Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	1,143,601	T→C	11.4%	I175I (ATT→ATC)	plsX →	putative phosphate acyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	1,143,601	0	T	C	11.4%	96.8 / 5.1	35	I175I (ATT→ATC)	plsX	putative phosphate acyltransferase
Reads supporting (aligned to +/- strand):  ref base T (15/16);  new base C (2/2);  total (17/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.88e-01

CAATGCGCGTGGCCCTGGAGCTGGTGAAAGAAGGTCGAGCGCAAGCCTGTGTCAGTGCCGGTAATACCGGGGCGCTGATGGGGCTGGCAAAATTATTACTCAAGCCCCTGGAGGGGATTGAGCGTCCGGCGCTGGTGACGGTATTACCACATCAGCAAAAGGGCAAAACGGTGGTCCTTGACTTAGGGGCCAACGTCGATTGTGACAGCACAATGCTGGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCGGTGCTTAAAACAATCCCTTCTATCAATTATATCGGCTATCTTGAAGCCAATGAGTTGTTAACTGGCAAGACAGATGTGCTGGTTTGTGACGGCTTTACAGGAAATGTCACATTAAAGACGATGGAAGGTGTTGTCAGGATGTTCCTTTCTCTGCTG  >  CP009273/1143333‑1143835                                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                           cAATGCGCGTGGCCCTGGAGCTGGTGAAAGAAGGTCGAGCGCAAGCCTGTGTCAGTGCCGGTAATACCGGGGCGCTGATGGGGCTGGCAAAATTATTACTCAAGCCCCTGGAGGGGATTGAGCGTCCGGCGCTGGTGACGGTATTACCACATCAGCAAAAGGGCAAAACGGTGGTCCTTGACTTAGGGGCCAACGTCGATTGTGACAGCACAATGCTGGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAAt                                                                                                                                                                                                                                      <  1:325663/275‑1 (MQ=255)                                                                  accctggCGCTGATGGGGTTGGCAAAATTATTACTCAAGCCCCTGGAGTGGATTTAGCGTCCTGCGCGGGTGACGGTATTACCACATCAGCAAAAAGGCAAAACGGTGGTCCTTGANTTAGGGGCCAACGTTGATTGTGGCAGCACAATGCTTGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGc                                                                                                                                                                     <  1:684557/270‑1 (MQ=255)                                                                                                                         aGCGTCCGGCGCTGGTGACGGTATTACCACATCAGCAAAAGGGCAAAACGGTGGTCCTTGACTTAGGGGCCAACGTCGATTGTGACAGCACAATGCTGGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGt                                                                                                                                                                                                                         >  2:483803/1‑168 (MQ=255)                                                                                                                             tCCGGCGCTGGTGACGGTATTACCACATCAGCAAAAGGGCAAAACGGTGGTCCTTGACTTAGGGGCCAACGTCGATTGTGACAGCACAATGCTGGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGCTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCt                                                                                                                                                                                                                     <  1:483812/168‑1 (MQ=255)                                                                                                                                                        tCAGCAAAAGGGCAAAACGGTGGTCCTTGACTTAGGGGCCAACGTCGATTGTGACAGCACAATGCTGGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGCTGCCTCAGCGGTGCTTaaaa                                                                                                                                                    >  2:514968/1‑206 (MQ=255)                                                                                                                                                        tCAGCAAAAGGGCAAAACGGTGGTCCTTGACTTAGGGGCCAACGTCGATTGTGACAGCACAATGCTGGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATCCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCGGTGCTTAAAACAATccc                                                                                                                                             >  1:673796/1‑213 (MQ=255)                                                                                                                                                            cAAAAGGGCAAAACGGTGGTCCTTGACTTAGGGGCCAACGTCGATTGTGACAGCACAATGCTGGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGTTGCCTCAGCGGTGCTTAAAACAAt                                                                                                                                                <  1:514977/206‑1 (MQ=255)                                                                                                                                                            cAAAAGGGCAAAACGGTGGTCCTTGACTTAGGGGCCAACGTCGATTGTGACAGCACAATGCTGGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATCCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCGGTGCTTAAAACAATCCCTTCt                                                                                                                                         <  2:673782/213‑1 (MQ=255)                                                                                                                                                                   ataagagacaggtCCTTGACTTAGGGGACAACGTCGATTGTGACAGCACAATGCTGGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGCGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCTGGATGCCTCAGCGGTGCTTAAAACAATCCCTTCTATCAATTATATCGGCTATCTTGAAGCCAATGAGTTGTTAACTGGCAAGACAGATGTGCTGGTTTGTGa                                                                     <  1:411561/264‑1 (MQ=255)                                                                                                                                                                                 cTTGACTTAGGGGCCAACGTCGATTGTGACAGCACAATGCTGGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTgaa                                                                                                                                                                                                        >  1:675784/1‑129 (MQ=255)                                                                                                                                                                                     aCTTAGGGGCCAACGTCGATTGTGACAGCACAATGCTGGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTgaagaag                                                                                                                                                                                                    <  2:675770/129‑1 (MQ=255)                                                                                                                                                                                         aGGGGCCAACGTCGATTGTGACAGCACAATGCTGGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCGGTGCTTAAAACAATCCCTTCNATCAATTANATCGGCTATCTTGAAGCCAATGAGTTGTTAACTGGCAAGACAGATGTGCTGGTTTGTGACGGCTTTAAAGGAAATGTCACAt                                              >  1:495971/1‑275 (MQ=255)                                                                                                                                                                                               cAACGTCGATTGTGACAGCACAATGCTGGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTgaagaagaa                                                                                                                                                                                                  >  1:347384/1‑121 (MQ=255)                                                                                                                                                                                                   gTCGATTGTGACAGCACAATGCTGGTGCAATTTGCCATGATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTaa                                                                                                                                                                                              <  2:347378/121‑1 (MQ=255)                                                                                                                                                                                                                 cacaATGCTGGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTc                                                                                                                                                                  >  2:165190/1‑135 (MQ=255)                                                                                                                                                                                                                     aTGCTGGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCg                                                                                                                                                              <  1:165192/135‑1 (MQ=255)                                                                                                                                                                                                                           gTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCGGTGCTTAAAACAATCCCTTCTATCAATTATATCGGCTATCTTGAAGCCAATGAGTTGTTAACTGGCAAGACAGATGTGCTGGTTTGTGACGGCTTTACAGGAAATGTCACATTAAAGACGATg                                   >  1:100488/1‑252 (MQ=255)                                                                                                                                                                                                                           gTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCGGTGCTTAAAACAATCCCTTCTATCAATTATATCGGCTATCTTGAAGCCAATGAGTTGTTAACTGGCAAGACAGATGTGCTGGTTTGTGACGGCTTTACAGGAAATGTCACATTAAAGACGATGGACGATGTTTGCAGGATGTTcc             >  1:12953/1‑274 (MQ=255)                                                                                                                                                                                                                               aaTTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCGGTGCTTAAAACAATCCCTTCTATCAATTATATCGGCTATCTTGAAGCCAATGAGTTGTTAACTGGCAAGACAGATGTGCTGGTTTGTGACGGCTTTACAGGAAATGTCACATTAAAGACGATGGAAg                               <  2:100487/252‑1 (MQ=255)                                                                                                                                                                                                                                aTTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGtc                                                                                                                                                                                        >  1:682483/1‑98 (MQ=255)                                                                                                                                                                                                                                aTTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTc                                                                                                                                                                  >  1:641754/1‑120 (MQ=255)                                                                                                                                                                                                                                    gCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGa                                                                                                                                                                                    <  2:682469/98‑1 (MQ=255)                                                                                                                                                                                                                                    gCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCg                                                                                                                                                              <  2:641740/120‑1 (MQ=255)                                                                                                                                                                                                                                     ccATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCggg                                                                                                                                                                         >  1:298227/1‑108 (MQ=255)                                                                                                                                                                                                                                         tATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGc                                                                                                                                                                     <  2:298222/108‑1 (MQ=255)                                                                                                                                                                                                                                                  aGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCGGTGCTTAAAACAATCCCTTCTATCAATTATATc                                                                                                                             >  1:297464/1‑139 (MQ=255)                                                                                                                                                                                                                                                     tCTGGCTGAAGAGGTGGTGGAAATCCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTaaa                                                                                                                                                                                             >  2:607023/1‑72 (MQ=255)                                                                                                                                                                                                                                                      cTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCGGTGCTTAAAACAATCCCTTCTATCAATTATATCGGCt                                                                                                                         <  2:297459/139‑1 (MQ=255)                                                                                                                                                                                                                                                         gCTGAAGAGGTGGTGGAAATCCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGt                                                                                                                                                                                         <  1:607036/72‑1 (MQ=255)                                                                                                                                                                                                                                                              agagGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCGGTGCTTAAAACAATCCCTTCTATCAATTATATCGGCTATCTTGAAGCCAATGAGTTGTTAACTGGCAAGACAGATGTGCTGGTTTGTGACGGCTTTACAGGAAATGTCACATTAAAGACGATGGAAGGTGTTGTCAGGATGTTCCTTTctct      >  1:142703/1‑246 (MQ=255)                                                                                                                                                                                                                                                                  gtggtgGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCGGTGCTTAAAACAATCCCTTCTATCAATTATATCGGCTATCTTGAAGCCAATGAGTTGTTAACTGGCAAGACAGATGTGCTGGTTTGTGACGGCTTTACAGGAAATGTCACATTAAAGACGATGGAAGGTGTTGTCAGGATGTTCCTTTCTctgctg  <  2:142702/246‑1 (MQ=255)                                                                                                                                                                                                                                                                     gtggAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGtc                                                                                                                                                                                        >  1:308144/1‑61 (MQ=255)                                                                                                                                                                                                                                                                       ggAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCGGTGCTTAAAACAATccc                                                                                                                                             >  2:318267/1‑102 (MQ=255)                                                                                                                                                                                                                                                                         aaaTTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGa                                                                                                                                                                                    <  2:308139/61‑1 (MQ=255)                                                                                                                                                                                                                                                                           aTTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCGGTGCTTAAAACAATCCCTTCt                                                                                                                                         <  1:318273/102‑1 (MQ=255)                                                                                                                                                                                                                                                                            ttCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCGGTGCTTAAAACAATCCCTTCTATCAATTATATCGGCTATc                                                                                                                      >  1:218256/1‑120 (MQ=255)                                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                           CAATGCGCGTGGCCCTGGAGCTGGTGAAAGAAGGTCGAGCGCAAGCCTGTGTCAGTGCCGGTAATACCGGGGCGCTGATGGGGCTGGCAAAATTATTACTCAAGCCCCTGGAGGGGATTGAGCGTCCGGCGCTGGTGACGGTATTACCACATCAGCAAAAGGGCAAAACGGTGGTCCTTGACTTAGGGGCCAACGTCGATTGTGACAGCACAATGCTGGTGCAATTTGCCATTATGGGCTCAGTTCTGGCTGAAGAGGTGGTGGAAATTCCCAATCCTCGCGTGGCGTTGCTCAATATTGGTGAAGAAGAAGTAAAGGGTCTCGACAGTATTCGGGATGCCTCAGCGGTGCTTAAAACAATCCCTTCTATCAATTATATCGGCTATCTTGAAGCCAATGAGTTGTTAACTGGCAAGACAGATGTGCTGGTTTGTGACGGCTTTACAGGAAATGTCACATTAAAGACGATGGAAGGTGTTGTCAGGATGTTCCTTTCTCTGCTG  >  CP009273/1143333‑1143835

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑