Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006584	793,877	T→C	C358R (TGT→CGT)	LY180_03720 →	rhsA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006584	793,877	0	T	C	92.9%	23.9 / ‑3.7	14	C358R (TGT→CGT)	LY180_03720	rhsA
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (7/6);  total (8/6)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

AGTGTATGACCGCAGCAATACACAGGTGCGCAGCTTTACTTACGATGATAAATACCGGGGCCGGATGGTGGCGCACCGTCACACGGGCCGACCGGAAATCTGTTACCGTTACGACAGCGACGGGCGGGTGACAGAACAGCTAAACCCGGCAGGCTTAAGTTACACGTATCAGTATGAAAAAGACCGCATCACCATCACCGACAGCCTGAACCGCCGTGAAGTGCTGCACACGCAGGGCGAAGCCGGGCTGAAGCGGGTGGTGAAAAAGGAACACGCGGACGGCAGCGTCACACAGAGTCAGTTTGACGCCGTGGGCAGGCTCAGGGCACAGACGGATGCCGCAGGCAGGACAACAGAGTACAGCCCGGATGTGGTGAC  >  CP006584/793777‑794154                                                                                                     |                                                                                                                                                                                                                                                                                      aGTGTATGACCGCAGCAATACACAGGTGCGCAGCTTTACTTACGATGATAAATACCGGGGCCGGATGGTGGCGCACCGTCACACGGGCCGACCGGAAATCCGTTACCGTTACGACAGCGACGGGCGGGTGACAGAACAGCTAAACCCGGCAGGCTTAAGCTACACGTATCAGTATGAGAAAGACCGCATCACCATCACCGACAGCCTGGACCGCCGTGAAGTGCTGCACACGCAGGGCGAAGCCGGGCTGAAGCGGGTGGTGAAAAAGGAACACGCGGACGGCAGCGTCACACAGAGt                                                                                  <  1:380155/298‑1 (MQ=14)            gcagcaATACACAGGTGCGCAGCTTTACTTACGATGATAAATACCGGGGCCGGATGGTGGCGCACCGTCACACGGGCCGACCGGAAATCCGTTACCGTTACGACAGCGACGGGCGGGTGACAGAACAGCTAAACCCGGCAGGCTTAAGCTACACGTATCAGTATGAGAAAGACCGCATCACCATCACCGACAGCCTGGACCGCCGTGAAGTGCTGCACACGCAGGGCGAAGCCGGGCTGAAGCGGGTGGTGAAAAAGGAACACGCGGACGGCAGCGTCACACAGAGTCAGTTTGACGc                                                                       >  1:394473/1‑298 (MQ=14)               gcaATACACAGGTGCGCAGCTTTACTTACGATGATAAATACCGGGGCCGGATGGTGGCGCACCGTCACACGGGCCGACCGGAAATCCGTTACCGTTACGACAGCGACGGGCGGGTGACAGAACAGCTAAACCCGGCAGGCTTAAGCTACACGTATCAGTATGAGAAAGACCGCATCACCATCACCGACAGCCTGGACCGCCGTGAAGTGCTGCACACGCAGGGCGAAGCCGGGCTGAAGCGGGTGGTGAAAAAGGAACACGCGGACGGCAGCGTCACACAGAGTCAGTTTGACGCCGt                                                                    <  1:129225/298‑1 (MQ=17)                   tACACAGGTGCGCAGCTTTACTTACGATGATAAATACCGGGGCCGGATGGTGGCGCACCGTCACACGGGCCGACCGGAAATCCGTTACCGTTACGACAGCGACGGGCGGGTGACAGAACAGCTAAACCCGGCAGGCTTAAGCTACACGTATCAGTATGAGAAAGACCGCATCACCATCACCGACAGCCTGGACCGCCGTGAAGTGCTGCACACGCAGGGCGAAGCCGGGCTGAAGCGGGTGGTGAAAAAGGAACACGCGGACGGCAGCGTCACACAGAGTCAGTTTGACGCCGTGGGc                                                                >  1:374645/1‑298 (MQ=17)                   tACACAGGTGCGCAGCTTTACTTACGATGATAAATACCGGGGCCGGATGGTGGCGCACCGTCACACGGGCCGACCGGAAATCCGTTACCGTTACGACAGCGACGGGCGGGTGACAGAACAGCTAAACCCGGCAGGCTTAAGCTACACGTATCAGTATGAGAAAGACCGCATCACCATCACCGACAGCCTGGACCGCCGTGAAGTGCTGCACACGCAGGGCGAAGCCGGGCTGAAGCGGGTGGTG‑AAAAGGAACACGCGGACGGCAGCGTCACACAGAGTCAGTTTGACGCCGTGGGCa                                                               <  1:271203/298‑1 (MQ=12)                      acaGGTGCGCAGCTTTACTTACGATGATAAATACCGGGGCCGGATGGTGGCGCACCGTCACACGGGCCGACCGGAAATCCGTTACCGTTACGACAGCGACGGGCGGGTGACAGAACAGCTAAACCCGGCAGGCTTAAGCTACACGTATCAGTATGAGAAAGACCGCATCACCATCACCGACAGCCTGGACCGCCGTGAAGTGCTGCACACGCAGGGCGAAGCCGGGCTGAAGCGGGTGGTGAAAAAGGAACACGCGGACGGCAGCGTCACACAGAGTCAGTTTGACGCCGTGGGCAgg                                                             >  1:407787/1‑298 (MQ=17)                                 gCTTTACTTACGATGATAAATACCGGGGCCGGATGGTGGCGCACCGTCACACGGGCCGACCGGAAATCCGTTACCGTTACGACAGCGACGGGCGGGTGACAGAACAGCTAAACCCGGCAGGCTTAAGCTACACGTATCAGTATGAGAAAGACCGCATCACCATCACCGACAGCCTGGACCGCCGTGAAGTGCTGCACACGCAGGGCGAAGCCGGGCTGAAGCGGGTGGTGAAAAAGGAACACGCGGACGGCAGCGTCACACAGAGTCAGTTTGACGCCGTGGGCAGGCTCAGGGcaca                                                  <  1:169949/298‑1 (MQ=21)                                  cTTTACTTACGATGATAAATACCGGGGCCGGATGGTGGCGCACCGTCACACGGGCCGACCGGAAATCTGTTACCGTTACGACAGCGACGGGCGGGTGACAGAACAGCTAAACCCGGCAGGCTTAAGTTACACGTATCAGTATGAAAAAGACCGCATCACCATCACCGACAGCCTGAACCGCCGTGAAGTGCTGCACACGCAGGGCGAAGCCGGGCTGAAGCGGGGGGTGCAAAAGGAACACGCGGACGGCAGCGGCCCGCAGCGCCAGGTTGACCGCGTGGGCCGGccgaaggccaca                                                 >  2:127237/1‑287 (MQ=1)                                     tacttacGATGATAAATACCGGGGCCGGATGGTGGCGCACCGTCACACGGGCCGACCGGAAATCCGTTACCGTTACGACAGCGACGGGCGGGTGACAGAACAGCTAAACCCGGCAGGCTTAAGCTACACGTATCAGTATGAGAAAGACCGCATCACCATCACCGACAGCCTGGCCCGCCGTGAAGTGCTGCACACTCCGCGCGAAGCCGGGCTGACGCGGGGGGTGGAAAAGGAACACGCGGACCGCCGCGTCCCCCACAGTCAGTTTCACCGCGTGGGCCGGCCCggggaccagccg                                              >  2:612014/1‑290 (MQ=11)                                            gatgatAAATACCGGGGCCGGATGGTGGCGCACCGTCACACGGGCCGACCGGAAATCCGTTACCGTTACGACAGCGACGGGCGGGTGACAGAACAGCTAAACCCGGCAGGCTTAAGCTACACGTATCAGTATGAGAAAGACCGCATCACCATCACCGACAGCCTGCACCGCCGTGAAGTGCTGCCCACGCAGGGCGAAGCCCGGCTGAAGCGGGGGGGGAAAAAGGAACACCCGGACCGCCGCCTCACACAGAGGCACTTTGACCCCGTCGGACGACCCAGGGcaccaccgggagccc                                       >  2:354567/1‑286 (MQ=11)                                                 tAAATACCGGGGCCGGATGGTGGCGCACCGTCACACGGGCCGACCGGAAATCCGTTACCGTTACGACAGCGACGGGCGGGTGACAGAACAGCTAAACCCGGCAGGCTTAAGCTACACGTATCAGTATGAGAAAGACCGCATCACCATCACCGACAGTCTGGACCGCCGTGAAGTGCTGCACACGCAGGGCGAAGCCGGGCTGAAGCGGGGGGTGAAAAAGGAACACGCGGACGGCAGCGTCACACAGAGTCAGTTTGACGCCGTGGGCAGGCTAAGGGCACAGACGGATGGCgcaggc                                  >  1:186921/1‑298 (MQ=255)                                                             ccggctctgcgcgcACAGTCCCACGTGCGGATCAGAAATCCATTAACATTACGACAGCCGCGGGGGGGGGACAGAACAGGTAACCCCGGCAGGCTTAAGGTACACGTATCAGTATGAGAATGACCTCAGCTCCATCACCGACAGTCTGGACCGCCGTGAAGTGCTGCACACGCAGGGCGAAGCCGGGCTGAAGCGGGTGGTGAAAAAGGAACACGCGGACGGCAGCGTCACACAGAGTCAGTTTGACGCCGTGGGCAGGCTAAGGGCACAGACGGATGCCGCAGGCAGGACAACagag                      <  2:186921/288‑1 (MQ=11)                                                                               tCACACGGGCCGACCGGAAATCCGTTACCGTTACGACAGCGACGGGCGGGTGACAGAACAGCTAAACCCGGCAGGCTTAAGCTACACGTATCAGTATGAGAAAGACCGCATCACCATCACCGACAGCCTGGACCGCCGTGAAGTGCTGCACACGCAGGGCGAAGCCGGGCTGAAGCGGGTGGTGAAAAAGGAACACGCGGACGGCAGCGTCACACAGAGTCAGTTTGACGCCGTGGGCAGGCTCAGGGCACAGACGGATGCCGCAGGCAGGACAACAGAGGACAGCCCGGATggggtg    >  1:356436/1‑298 (MQ=255)                                                                                 ccacTGGCCGACCGGAAATCCGTTACCGTTACGACAGCCACGTGCGGGTGACAGAACAGCTAAACCCGGCAGGCTTAAGCTACACGTATCAGTATGAGAAAGACCGCATCACCATCACCGACAGCCTGGACCGCCGTGAAGTGCTGCACACGCAGGGCGAAGCCGGGCTGAAGCGGGTGGTGAAAAAGGAACACGCGGACGGCAGCGTCACACAGAGTCAGTTTGACGCCGTGGGCAGGCTCAGGGCACAGACGGATGCCGCAGGCAGGACAACAGAGTACAGCCCGGATGTGGTGAc  <  1:256634/297‑1 (MQ=255)                                                                                                     |                                                                                                                                                                                                                                                                                      AGTGTATGACCGCAGCAATACACAGGTGCGCAGCTTTACTTACGATGATAAATACCGGGGCCGGATGGTGGCGCACCGTCACACGGGCCGACCGGAAATCTGTTACCGTTACGACAGCGACGGGCGGGTGACAGAACAGCTAAACCCGGCAGGCTTAAGTTACACGTATCAGTATGAAAAAGACCGCATCACCATCACCGACAGCCTGAACCGCCGTGAAGTGCTGCACACGCAGGGCGAAGCCGGGCTGAAGCGGGTGGTGAAAAAGGAACACGCGGACGGCAGCGTCACACAGAGTCAGTTTGACGCCGTGGGCAGGCTCAGGGCACAGACGGATGCCGCAGGCAGGACAACAGAGTACAGCCCGGATGTGGTGAC  >  CP006584/793777‑794154

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑