Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,737,631:1	+A	61.5%	coding (33/48 nt)	pheL →	phe operon leader peptide

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,737,631	1	.	A	61.5%	45.1 / 32.2	26	coding (33/48 nt)	pheL	phe operon leader peptide
Reads supporting (aligned to +/- strand):  ref base . (8/2);  new base A (8/8);  total (16/10)
Fisher's exact test for biased strand distribution p-value = 2.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

GTCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTT‑TTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCGGGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACT  >  NC_000913/2737495‑2737767                                                                                                                                          |                                                                                                                                         gtCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACGGTACGGGTACTGTACTAAAGTCACGTGAGGAAACAAACATGGAACACATACCGCCATTCTTCGCATTCctt‑atttat                                                                                                                                    >  1:209373/1‑140 (MQ=255)         tatTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTATTTACCTTCCCCt                                                                                                                             <  2:494059/143‑1 (MQ=255)            tGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTATTTACCTTCCCCTGaa                                                                                                                          <  1:491760/143‑1 (MQ=255)              aGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGATGTCGGTGCGGATACTGTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTT‑TTTACCTTCCCCTGAATgg                                                                                                                       <  1:262761/143‑1 (MQ=255)                    tCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGTCACTCAAGGAAACAAACATGAAACACACAGCCATATTCCTCGCATTCTTTATTTACCTTCCCCTGAATGGTAGGc                                                                                                                  >  2:551529/1‑143 (MQ=255)                      gCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTT‑TTTACCTTCCCCGGAATGGCAGCCGtt                                                                                                               >  1:430217/1‑143 (MQ=255)                            gcgcCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTATTTACCTTCCCCTGAATGGGAGGCGTTtcgtc                                                                                                          <  1:527830/143‑1 (MQ=255)                               ccTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAGGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTGT‑TTTACCTTCCCCTGCATGGGAGGCGTTTCGTCgtgt                                                                                                      >  1:161799/1‑143 (MQ=255)                                    gggCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGAAACAAACATGAGACACATACCGTTTTTCTTCGCATTCTTTATTTAACTTCACGTGAATGGGAGGCGTTTCGTCGTGTGaaa                                                                                                  >  2:4708/1‑143 (MQ=255)                                          gTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGTCACTTGAGGACACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTATTTACCTTCCCCTCAATGGGAGGCGTTTCGTCGTGTGAAACAGAAt                                                                                            >  1:358934/1‑143 (MQ=255)                                                  ttgACAGCGTGAAAACAGTACGGGTACGGTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTATTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGAc                                                                                    <  1:177276/143‑1 (MQ=255)                                                          gTGAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTT‑TTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAGCAGAATGCGAAGTCGAACAAtta                                                                           >  1:230768/1‑141 (MQ=255)                                                            gAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTT‑TTTACTTTCCCCTCAATGGGAGGCGTTTCGTCGTGTGAAGCAGAATGCGAAGACGAACAATAAgg                                                                         >  1:465539/1‑143 (MQ=255)                                                            gAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTT‑TTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAgg                                                                         >  1:401956/1‑143 (MQ=255)                                                                            ctgtactAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTATTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCgggg                                                          <  1:458248/143‑1 (MQ=255)                                                                                    aaGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTATTTACCTTCCCCTGAATAGGAGGCGTTTCGTCGTGTGAACCAGAATGCGAAGACGCACAATAAGGCCTCCCACACCGGGTGGCGtttt                                                  >  2:36883/1‑143 (MQ=255)                                                                                         aCTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTATTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCGGGGGGCCTTTTTTAtt                                             <  1:452783/143‑1 (MQ=255)                                                                                         aCTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTATTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCGGGGGGCCTTTTTTAtt                                             >  1:36183/1‑143 (MQ=255)                                                                                           ttAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTT‑TTTACCTTCCACTGAATGGGAGGCGTTTCGTTGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCGGGGAGCCTTTTTTATTGAt                                          >  2:254353/1‑143 (MQ=255)                                                                                                      aacaTGAAACACATACCGTTTTTCTTCGCATTCTTTATTTACCTTCCCCTGAATGAGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCGGGGGGCCTTTTTTATTAATAACAAAAAgg                                >  1:307320/1‑143 (MQ=255)                                                                                                        cctGAAACACATACCGTGTTTCTTCGCATTCTTT‑TTTACCTGCCCCTGAATGTGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCGGGGGGCCTTTTTTATTGATAACAAAAAGGCaa                             <  2:401956/141‑1 (MQ=255)                                                                                                                      cGTTTTTCTTCGCATTCTTTATTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCGGGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCg                >  1:487539/1‑143 (MQ=255)                                                                                                                       gTTTTTCTTCGCATTCTTT‑TTTAACTTCCCCTGAATGGGAGGCGTCTAGTCGTGTGAAACAGAATGCGAAGACGAACAATAGGACCTCCCAAATAGGCGAGGCATTTTTATTGATAACAAAACGGCAACACAATGACACCgca              >  2:141228/1‑141 (MQ=255)                                                                                                                              tgcGCATTCTTT‑TTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCGGGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCg       >  1:110654/3‑143 (MQ=255)                                                                                                                                cGCATTCTTTATTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCGGGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGt      >  1:31496/1‑143 (MQ=255)                                                                                                                                  cATTCTTTATTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCGGGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTa    <  2:36183/143‑1 (MQ=255)                                                                                                                                    ttCTTTATTTACCTTCACCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGTGAAGACGAACAATAAGGCCTCCCAAATCGGGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACt  <  1:129156/143‑1 (MQ=255)                                                                                                                                          |                                                                                                                                         GTCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTT‑TTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCGGGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACT  >  NC_000913/2737495‑2737767

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑