Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AE015451	3,319,193	G→A	16.7%	intergenic (‑157/+35)	treSA ← / ← PP_2919	trehalose synthase A/Transcriptional regulator, LysR family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451	3,319,193	0	G	A	16.7%	65.9 / 7.7	30	intergenic (‑157/+35)	treSA/PP_2919	trehalose synthase A/Transcriptional regulator, LysR family
Reads supporting (aligned to +/- strand):  ref base G (9/16);  new base A (2/3);  total (11/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.87e-01

CGGGCTGGGTCATTTCGCGTCCTCTTTGCGTGTCGGCACCGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAGGCCAACCCCACGCTCATCGGCGTGACCGGGTCGCTGATGGTCACCGTCTCGATGCGCTTGCCCTCCAGCGACCACGGCCGGTGCACCAGGTCCGA  >  AE015451/3319024‑3319422                                                                                                                                                                           |                                                                                                                                                                                                                                      cGGGCTGGGTCATTTCGCGTCCTCTTTGCGTGTCGGCACCGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGCCCCTGTGGGAGCGGGCGCGCCCGCGGAGAGGCCggg                                                                                                                                                                                                                    >  1:391590/1‑189 (MQ=255)  gggCTGGGTCATTTCGCGTCCTCTTTGCGTGTCGGCACCGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGTGCAGCGCAAATCTTCAGCGGTATG‑TCCGCCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCa                                                                                                                                                                     >  1:950321/1‑235 (MQ=25)  gggCTGGGTCATTTCGCGTCCTCTTTGCGTGTCGGCACCGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGGGCCa                                                                                                                                                                     >  1:244336/1‑235 (MQ=255)                  cgTCCTCTTTGCGTGTCGGCACCGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCAAGCCCGCGa                                                                                                                                                                                                                              <  1:570319/162‑1 (MQ=255)                       tctTTGCGTGTCGGCACCGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGcat                                                                                                                                                            <  1:668109/223‑1 (MQ=255)                         tttGCGTGTCGGCACCGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGa                                                                                                                                                                                                                              >  1:884297/1‑155 (MQ=255)                                      aCCGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAActgctg                                                                                                                                                                             >  2:367977/1‑191 (MQ=255)                                        cGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAgc                                                                                                                                                                                                <  1:598883/170‑1 (MQ=255)                                              aGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGcc                                                                                                                                                                                        <  2:286842/172‑1 (MQ=255)                                                        ggCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCAAGccc                                                                                                                                                                                                                                  <  1:549304/120‑1 (MQ=255)                                                        ggCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCAAGccc                                                                                                                                                                                                                                  >  2:549301/1‑120 (MQ=255)                                                                           tgtgCTCAAGATGGGTGTTGGTTGCTTCGCGGGCTTGCGCGCTGCCACAGGCGGA‑CATACCGCTGAAGATTGGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAg                                                                                                                                                                    <  1:344258/160‑1 (MQ=255)                                                                                  aaGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGCACCGGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCgg                                                                                                                                                                                           <  2:115971/133‑1 (MQ=255)                                                                                                 ttcttcGCGGGCTTGCCCGCTCCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGGGc                                                                                                                                                                       >  2:192336/1‑138 (MQ=255)                                                                                                     tcGCGGGCTTGCCCGCTCCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGAACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAGGCCAACCCCACGc                                                                                    <  1:852464/217‑1 (MQ=255)                                                                                                           gCTTGCCCGCTCCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAGGCCAACCCCACGCTCATCGGCGTGACCGGGTCGCTGAt                                                           <  1:673802/236‑1 (MQ=255)                                                                                                                cccGCTGCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCTAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAGGCCAACCCCACGCTCATCGGCGTGACCGGGTCGCTGATGGTc                                                       <  1:603130/235‑1 (MQ=255)                                                                                                                 ccGCTCCCACAGGCGCA‑CATACAGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGcc                                                                                                                                                                                                                       >  1:380975/1‑74 (MQ=255)                                                                                                                           aGGCGGA‑CATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCAAGCCcgc                                                                                                                                                                                                                                <  2:91872/55‑1 (MQ=25)                                                                                                                                     tACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTg                                                                                                                                              >  2:1035686/1‑128 (MQ=255)                                                                                                                                     tACCGCTGAAGAGTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCgg                                                                                                                                                                                                                     <  2:304531/57‑1 (MQ=255)                                                                                                                                      aCCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAGGCCAACCCCACGCTCATCGGCGTGACCGGGTCGCTGATGGTCACCGTCTCGATGCGCTTGCCCt                                 <  1:337106/236‑1 (MQ=255)                                                                                                                                               gATTTGCGCTGCACCTGTGGGAGCGGGCACGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAGGCCAACCCCACGCTCATCGGCGTGACCGGGTCGCTGATGGTCACCGTCTCGATGCGCt                                       >  2:720775/1‑221 (MQ=255)                                                                                                                                                          cACCTGTGGGCGCGGGCGCGCCcgc                                                                                                                                                                                                                                <  2:320310/25‑1 (MQ=255)                                                                                                                                                               gtgGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGaa                                                                                                                                                                  <  2:692955/82‑1 (MQ=255)                                                                                                                                                                ggggAGGGGGCGGGCCCGCGAAGAGGCCGGGCCTGCaaa                                                                                                                                                                                                            <  2:184076/38‑1 (MQ=17)                                                                                                                                                                   gggCGGGCGCGCACGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGc                                                                                                                                      <  1:2296/104‑1 (MQ=255)                                                                                                                                                                      cGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAGGCCAACCCCACGCTCATCGGCGTGACCGGGTCGCTGATGGTCACCGTCTCGATGCGCTTGCCCTCCAGCGACCACgg                    <  1:81330/217‑1 (MQ=255)                                                                                                                                                                      cGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAGGCCAACCCCACGCTCATCGGCGTGACCGGGTCGCTGATGGTCACCGTCTCGATGCGCTTGCCCTCCAGCGACCACGGCCGGTGCACCAGGTCCGa  <  1:367980/235‑1 (MQ=255)                                                                                                                                                                       gggCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAGGCCAACCCCACGCTCATCGGCGTGACCGGGTCGCTGATGGTCACCGTCTCGATGCGCTTGCCCTCCAGCGACCACGGCCg                 >  2:467393/1‑219 (MQ=255)                                                                                                                                                                           |                                                                                                                                                                                                                                      CGGGCTGGGTCATTTCGCGTCCTCTTTGCGTGTCGGCACCGGCTCAGGTTATGACGGCGCTGCGGCCTGAACGTTCGGCTCAAGATGGGTGTTGGTTTCTTCGCGGGCTTGCCCGCTCCCACAGGCGGA‑CATACCGCTGAAGATTTGCGCTGCACCTGTGGGAGCGGGCGCGCCCGCGAAGAGGCCGGGCCTGCAAAGGCAGGATCAGCGCCGGGCCGACAACTGCTGCGGTGCCAGAAACGCATCATGGAAGTAATTGCGCACCGCCTGCATCGCCGGGCTGAATGCCCGTTCCCGGTGCCAGGCCAACCCCACGCTCATCGGCGTGACCGGGTCGCTGATGGTCACCGTCTCGATGCGCTTGCCCTCCAGCGACCACGGCCGGTGCACCAGGTCCGA  >  AE015451/3319024‑3319422

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑