Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	1,229,969	G→T	22.1%	L69M (CTG→ATG)	nhaB ←	sodium:proton antiporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	1,229,969	0	G	T	22.1%	32.9 / 3.4	18	L69M (CTG→ATG)	nhaB	sodium:proton antiporter
Reads supporting (aligned to +/- strand):  ref base G (7/7);  new base T (2/2);  total (9/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACAGCTGTTTCATAAAATAGATACCCGCCACCATAAACATCAGTAACAGCAAGACTTCAAGATTTGCCGCCACCTCTTCACGGACGTGTTCCGCGCTGGTCATGCCGATGAATACCGCTTCGATAGCCAACAGACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGAAAATAAATTCCGCTACCAGCAACCAGCCCGCGACGAAAGGGCTGATGAGGAAAATTAACGGGTTTACGATTAAGAAAATGATG  >  CP009273/1229836‑1230099                                                                                                                                      |                                                                                                                                   aacagcTGTTTCATAAAATAGATACCCGCCACCATAAACATCAGTAACAGCAAGACTTCAAGATTTGCCGCCACCTCTTCACGGACGTGTTCCGCGCTGGTCATGCCGATGAATACCGCTTCGATAGCCAACAGaccacc                                                                                                                              >  1:547360/1‑140 (MQ=255) aacagcTGTTTCATAAAATAGATACCCGCCACCATAAACATCAGTAACAGCAAGACTTCAAGATTTGCCGCCACCTCTTCACGGACGTGTTCCGCGCTGGTCATGCCGATGAATACCGCTTCGATAGCCAACAGaccacc                                                                                                                              >  1:460834/1‑140 (MQ=255)                                          cAGTAACAGCAAGACTTCAAGATTTGCCGCCACCTCTTCACGGACGTGTTCCGCGCTGGTCATGCCGATGAATACCGCTTCGATAGCCAACAGACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGa                                                                                     >  2:318671/1‑140 (MQ=255)                                           aGTAACAGCAAGACTTCAAGATTTGCCGCCACCTCTTCACGGACGTGTTCCGCGCTGGTCATGCCGATGAATACCGCTTCGATAGCCAACAGACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGaa                                                                                    >  1:104268/1‑140 (MQ=255)                                                       aCTTCAAGATTTGCCGCCACCTCTTCACGGACGTGTTCCGCGCTGGTCATGCCGATGAATACCGCTTCGATAGCCAACAGACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGAAAATAAATTCCGc                                                                        <  2:547360/140‑1 (MQ=255)                                                       aCTTCAAGATTTGCCGCCACCTCTTCACGGACGTGTTCCGCGCTGGTCATGCCGATGAATACCGCTTCGATAGCCAACAGACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGAAAATAAATTCCGc                                                                        <  2:460834/140‑1 (MQ=255)                                                           cAAGATTTGCCGCCACCTCTTCACGGACGTGTTCCGCGCTGGTCATGCCGATGAATACCGCTTCGATAGCCAACAGACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGAAAATAAATTCCGCTAcc                                                                    >  1:552589/1‑140 (MQ=255)                                                                      gccACCTCTTCACGGACGTGTTCCGCGCTGGTCATGCCGATGAATACCGCTTCGATAGCCAACAGACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGAAAATAAATTCCGCTACCAGCAACCAGcc                                                         <  1:428686/140‑1 (MQ=255)                                                                                 aCGGACGTGTTCCGCGCTGGTCATGCCGATGAATACCGCTTCGATAGCCAACAGACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGAAAATAAATTCCGCTACCAGCAACCAGCCCGCGACGAAAg                                              <  1:383890/140‑1 (MQ=255)                                                                                               cgcTGGTCATGCCGATGAATACCGCTTCGATAGCCAACATACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGAAAATAAATTCCGCTACCAGCAACCAGCCCGCGACGAAAGGGCTGATGAGGaaa                                >  1:249214/1‑140 (MQ=255)                                                                                               cgcTGGTCATGCCGATGAATACCGCTTCGATAGCCAACATACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGAAAATAAATTCCGCTACCAGCAACCAGCCCGCGACGAAAGGGCTGATGAGGaaa                                >  1:103006/1‑140 (MQ=255)                                                                                               cgcTGGTCATGCCGATGAATACCGCTTCGATAGCCAACAGACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGAAAATAAATTCCGCTACCAGCAACCAGCCCGCGACGAAAGGGCTGATGAGGaaa                                >  1:473491/1‑140 (MQ=255)                                                                                               cgcTGGTCATGCCGATGAATACCGCTTCGATAGCCAACAGACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGAAAATAAATTCCGCTACCAGCAACCAGCCCGCGACGAAAGGGCTGATGAGGaaa                                >  1:503069/1‑140 (MQ=255)                                                                                                                aaTACCGCTTCGATAGCCAACAGACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGAAAATAAATTCCGCTACCAGCAACCAGCCCGCGACGAAAGGGCTGATGAGGAAAATTAACGGGTTTACGAt               <  2:104268/140‑1 (MQ=255)                                                                                                                             tAGCCAACATACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGAAAATAAATTCCGCTACCAGCAACCAGCCCGCGACGAAAGGGCTGATGAGGAAAATTAACGGGTTTACGATTAAGAAAatgatg  <  2:103006/140‑1 (MQ=255)                                                                                                                             tAGCCAACATACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGAAAATAAATTCCGCTACCAGCAACCAGCCCGCGACGAAAGGGCTGATGAGGAAAATTAACGGGTTTACGATTAAGAAAatgatg  <  2:249214/140‑1 (MQ=255)                                                                                                                             tAGCCAACAGACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGAAAATAAATTCCGCTACCAGCAACCAGCCCGCGACGAAAGGGCTGATGAGGAAAATTAACGGGTTTACGATTAAGAAAatgatg  <  2:473491/140‑1 (MQ=255)                                                                                                                             tAGCCAACAGACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGAAAATAAATTCCGCTACCAGCAACCAGCCCGCGACGAAAGGGCTGATGAGGAAAATTAACGGGTTTACGATTAAGAAAatgatg  <  2:503069/140‑1 (MQ=255)                                                                                                                                      |                                                                                                                                   AACAGCTGTTTCATAAAATAGATACCCGCCACCATAAACATCAGTAACAGCAAGACTTCAAGATTTGCCGCCACCTCTTCACGGACGTGTTCCGCGCTGGTCATGCCGATGAATACCGCTTCGATAGCCAACAGACCACCGGGGAGCAGCGGGTAGCATTTCAGGGCCATCGCCAGAGTGAAAATAAATTCCGCTACCAGCAACCAGCCCGCGACGAAAGGGCTGATGAGGAAAATTAACGGGTTTACGATTAAGAAAATGATG  >  CP009273/1229836‑1230099

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑