Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,448,179	G→A	12.9%	G193G (GGC→GGT)	gspA ←	general secretory pathway component, cryptic

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,448,179	0	G	A	12.9%	77.7 / 3.4	31	G193G (GGC→GGT)	gspA	general secretory pathway component, cryptic
Reads supporting (aligned to +/- strand):  ref base G (13/14);  new base A (2/2);  total (15/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.58e-01

CACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGTAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGACCTTCAAGGATGCTTGCCTTAAGTTCGTGCTCCGTCAGACGTCCTATCGAGACAAGTTCAATGCCCTGTTTTTTAAAATCACGTTCGACTTTTCGATCGGGTCTGCCGATCAGCAAAAATTGACCGTCAGGAATAAGAGATATTGCGCGTTGGAG  >  CP009273/3448001‑3448406                                                                                                                                                                                   |                                                                                                                                                                                                                                    cacaGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGTAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAgg                                                                                                                                                                                     >  2:527980/1‑227 (MQ=255)     ggTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGTAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGAt                                                                                                                                                                                 <  1:527991/227‑1 (MQ=255)              gATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGTAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCAcc                                                                                                                                                                                                                                   >  1:305091/1‑168 (MQ=255)                  aTGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGTAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCACCCCGa                                                                                                                                                                                                                               <  2:305086/168‑1 (MQ=255)                                     cGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGTAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGACCTTCAAGGATGCTTGCCTTAAGTTCGTGCTCCGTCAGACGTCCTATCGAGACAAGTTCa                                                                                                 >  2:651835/1‑275 (MQ=255)                                                      cGGGGGCGGTTATCACCCAATATGCGGTAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACataat                                                                                                                                                                                                                         >  2:35428/1‑138 (MQ=255)                                                         gggCGGTTATCACCCAATATGCGGTAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCTGGTTGGTCAATATTCTTACCTTCAAGGATGCTTGCCTTAAGTTCGTGCTCCTTCAGACGTCCTATCGAGACAAGTTCAAGGCCCTGTTTTTTataa                                                                               >  2:624340/1‑273 (MQ=255)                                                          ggCGGTTATCACCCAATATGCGGTAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAg                                                                                                                                                                                                                     <  1:35428/138‑1 (MQ=255)                                                                     cccAATATGCGGTAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCAcc                                                                                                                                                                                                                                   >  1:425747/1‑113 (MQ=255)                                                                         atatGCGGTAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCACCCCGa                                                                                                                                                                                                                               <  2:425741/113‑1 (MQ=255)                                                                           atGCGGTAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGTCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGACCTTCAAGGATGCTTGCCTTAAGTTCGTGCTCCGTCAGACGTCCTATCGAGACAAGTTCAATGCCCTGTTTTTTAAAATCACGTTCTACTTTTCGAt                                                            <  1:651846/274‑1 (MQ=255)                                                                                gTAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGACCTTCAAGGATGCTTGCCTTAAGTTCg                                                                                                                                  >  1:499978/1‑199 (MQ=255)                                                                                    aTCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGc                                                                                                                                                                                                                                    <  1:94236/97‑1 (MQ=255)                                                                                    aTCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGACCTTCAAGGATGCTTGCCTTAAGTTCGTGCt                                                                                                                              <  2:499969/199‑1 (MQ=255)                                                                                                       cTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTg                                                                                                                                                                          >  1:183656/1‑136 (MQ=255)                                                                                                           gAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCa                                                                                                                                                                      <  2:183652/136‑1 (MQ=255)                                                                                                            aaaaCGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGACCTTCAAGGATGCTTGCCTTAAGTTCGTGCTCCGTCAGACGTCCTATCGAGACAAGTTCAATGCCCTGTTTTTTAAAATCACGTTCGACTTTTCGATCGGGTCTTCCGATCAGCAAAAATTGACCGTCAg                           >  2:592761/1‑274 (MQ=255)                                                                                                                     gTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCACGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGACCTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGACCTTCAAGGATGCTTGCCTTAAGTTCGTGCTCCGTAAGACGTCCTATCGAGACAAGTTAAATGCCCTGTTTTTTAAAATCACGTTCGCAtttt                                                                >  2:584404/1‑228 (MQ=255)                                                                                                                         gCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCCTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGACCTTCAAGGATGCTTGCCTTAAGTTCGTGCTCCGTCAGACGTCCTATCGAGACAAGTTCAATGCCCTGTTTTTTAAAATCACGTTCGACTTTTCGAt                                                            <  1:584415/228‑1 (MQ=255)                                                                                                                                  gCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGATCTTCAAGGATGCTTGCCTTAAGTTCGTGCTCCGTCAGACGTCCTATCGAGACAAGTTCAATGCCCTGTTTTTTAAAATCACGTTCGACTTTTCGATCGGGTCTGCCGATCAGCAAAAATTGACCGTCAGGAATAAGAGATATTGCGCGTTgg    <  1:592772/275‑1 (MQ=255)                                                                                                                                     gttataaGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAAGTCTGGCGGTTAAAAGGAGATCTGGTTGGTCAATATTCTGACCATCAAGGATGCTTGCCTTAAGTTCGTGCTCCGTCAGACGTCCTATCGAGACAAGTTCAATGCCCTGTTTTTTAAAATCACGTTCGACTTTTCGATCGGGTCTGCCGATCAGCAAAAATTGACCGTCAGGAATAAGAGATATTGCGCGTTGgag  <  1:624351/271‑1 (MQ=255)                                                                                                                                             cGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGcc                                                                                                                                                                                                                                   >  2:176652/1‑41 (MQ=255)                                                                                                                                                aTTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGAt                                                                                                                                                                                 >  2:580265/1‑88 (MQ=255)                                                                                                                                                 ttGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGa                                                                                                                                                                                                                               <  1:176656/41‑1 (MQ=255)                                                                                                                                                    tttCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCggg                                                                                                                                                                             <  1:580276/88‑1 (MQ=255)                                                                                                                                                       cGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAata                                                                                                                                                                   >  1:215957/1‑95 (MQ=255)                                                                                                                                                       cGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTc                                                                                                                                                                >  2:612090/1‑98 (MQ=255)                                                                                                                                                           ggCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCt                                                                                                                                                               <  2:215953/95‑1 (MQ=255)                                                                                                                                                           ggCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGAc                                                                                                                                                            <  1:612101/98‑1 (MQ=255)                                                                                                                                                                              cGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAAct                                                                                                                                                                                                    >  1:296343/1‑39 (MQ=255)                                                                                                                                                                                  cGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTgg                                                                                                                                                                                                <  2:296338/39‑1 (MQ=255)                                                                                                                                                                                   |                                                                                                                                                                                                                                    CACAGGTAAGAGCGATAATGGTTCCACTCATCACCACGGCAAGCTGCATTTTCCGGGGGCGGTTATCACCCAATATGCGGTAAATCATTCGCCATTGTTTTGCTGTGAAAACGCTGGTCTGCTCGGCTTGCTGTAATAAGCGAATTGTTTCGCCGGCAAGCGCCAGCTTTCTGCGATCGCCCCGACATAATAAAGCTATCCGTTTCAGAACTCTGGCGGTTAAAAGGAGATCGGGTTGGTCAATATTCTGACCTTCAAGGATGCTTGCCTTAAGTTCGTGCTCCGTCAGACGTCCTATCGAGACAAGTTCAATGCCCTGTTTTTTAAAATCACGTTCGACTTTTCGATCGGGTCTGCCGATCAGCAAAAATTGACCGTCAGGAATAAGAGATATTGCGCGTTGGAG  >  CP009273/3448001‑3448406

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑