Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	982,565	T→A	35.8%	intergenic (‑127/+476)	ompF ← / ← asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	982,565	0	T	A	35.8%	6.4 / 9.8	14	intergenic (‑127/+476)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base T (7/2);  new base A (2/3);  total (9/5)
Fisher's exact test for biased strand distribution p-value = 2.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.92e-01

CAGAATATTGCGCTTCATCATTATTTATTACCCTCATGGTTTTTTTTATGACACCTGCCACTGCCGTCAATAAGTTCTGTCAATAAAAATTTACGGAACTATTGATGAGAGTTTGGTGTCTTTATGTGTCTGCAGGCATCTTTCCATTCAAACTAACGTTTCGCTACCGTGAAAGTGCTACAAAGATAAAGATTTGGTTTCAAAAAGAAAAAATATGTAACCAAAAGTAAAATTTAAGGAACTTTGTGAACACCGTCATATTTCCATAGAGACGTGATGATATTTA  >  CP009273/982418‑982703                                                                                                                                                    |                                                                                                                                           cAGAATATTGCGCTTCATCATTATTTATTACCCTCATGGTTTTTTTTATGACACCTGCCACTGCCGTCAATAAGTTCTGTCAATAAAAATTTACGGAACTATTGATGAGCGTTTGGTGTCTTTATTGGTCTGCAGGCATCTTTCCATTc                                                                                                                                           >  1:287610/1‑149 (MQ=255)            gcTTCATCATTATTTATTACCCTCATGGTTTTTTTTATGACACCTGCCACTGCCGTCAATAAGTTCTGTCAATAAAAATTTACGGAACTATTGATGAGAGTTTGGTGTCTTTATGTGTCTGCAGGCCTCTTTCCATTCACACTTACGtt                                                                                                                                >  1:37444/1‑149 (MQ=255)                     ttatttatTACCCTCATGGTTTTTTTTATGACACCTGCCACTGCCGTCAATAAGTTCTGTCAATAAAAATTTACGGAACTATTGATGAGAGTTTGGTGTCTTTATGTGTCTGCAGGCATCTTTCCATTCAAACTAACGTTTCGCTACCg                                                                                                                       >  2:166874/1‑149 (MQ=255)                     ttatttatTACCCTCATGGTTTTTTTTATGACACCTGCCACTGCCGTCAATAAGTTCTGTCAATAAAAATTTACGGAACTATTGATGAGAGTTTGGTGTCTTTATGTGTCTGCAGGCATCTTTCCATTCAAACTAACGTTTCGCTACCg                                                                                                                       >  2:24991/1‑149 (MQ=255)                                        atttttttATGACACCTGCCACTGCCGTCAATAAGTTCTGTCAATAAAAATTTACGGAACTATTGATGAGAGGTTGGTGTCTTTATGTGTCTGCAGGCATCTTTCCATTCAAACTGACGTTTCGCTACCGTCAAAGTGCTACaacaata                                                                                                    >  1:66745/2‑144 (MQ=255)                                            ttttATGACACCTGCCACTGCCGTCAATAAGTTCTGTCAATAAAAATTTACGGAACTATTGATGAGAGTTTGGTGTCTTTATGTGTCTGCAGGCATCTTTCCATTCAAACTAACGTTTCGCTACCGTGAAAGTGCTACaaagataaaga                                                                                                >  1:272022/1‑149 (MQ=255)                                                          ccACTGCCGTCAATAAGTTCTGTCAATAAAAATTTACGGAACTATTGATGAGAGTTTGGTGTCTTTATGTGTCTGCAGGCATCTTTCCATACAAACTAACGTTTCGCTACCGTGAAAGTGCTACAAAGATAAAGATTTGGTTTCaaaaa                                                                                  >  1:286534/1‑149 (MQ=255)                                                                  actaaTATGTTCTGTCAATAAAAATTTACGGAACTATTGATGAGAGTTTGGTGTCTTTATGTGTCTGCAGGCATCTCTCCATTCAAACTAACGTTTCGCTACCGTGAAAGTGCTACAAAGATAAAGATTTGGTTTCAAAAAGAAAAAat                                                                          <  1:297820/146‑1 (MQ=255)                                                                       tAAGTTCTGTCAATAAAAATTTACGGAACTATTGATGAGAGTTTGGTGTCTTTATGTGTCTGCAGGCATCTTTCCATACAAACTAACGTTTCGCTACCGTGAAAGTGCTACAAAGATAAAGATTTGGTTTCAAAAAGAAAAAATATGTa                                                                     >  2:41706/1‑149 (MQ=255)                                                                                                         atgaGAGTTTGGTGTCTTTATGTGTCTGCAGGCATCTTTCCATTCAAACTAACGTTTCGCTACCGTGAAAGTGCTACAAAGATAAAGATTTGGTTTCAAAAAGAAAAAATATGTAACCAAAAGTAAAATTTAAGGAACTTTGTGAacac                                   >  2:106158/1‑149 (MQ=255)                                                                                                                    gtgtCTTTATGTGTCTGCAGGCATCTTTCCATTCAAACTAACGTTTCGCTACCGTGAAAGTGCTACAAAGATAAAGATTTGGTTTCAAAAAGAAAAAATATGTCAACAAAAGTAAAATTTAAGGAACTTTGTGAACACCGTCATATTTc                        <  2:174333/149‑1 (MQ=255)                                                                                                                               tttCTGCAGGCATCTTTCCATACAAACTAACGTTTCGCTACCGTGAAAGTGCTACAAAGATAAAGATTTGGTTTCAAAAAGAAAAAATATGTAACCAAAAGTAAAATTTAAGGAACTTTGTGAACACCGTCATATTTCCATAGAGACGt             <  2:293305/147‑1 (MQ=255)                                                                                                                               tgccTGCAGGCATCTTTCCATACAAACTAACGTTTCGCTACCGTGAAAGTGCTACAAAGATAAAGATTTGGTTTCAAAAAGAAAAAATATGTAACCAAAAGTAAAATTTAAGGAACTTTGTGAACACCGTCATATTTCCATAGAGACGt             <  2:293350/146‑1 (MQ=255)                                                                                                                                          aTCTTTCCATACAAACTAACGTTTCGCTACCGTGAAAGTGCTACAAAGATAAAGATTTGGTTTCAAAAAGAAAAAATATGTAACCAAAAGTAAAATTTAAGGAACTTTGTGAACACCGTCATATTTCCATAGAGACGTGATGATATTTa  <  2:278379/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                           CAGAATATTGCGCTTCATCATTATTTATTACCCTCATGGTTTTTTTTATGACACCTGCCACTGCCGTCAATAAGTTCTGTCAATAAAAATTTACGGAACTATTGATGAGAGTTTGGTGTCTTTATGTGTCTGCAGGCATCTTTCCATTCAAACTAACGTTTCGCTACCGTGAAAGTGCTACAAAGATAAAGATTTGGTTTCAAAAAGAAAAAATATGTAACCAAAAGTAAAATTTAAGGAACTTTGTGAACACCGTCATATTTCCATAGAGACGTGATGATATTTA  >  CP009273/982418‑982703

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: ‑