Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP006881	3,476,688	G→T	27.1%	S20Y (TCT→TAT)	U712_17855 ←	putative undecaprenyl‑phosphate galactose phosphotransferase‑like Protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	3,476,688	0	G	T	27.1%	38.1 / 3.3	47	S20Y (TCT→TAT)	U712_17855	putative undecaprenyl‑phosphate galactose phosphotransferase‑like Protein
Reads supporting (aligned to +/- strand):  ref base G (20/11);  new base T (3/9);  total (25/22)
Fisher's exact test for biased strand distribution p-value = 3.87e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTCTCCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAGACGGATGTTAATTG  >  CP006881/3476555‑3476821                                                                                                                                      |                                                                                                                                      cGTCTCCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGt                                                                                                                                  <  4:180939/139‑1 (MQ=255)     tcCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATTTAAAAGAATGTAttt                                                                                                                              >  6:388225/1‑139 (MQ=255)              aTCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTGGATTCAGATAAAGGAAAAGAATGTATTTTTTGAAcgg                                                                                                                     >  3:113075/1‑137 (MQ=255)                 aaaaTTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTGGTTTCTGATAATGTAAAAAAAAGTATTTGTTGATCagag                                                                                                                   >  2:334664/1‑138 (MQ=255)                        aaaaTACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCATATAAAGTAAAATAAATTATTTTTTGAACTGAGaaataacc                                                                                                           >  4:80219/1‑133 (MQ=255)                                  aaTCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCGTTTAAGCTAATTTAAAAAAATGTATTTTTTGTACTGATGATTCACGAAGCACAtt                                                                                                  >  1:405397/1‑138 (MQ=255)                                       ttGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTCACGACTCACATTCATGCt                                                                                            <  7:372579/139‑1 (MQ=255)                                       ttGGCAGCGCAATCGCAAATCCAATGAGCGCAAACAAAATATCCATTACGCGCTTTATTCCAAAATAACGCGCCGTCTTTTCATATAATTAAAAAGAATGTATTTGTTCAACTGACAATCCACGACTCACATTCATGCt                                                                                            <  4:135001/139‑1 (MQ=255)                                       agaccggcgaAATCGCAAATCAATTGACCGCAAACAAAAAATCAATTACGCGCTTTATTACAAAATACGGCGCCTTATTTTCATAAAATTTAAAAGATTTTTTTTGTGTAACTTATAATGCACGACTCACATTCATGCt                                                                                            <  2:44864/133‑1 (MQ=255)                                            aGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATTTAAAAGAATGTATTTGTTGTACTGAGAATTAACGAATCACATTCATGCtttta                                                                                        >  4:359220/1‑137 (MQ=255)                                              cgcAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTTTTGAACTGAGAATTAACGACTCACATTCATGCTTTTctct                                                                                     >  8:71287/1‑139 (MQ=255)                                              cgcAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGAGTATGTAAAAGAATGTTTTTGTTGAACTGAGAATTGACGACTCACATTCATGCTTTTatct                                                                                     >  5:412535/1‑139 (MQ=255)                                                cAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTGGTTTGAGATATTGTAAAAGAATTTATTTTTTGAACTGAGAATTCAAGCAGCACATTAATTCttttatatgg                                                                                   >  5:50135/1‑133 (MQ=255)                                                cAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTCACGACTCACATTCATGCTTTTATCTGc                                                                                   >  2:64680/1‑139 (MQ=255)                                                 actCGCAAATCCTATGCGAGAAAACAAAATTTCAATTACGAGTTTTTTAGAAAAATAACAAGCGTTCTTTTCTTATAATTTAAATTAATTTTTTTTTTTAACTTTTAATCCACGACTCACATTCATGCTTTTCTCTGca                                                                                  <  8:172592/137‑1 (MQ=255)                                                 aaccGCCAACCAAATGAGCGAAAACCAAATATCCATACCGCGCTTAATTGCCAAATAACCAGCCTTCTTTACAGAAAATTTAAAATATTTTATTTGTTCAACTTACAATCCACGACTCACATTCATGCTTTTCTCTGca                                                                                  <  3:31736/136‑1 (MQ=255)                                                   tCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTGACGACTCACATTCATGCTTTTCTCTGcccg                                                                                >  1:8859/1‑136 (MQ=255)                                                     gCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCATAAAATGTAAAACAATGTATTTGTTGAACTGAGAATCCACGACTCACATTCATGCTTTTCTCTGcactca                                                                              <  3:195095/139‑1 (MQ=255)                                                        aatccaatGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTTTTGAACTTAGAATTCACGACTCACATACATGCTTTTATCTGcacctgtc                                                                            >  1:44864/1‑133 (MQ=255)                                                        aatccaatGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCGTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGATCATTCACGACTCACATTCATGCTTTTATCTGcactcact                                                                            >  3:51279/1‑138 (MQ=255)                                                             attgcgcgaAAACAAAAAAGCTATAACGCGATTTATTCCCAAAAAACGAGACCTCTTTTAATAAAATTTAAAATAATTAATTTTTTGTACTCCGAATGCACGACTCACATTCATGCTTTTCTCTGCACTCACTGacaca                                                                      <  4:429041/134‑1 (MQ=255)                                                               tGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTGGTTTTAGATAATTTAAAAGAAATTATTTTTTGAAATGAGTATTAAAGCCTCACATTCAAGGTTTTGTGTGCGCTCACGGacacacc                                                                    >  1:225833/1‑138 (MQ=255)                                                               tGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTTAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGacacaca                                                                    >  7:15729/1‑139 (MQ=255)                                                                 acccaaaaCAAAAAATCAATTCCGCGTTTAATTCCAAAATACCGCGCCTTATTTTCATATAATTTAAAATATTTTATTTGTTTAAATTACAATCCACGACTCACATTCATGCTTTTCTCTGCACTCACTGacacacac                                                                   <  5:133840/133‑1 (MQ=255)                                                                   cgcAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTGTGTTAACATAATGTAAAATAATGTATTTTTTTAACTTAGAAATAAAGACACACAATAATGCTTTTTTCTGCACTCACTGCCCCCCAcccc                                                                >  6:268605/1‑137 (MQ=255)                                                                       aaCCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATTTAAAAGAATGTATTTGTTGAACTGAGTATTCACGACTCACATTCATGCGTTTCTCTGCGCTCGCTGACACCCACCTCAc                                                              >  3:53219/1‑137 (MQ=255)                                                                                  cATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATTTAAAATAATGTATTTGTTGAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTggg                                                  <  7:69975/138‑1 (MQ=255)                                                                                   aTTACGCTATTTATTGCAAAATAAGGCGCATTATTTTCATATAATTAAAAATAATTTTTTTTTTAAACTTATAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGAt                                                <  3:80219/139‑1 (MQ=255)                                                                                    ttccgcgCTTTATAGCCAAATCACGAGCCGTCTTTTCATATAATTAAAACTAATTTATTTGTTCAACTTACAATCCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATg                                               <  4:265771/136‑1 (MQ=255)                                                                                    ttACGCGCTTTATTGCCAAATAACGAGCCGTGTTTTCAGATAATGTTAAAGAATGTATTTGTTGAACTGAGAATTCACGACTCACATTCATTCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATg                                               >  3:168250/1‑139 (MQ=255)                                                                                    ttACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTCACGACTCCCATTCATGCTTTTCTCTGCACTCACTGACACACCCCTCACGATTTGTTTGGGATg                                               >  7:247441/1‑139 (MQ=255)                                                                                         cgcTTTATTCCAAAAAAACGCGCCTTTTTTTCATATAATGAAAAAGAATGTTTTTGTTGAACTTAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTatg                                          <  6:388086/139‑1 (MQ=255)                                                                                         cgcTTTATATCCAAATAACGAGACTTTTTTTCAGATAATTTAAAACTATTTATTTGTTGAACGGATAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTatg                                          <  5:111092/139‑1 (MQ=255)                                                                                          tatttATTGCAAAAAAACGACCGTTTTTTTAAGATATTTAAAAAGATTTTTTTTGTTCAACTGATAATCCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTatga                                         <  6:50135/137‑1 (MQ=255)                                                                                          gatttATTGAAAATTAACGAGCTGTATTTACTTATATTTAAAAATAATGTATTTGTTGAAATTACAATACACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTatga                                         <  5:362829/137‑1 (MQ=255)                                                                                               atcccaaaaTAACCCGCCTTATTTACAGAAAATTAAAAAGATTTTTTTTTTTCAACTGAGAAACCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGAc                                     <  1:334664/132‑1 (MQ=255)                                                                                               aTTGCCAAATACCGAGCCGTCTTTTCATATAATTTAAAAGAATTTATTTGTTCAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGAc                                     <  5:217909/138‑1 (MQ=255)                                                                                                 tGCCAAATAACGAGCCGTCGTTTGAGATTATTTAAAATAATGTATTTGTTTAACTGATAATTAACGACTCACATTGATGAGTTTCTCGGCACAAACTGACACACACCGACCGCTTTGTTTGGGGTGTTATTATGACATa                                  >  6:5126/1‑139 (MQ=255)                                                                                                   ccAAATAACGAGCCGTGTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTCCCGACTCACATTGCTGCTTTTCTCTGCACTCACTGACACCCACCGCCCGATTTGGTTGGGATGGTTTGATGACCTATg                                >  7:124305/1‑139 (MQ=255)                                                                                                      aaacaCGCGCCGTCTTTTCATAAACTGAAAAAGATTGTATTTGTTGAACTGAGACATCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCca                             <  8:247441/135‑1 (MQ=255)                                                                                                                cGTCTTTCCATATAATTAAAAAGAATGTATTTGTTCAACTTCCAACCCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAg                   <  4:53219/139‑1 (MQ=255)                                                                                                                  tcgtttAAGATAATGTAAAAGAATGTATTTGTTTTAATTAGAATTAACGCCTCACAATAATGAGTTTCTCTGCACTCCCGGACACACACCAACCGCATTGTTTTGGATGTTATTATTACCTATAGAACTCAGTTTATCa                 >  4:376042/4‑139 (MQ=255)                                                                                                                  tCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCGCACGATTTGTTTGGGTTGTTATGATGACCTATGCCAGTCAGTTTAg                   >  2:37361/1‑137 (MQ=255)                                                                                                                              ttGTAAAAGATTGTTTTTTTTGAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAGACGGATGTTaa     <  4:51279/138‑1 (MQ=255)                                                                                                                              aTGTAAAAGAATGTATTTGTTGAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAGACGGATGTTaa     >  7:267596/1‑139 (MQ=255)                                                                                                                              aTGTAAAAGAATGTATTTGTTGAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGAAGACGGATGTTaa     >  3:118274/1‑139 (MQ=255)                                                                                                                                  aaaaTAATTTATTTGTTCAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAGACGGATGTTAATTg  <  7:71287/138‑1 (MQ=255)                                                                                                                                      |                                                                                                                                      CGTCTCCAAACAAATCAAAATTGAAAATACCGCAATCATTGGCAGCGCAATCGCCAATCCAATGAGCGCAAACCAAATATCCATTACGCGCTTTATTGCCAAATAACGAGCCGTCTTTTCAGATAATGTAAAAGAATGTATTTGTTGAACTGAGAATTCACGACTCACATTCATGCTTTTCTCTGCACTCACTGACACACACCTCACGATTTGTTTGGGATGTTATGATGACCTATGCCAGTCAGTTTAGCAGACGGATGTTAATTG  >  CP006881/3476555‑3476821

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑