAGTTGGCCCTGACCGAAGCGGCCAATTTTATTTTTGTCGTTATTTACACCGCGGTTTCTCATTCATTGCCTGATGCGACGTTTACACCCGTCCGTAGCGATCAGCGAAACGCACCACATCATCCTCTTCGATATAAGAGCCGGAGCGCACTTCAATTAAATCGAGCGGAATTTTCCCCGGGTTTTCCAGGCAATGCGTCGCCCCCAGCGGAATATAAATGGACTCGTTTTCACCAAGCAGTTTGATATCACCATCAATGGTGACTTTTGCCg                                                       <  1:189508/274‑1 (MQ=255)                                                                                                                                                                                                                     aCCGAAGCGGCCAATTTTATTTTTGTCGGTATTTACACCGCGGTTTCGCATTCATTGCCTGATGCGACGTTTACACCCGTCCGTAGCGATCCGCGAAACGCACCAcat                                                                                                                                                                                                                >  1:432991/1‑108 (MQ=255)                                                                                                                                                                                                                         aaGCGGCCAATTTTATTTTTGTCGTTATTTACACCGCGGTTTCGCATTCATTGCCTGATGCGACGTTTACACCCGTCCGTAGCGATCCGCGAAACGCACCACatcatc                                                                                                                                                                                                            <  2:432984/108‑1 (MQ=255)                                                                                                                                                                                                                                        tttttGTCGTTATTTACACCGCGGTTTCGCATTCATTGCCTGATGCGACGTTTACACCCGTCCGTAGCGATCCGCGAAACGCACCACATCATCCTCTTCGAGATAAGAGCCGGAgc                                                                                                                                                                                     >  1:288196/1‑116 (MQ=255)                                                                                                                                                                                                                                            tGTCGTTATTTACACCGCGGTTTCGCATTCATTGCCTGATGCGACGTTTACACCCGTCCGTAGCGATCCGCGAAACGCACCACATCATCCTCTTCGAGATAAGAGCCGGAGCGCAc                                                                                                                                                                                 <  2:288193/116‑1 (MQ=255)                                                                                                                                                                                                                                                   aTTTACACCGCGGTTTCGCATTCATTGCCTGATGCGACGTTTACACCCGTCCGTAGCGATCCGCGAAACGCACCACATCATCCTCTTCGAGATAAGAGCCGGAGCGCACTTCAATTAAATCGAGCGGAATTTTCCCCGGGTTTTCCa                                                                                                                                           >  1:502444/1‑147 (MQ=255)                                                                                                                                                                                                                                                       acacCGCGGTTTCGCATTCATTGCCTGATGCGACGTTTACACCCGTCCGTAGCGATCCGCGAAACGCACCACATCATCCTCTTCGAGATAAGAGCCGGAGCGCACTTCAATTAAATCGAGCGGAATTTTCCCCGGGTTTTCCAGGCa                                                                                                                                       <  2:502437/147‑1 (MQ=255)                                                                                                                                                                                                                                                             cgGTTTCGCATTCATTGCCTGATGCGACGTTTACACCCGTCCGTAGCGATCCGCGAAACGCACCACATCATCCTCTTCGAGATAAGAGCCGGAgc                                                                                                                                                                                     >  1:18080/1‑95 (MQ=255)                                                                                                                                                                                                                                                             cgGTTTCGCATTCATTACCTGATGCGACGTTTACACCCGTCCGTAGCGATCCGCGAAACGCACCACATCATCCTCTTCGAGATAaga                                                                                                                                                                                             >  1:488629/1‑87 (MQ=255)                                                                                                                                                                                                                                                             cgGTTGCGCATTCATTGCCGGAGTCGCCGCTGACACCCGTCCGGTGTGATCCGCGAAACGCACCACATCATCCGCTTTGAGAGAATGGCCGGAGCGCACTTCAATTAAATCGAGCGGAATTTTCCCCGGGTTTGCCAGGCAATTCGTCGCCCTCTGCGGAATAGAAATGGACTCGTTTTCACCAAGCAGTTTGATATCACCATCATTGGTGTCTTTGGCCGATCCCGCGACAATCACCCAGTGTTCCTCGCGGTGATTGTGCATCTGTACCGAc  <  2:191505/274‑1 (MQ=255)                                                                                                                                                                                                                                                                 ttCGCATTCATTGCCTGATGCGACGTTTACACCCGTCCGTAGCGATCCGCGAAACGCACCACATCATCCTCTTCGAGATAAGAGCCGGAGCGCAc                                                                                                                                                                                 <  2:18080/95‑1 (MQ=255)                                                                                                                                                                                                                                                                 ttCGCATTCATTACCTGATGCGACGTTTACACCCGACCGTAGCGATCCGCGAAACGCACCACATCATCCTCTTCGAGATAAGAGCCg                                                                                                                                                                                         <  2:488622/87‑1 (MQ=255)                                                                                                                                                                                                                                                                     cattcattGCCTGATGCGACGTTTACACCCGTCCGTAGCGATCCGCGAAACGCACCACATCATCCTCTTCGAGATAAGAGCCGGAgc                                                                                                                                                                                     >  2:542152/1‑87 (MQ=255)                                                                                                                                                                                                                                                                         cattGCCTGATGCGACGTTTACACCCGTCCGTAGCGATCCGCGAAACGCACCACATCATCCTCTTCGAGATAAGAGCCGGAGCGCAc                                                                                                                                                                                 <  1:542160/87‑1 (MQ=255)                                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                                                  TCGCCAGCGCCAGTTTTAAGGTTTCGCTGGTGAGGCGGACATCACCGCCTAACACAATGGTTTTCGGTTTGAGAAATTCGCCATAGGCGCGACCAATGCGCCAGGCGATATCTTCATTCAGTTCTTCGCCTAATTTCCCGCGAATATCATAGGCTTTAAAGCAGGTTAATTTTTTCATATCGTTACCCTTTTTCAGGCAATAGTTGGCCCTGACCGAAGCGGCCAATTTTATTTTTGTCGTTATTTACACCGCGGTTTCGCATTCATTGCCTGATGCGACGTTTACACCCGTCCGTAGCGATCCGCGAAACGCACCACATCATCCTCTTCGAGATAAGAGCCGGAGCGCACTTCAATTAAATCGAGCGGAATTTTCCCCGGGTTTTCCAGGCAATGCGTCGCCCCCAGCGGAATATAAATGGACTCGTTTTCACCAAGCAGTTTGATATCACCATCAATGGTGACTTTTGCCGTTCCCGCGACAACCACCCAGTGTTCCGCGCGGTGATGGTGCATCTGTACCGAC  >  CP009273/2116283‑2116808

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑