Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP006881	1,653,867	G→A	13.0%	M237I (ATG→ATA)	U712_08495 →	GTP‑sensing transcriptional pleiotropic repressor CodY

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	1,653,867	0	G	A	13.0%	125.7 / 7.8	46	M237I (ATG→ATA)	U712_08495	GTP‑sensing transcriptional pleiotropic repressor CodY
Reads supporting (aligned to +/- strand):  ref base G (22/18);  new base A (2/4);  total (24/22)
Fisher's exact test for biased strand distribution p-value = 4.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

AGGAGCTTGACGGAAATGAAGGTCTTCTTGTTGCAAGTAAAATTGCTGACCGTGTCGGCATTACCCGTTCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCTTTTTTTATTTCAAATAAAGGAAATCAATAAGCT  >  CP006881/1653731‑1653998                                                                                                                                         |                                                                                                                                    aggggCTTGACGGAAATGAAGGTCTTCTTGTTGCAAGTAAAATTGCTGACCGTGTCGGCATTACCCGTTCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGaa                                                                                                                                   <  8:319585/139‑1 (MQ=255) acgagCTTTACGGAAATGAAGGTCTTCTTGTTGCAAGTAAAATTGCTGACCGTGTCGACATTACCAGATCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGaa                                                                                                                                   <  2:57917/137‑1 (MQ=255)   gagCTTGACGGAAATGAAGGTCTTCTTGTTGCAAGTAAAATTGCTGACCGTGTCGACATTACCCGTTCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAg                                                                                                                                 <  8:12000/139‑1 (MQ=255)   gagCTTGAAGGAAATGAAGGTCTTCTTGTTGCAAGTAAAATTTCTGACCGTGTCGGGATTAGCCGTTCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAg                                                                                                                                 <  2:168353/139‑1 (MQ=255)    agCTTGACGGAAATGAAGGTCTTCTTGTTGCAAGTAAAATTGCTGACCGTGTCGACATTACCCGTTCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAgg                                                                                                                                >  4:225900/1‑139 (MQ=255)       ttGACGGAAATGAAGGTCTTCTTGTTGCAAGTAAAATTGCTGACCGTGTCGGCATTACCCGTTCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATAAAAGGTAc                                                                                                                             <  3:206212/139‑1 (MQ=255)         gACGGAAATGAAGGTCTTCTTGTTGCAAGTAAAATTGCTGACCGTGTCGGCATTACCCGTTCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATAAAAGGTAc                                                                                                                             <  5:294836/137‑1 (MQ=255)               aaTGCAGGTCTTCTTGTTGCAAGTAAAATTGCTGACCGTGTCGACATTACCCGTTCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCa                                                                                                                     <  7:161013/139‑1 (MQ=255)               aaTGAAGGTCTTCTTGATGCAAGTAAAATTGCTGACCGTGTCGACATTACCCGTTCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCa                                                                                                                     <  5:243861/139‑1 (MQ=255)                        cttcttGTTGCAACTAAAATTGCTGACCGTGTCGGCAATACCCGTACTGATATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGAGTTATCGAGTCTAGATCATTAGGAATGAAAGCTACTTATATCAAGGTACTa                                                                                                             >  6:56240/1‑138 (MQ=255)                              gttgCAAGTAAAATTGCTGACCGTGTCGACATTACCCGTTCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAaacaac                                                                                                       <  3:225900/138‑1 (MQ=255)                                        aaaTTGCTGACCGTGTCGACATTACCCGTTCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTaa                                                                                             <  4:150296/138‑1 (MQ=255)                                                  ccGTGTAGACATTACCCGTTCTGTTATTGTGAACGCACTCAGTTAGCTGGAGAGCGCCGGTTTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGa                                                                                   <  4:243707/138‑1 (MQ=255)                                                                     tCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTaa                                                                >  3:71235/1‑138 (MQ=255)                                                                     tCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTaa                                                                >  3:76300/1‑138 (MQ=255)                                                                     tCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTaa                                                                >  8:173437/1‑138 (MQ=255)                                                                            ttGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACaaa                                                         <  1:33990/138‑1 (MQ=255)                                                                              gtgAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATAAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACaaa                                                         >  1:220627/1‑136 (MQ=255)                                                                                 aaCGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAgg                                                                                                                  <  2:64001/76‑1 (MQ=255)                                                                                 aaCGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAgg                                                                                                                  >  1:64001/1‑76 (MQ=255)                                                                                 aaCGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAAc                                                   >  4:365103/1‑139 (MQ=255)                                                                                 aaCGCACTCAGAAAGCTGGAGAGCGACGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAAc                                                   >  1:224336/1‑139 (MQ=255)                                                                                   cGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCa                                                                                                                     <  8:83669/71‑1 (MQ=255)                                                                                   cGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCa                                                                                                                     >  7:83669/1‑71 (MQ=255)                                                                                      aCTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCttt                                              >  5:336168/1‑139 (MQ=255)                                                                                      aCTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCttt                                              >  6:169711/1‑139 (MQ=255)                                                                                                cTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTc                                    >  8:285634/1‑139 (MQ=255)                                                                                                cTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTc                                    >  2:191796/1‑139 (MQ=255)                                                                                                  ggAGCGCGCCGGTGGTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCtt                                  >  7:225680/1‑139 (MQ=255)                                                                                                        cgcCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCttttt                                            >  3:207991/1‑123 (MQ=255)                                                                                                        cgcCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCttttt                                            <  4:207991/123‑1 (MQ=255)                                                                                                           cGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCTTTTTTTAttt                         <  4:76300/139‑1 (MQ=255)                                                                                                           cGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCTTTTTTTAttt                         <  4:71235/139‑1 (MQ=255)                                                                                                                ttATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCTTTTTTTATTTCaaa                     <  7:173437/138‑1 (MQ=255)                                                                                                                  aTCGAGTCTAGATCATTAGGAATAAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCTTTTTTTATTTCAAATa                   >  4:325028/1‑138 (MQ=255)                                                                                                                        tCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCTTTTTTTATTTCAAATAAAGGaaa            >  7:323444/1‑139 (MQ=255)                                                                                                                        tCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCTTTTTTTATTTCAAATAAAGGaaa            >  1:129995/1‑139 (MQ=255)                                                                                                                        tCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCTTTTTTTATTTCAAATAAAGGaaa            >  7:337765/1‑139 (MQ=255)                                                                                                                             aTCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCTTTTTTTATTTCAAATAAAGGAAATCaa        >  5:261796/1‑138 (MQ=255)                                                                                                                             aTCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCTTTTTTTATTTCAAATAAAGGAAATCAAt       <  5:153368/139‑1 (MQ=255)                                                                                                                             aTCATTAGGAATAAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAACAACCCTTTTTGAGGGTTCTTTTTTTATTTCAAATAAAGGAAATCAAt       <  8:82565/139‑1 (MQ=255)                                                                                                                             aTCATTAGGAATAAAAGGGACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCTTTTTTTATTTCAAATAAAGGAAATCAAt       <  8:82562/139‑1 (MQ=255)                                                                                                                                 ttAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCTTTTTTTATTTCAAATAAAGGAAATCAAt       >  6:41751/1‑135 (MQ=255)                                                                                                                                  tAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCTTTTTTTATTTCAAATAAAGGAAATCAATa      >  7:314080/1‑135 (MQ=255)                                                                                                                                  tAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCTTTTTTTATTTCAAATAAAGGAAATCAATa      <  8:314080/135‑1 (MQ=255)                                                                                                                                  tAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCTTTTTTTATTTCAAATAAAGGAAATCAATAAGCt  >  1:293295/1‑139 (MQ=255)                                                                                                                                         |                                                                                                                                    AGGAGCTTGACGGAAATGAAGGTCTTCTTGTTGCAAGTAAAATTGCTGACCGTGTCGGCATTACCCGTTCTGTTATTGTGAACGCACTCAGAAAGCTGGAGAGCGCCGGTGTTATCGAGTCTAGATCATTAGGAATGAAAGGTACTTATATCAAGGTACTAAACAACAAATTCCTAATTGAATTAGAAAATCTAAAATCTCATTAATCACAAAAAGAACCCTTTTTGAGGGTTCTTTTTTTATTTCAAATAAAGGAAATCAATAAGCT  >  CP006881/1653731‑1653998

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑