Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,083,335	A→T	9.8%	intergenic (‑141/‑142)	yefM ← / → hisL	antitoxin of the YoeB‑YefM toxin‑antitoxin system/his operon leader peptide

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,083,335	0	A	T	9.8%	104.0 / 5.2	41	intergenic (‑141/‑142)	yefM/hisL	antitoxin of the YoeB‑YefM toxin‑antitoxin system/his operon leader peptide
Reads supporting (aligned to +/- strand):  ref base A (24/13);  new base T (2/2);  total (26/15)
Fisher's exact test for biased strand distribution p-value = 6.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.18e-01

GCATGTCAATCTCCTCTTTTGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGAATAAACATTCACAGAGACTTTTAT  >  CP009273/2083191‑2083478                                                                                                                                                  |                                                                                                                                                gCATGTCAATCTCCTCTTTTGTACAGTTCATTGTACACGCATTAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGT‑GCGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTcc                                                                                                                                             >  1:402985/1‑149 (MQ=255) gCATGTCAATCTCCTCTTTTGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTCTTTTTTGTGCCTTCAGCTAAGAGAACAGccc                                                                                                                                             >  1:22030/1‑149 (MQ=255)  cATGTCAATCTCCTCTTTTGTACCGTTCATTGTACAATGATTATCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCct                                                                                                                                            >  1:726387/1‑149 (MQ=255)  cATGTCAATCTCCTCTTTTGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCct                                                                                                                                            >  1:93107/1‑149 (MQ=255)   aTGTCAATCTCCTCTTTTGTACTGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCctc                                                                                                                                           <  1:492069/149‑1 (MQ=255)       caacccccaccttttTACCGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACTGTCCTCTTAg                                                                                                                                       <  2:64399/138‑1 (MQ=255)         aTCTCCTCTTTTGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTCAGAGGACAGTCCTCTTAGcc                                                                                                                                     >  2:832411/1‑149 (MQ=255)         aTCTCCTCTTTTGTACAGTTCATTGTAAAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACTGTCCTCTTAGct                                                                                                                                     <  2:401109/149‑2 (MQ=255)          tctcCTCTTTTGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGccc                                                                                                                                    >  2:320273/1‑149 (MQ=255)           ctcctcTTTTGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGcccc                                                                                                                                   >  2:214453/1‑149 (MQ=255)           atcctcTTTTGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGTCAGTCCTCTTAGcccc                                                                                                                                   >  2:388883/2‑149 (MQ=255)                                  tACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTGGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTa                                                                                                            >  1:209757/1‑149 (MQ=255)                                       tgttgggCGTTAATTAACTATTTATTTATTAGTTTGTTGTTCAAGGTATTGTCTGT‑GAGACGAATTTCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACaa                                                                                                       <  2:265269/143‑1 (MQ=255)                                       tgatgtGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCCAAGCATCCTCCTTTCCCCGCTCATTCATTAAACaa                                                                                                       <  2:859317/149‑1 (MQ=255)                                                            ttattaATTAGTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTATTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAatatat                                                                                  <  2:598709/149‑1 (MQ=255)                                                               ttaattaGTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGACCTCGATATTTATGGTGAAATCAGCCAACAGGCAAGTCCTATTAGCCCCCTCCCTTCCCCGCGCATGCATTAAACAAATCCATTGCCATAAAATATATaaa                                                                               >  1:722977/1‑149 (MQ=255)                                                                taattaGTTTGTAGCTCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATaaaaaa                                                                              >  1:23612/1‑149 (MQ=255)                                                                  attaGTTTGTAGATCAATGTATTGTCAGT‑GAGACGAAAATCCAGGCATCGAAAAAAAAAAAAACAACAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCCCCCCCCGCTAATTCATTAAACAAATCCATTGCCaaaaaaaaaaaaaaaaa                                                                            <  1:180199/149‑12 (MQ=255)                                                                      gTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGccc                                                                        >  2:499146/1‑149 (MQ=255)                                                                      gTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATCAAACAAATCCATTGCCATAAAATATATAAAAAAGccc                                                                        >  2:499120/1‑149 (MQ=255)                                                                       tttGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCAATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATATAATATATAAAAAAGCCCt                                                                       >  1:30244/1‑149 (MQ=255)                                                                         tggggATAAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATATTTGGTGCCATGAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTATACAACGCCCTTGCCCTAAAATCTATAAAAAACCACTTg                                                                     >  1:369478/5‑149 (MQ=255)                                                                         tGTAGATCAAGGTATTGTTAGT‑AAGACGAAAGTCCAGGATTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCATCATTTCCCAGCTCATTCATTAAACAAATCCATTGCCCTAAAATATATAAAAAAGCCCtcg                                                                     >  1:369407/1‑147 (MQ=255)                                                                         tGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTACCATCAGCTAAGAGGGCAGTCCTCTTAGCCACCTGCTTTCCCCGCTCATTCATTAAATAAATCCATTGCCATAAGAAAAATAAAAAAGACCGTg                                                                     >  2:327768/1‑149 (MQ=255)                                                                          gTAGATAAAGGGATTGT‑AGTAGACGCTAAAATCCTGGCTTCGCTATTTTTGGCGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAAGATATAAAAAATCCCTTGc                                                                    <  1:179339/149‑1 (MQ=255)                                                                              aTCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTc                                                                >  1:865048/1‑149 (MQ=255)                                                                                cAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTa                                                              <  1:707248/149‑1 (MQ=255)                                                                                         gTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAg                                                     >  2:867798/1‑149 (MQ=255)                                                                                                  gaCGAAAATCCAGGCTTCGCTATTTTTTTTTTTTTTTTCTAAGAAGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCGTTCCTTCCACAACTCCATTGCCATAAACTAAATAAAAAACCACTTGATTTTTTACTTGTTTGTGGTTTat                                             >  1:842853/1‑148 (MQ=255)                                                                                                   aCGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCAGAAAATCTATAAAAAAACCCTTGCTTTCTAACGAGAAAGTGGTTTAgg                                            >  1:830290/1‑149 (MQ=255)                                                                                                        aaTCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTaaa                                       >  2:791558/1‑149 (MQ=255)                                                                                                        aaTCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCGTGCTTTCTAACGTGAAAGTGGTTTAGGTTaaa                                       <  2:402985/149‑1 (MQ=255)                                                                                                         ctttgggtttCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTaaaa                                      <  1:216963/141‑1 (MQ=255)                                                                                                             aGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACa                                  <  1:326642/149‑1 (MQ=255)                                                                                                                cTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCCTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCa                               <  2:324436/149‑1 (MQ=255)                                                                                                                              gTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGAATAAACAtt                 <  2:865048/149‑1 (MQ=255)                                                                                                                                 gagggggCTAAGAGGACTGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATCAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGAATAAACATTcac              >  2:431662/7‑149 (MQ=255)                                                                                                                                    tCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGAATAAACATTCACaga           >  2:245303/1‑149 (MQ=255)                                                                                                                                        cTAAGAGGACTGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGAATAAACATTCACAGAGACt       >  2:502020/1‑149 (MQ=255)                                                                                                                                          aaGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCAGAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGAATAAACATTCACAGAGACttt     >  1:657203/1‑149 (MQ=255)                                                                                                                                             agGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTCCTAATTATCAGTTGAATAAACATTCACAGAGACTTTTAt  <  2:209757/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                GCATGTCAATCTCCTCTTTTGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGT‑GAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGAATAAACATTCACAGAGACTTTTAT  >  CP009273/2083191‑2083478

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑