Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AE015451	197,869	T→C	33.1%	G1125G (GGT→GGC)	PP_0168 →	putative surface adhesion protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451	197,869	0	T	C	33.1%	33.3 / 11.4	24	G1125G (GGT→GGC)	PP_0168	putative surface adhesion protein
Reads supporting (aligned to +/- strand):  ref base T (11/5);  new base C (3/5);  total (14/10)
Fisher's exact test for biased strand distribution p-value = 2.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01

TCGGTCGACACCACTACTGCGACCCTGACCGCCTCGCCAAGCGTGACCGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCTTGTCCAACGGCCAAACCATTACCGTTGAAGCGGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACGGGCGGCAACTTCGAACATCTGACTCCGAATCCGACCCCAGCCTCGACTGTCATCAATGACAGCATCGATACCGTCACCGTAAGTATTGTCAGCAATGGCAATGTGACCGAAGACCAGCAGCCTTCCTTTACTGTGAAAGTAA  >  AE015451/197720‑198101                                                                                                                                                      |                                                                                                                                                                                                                                         tCGGTCGACACCACTACTGCGACCCTGACCGCCTCGCCAAGCGTGACCGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCTTGTCCAACGGCCAAACCATTACCGTTGAAGCGGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAgcgc                                                                                                                                                    >  1:175044/1‑236 (MQ=255)                             ccGCCTCGCCAAGCGTGACCGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCTTGTCCAACGGCCAAACCATTACCGTTGAAGCGGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCt                                                                                                                                                                                            >  2:364803/1‑168 (MQ=255)                               gCCTCGCCAAGCGTGACCGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAATCCTGCCGAGACGCCGGTAACCGTGACCTTGTCCAACGGCCAAACCATTATCGTTGAAGCGGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCgg                                                                                                                                                                                                        >  2:123879/1‑154 (MQ=255)                                     ccAAGCGTGACCGAAGGCGGCGTGACCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCTTGTCCAACGGCCAAACCATTACCGTTGAAGCGGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACGGGCGGCAACtt                                                                                                                                     <  1:69492/215‑1 (MQ=255)                                                                  cTACACCGTGATCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCCTGTCCAACGGCCAAACCATTACCGTTGAAGCGGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACGGGCGGCAACTTCGAACATCTGACTCCGAATCCGACCCCAGCCTCGACTGTCATCAATGACa                                                                                   <  1:408194/236‑1 (MQ=255)                                                                         gTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCTTGTCCAACGGCCAAACCATTACCGTTGAAGCGGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACGGGCGGCAACTTCGAACATCTGACTCCGAATCCGACCCCAGCCTCGACTGtc                                                                                             <  2:175040/219‑1 (MQ=255)                                                                             cccTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCTTGTCCAACGGCCAAACCATTACCGTTGAAGCGGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACCACGGCTCGACCg                                                                                                                                                                          >  2:508928/1‑138 (MQ=255)                                                                                     aaTCCTGCCCAGACGCCGGTAACCGTGACCTTGTCCAACGGCCAAACCATTACCGTTGAAGCGGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACg                                                                                                                                                >  2:133114/1‑156 (MQ=39)                                                                                          tGCCCAGACGCCGGTAACCGTGACCTTGTCCAACGGCCAAACCATTACCGTTGAAGCGGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACGGGCGGCAACTTCGAACATCTGACTCCGAATCCGACCCCACCCTCGACt                                                                                                >  2:177391/1‑199 (MQ=255)                                                                                                    ccGGTAACCGTGACCTTGTCCAACGGCCAAACCATTACCGTTGAAGCGGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACGGGCGGCa                                                                                                                                         >  2:243832/1‑148 (MQ=39)                                                                                                     cGGTAACCGTGACCTTGTCCAACGGCCAAACCATTACCGTTGAAGCGGGTAAAGCCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACGGGCGGCAACTTCGAACATCTGACTCCGAATCCGACCCCAGCCTCGACTGTCATCAAt                                                                                       <  1:81552/197‑1 (MQ=255)                                                                                                         aaCCGTGACCTTGTCCAACGGCCAAACCATTACCGTTGAAGCGGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCCCCATCGAGAGCGCCACGGGCGGCAACTTCGAACATCTGACTCCGGATCCGACCCCAGCCTCGACt                                                                                                >  1:42288/1‑184 (MQ=255)                                                                                                                       ccAACGGCCAAACCATTACCGTTGAAGCGGGTAAAACCCa                                                                                                                                                                                                                                  >  2:41456/1‑40 (MQ=40)                                                                                                                        cAACGGCCAAACCATCACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACGGGCGGCAACTTCGAACATCTGACTCCGAATCCGACCCCAGCCt                                                                                                     <  2:502867/164‑1 (MQ=255)                                                                                                                         aaCGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGCTCGACTGTCAGCGTCACCATCGAGAACGCCACAGGCGGCAACTTCGAACAACTGACTCCGAATCCGACCCCAGCCTCGa                                                                                                  >  2:436969/1‑166 (MQ=11)                                                                                                                           cGGCCAAACCATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCGAATGACGTCTACAACAACGGTTCGACCGTCAGCGTCACCATCGAGAACGCCACGGGCGGCAACTTCGAACATCTGACTCCGAATCCGACCCCAGCCTCGACTGTCATCAATGACAGCATCGa                                                                            >  2:342078/1‑186 (MQ=14)                                                                                                                                  gccATCACCGTTGAAGCCGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACGGGCGGCAACTTCGAACATCTGACTCCGAATCCGACCCCAGCCTCGACTGTCATCAATGACAGCATCGATACCGTCACCGTAAGTATTGt                                                       <  1:386487/199‑1 (MQ=255)                                                                                                                                   ccATTACCGTTGAAGCCGGCAAGACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACGGGCGGCAACTTCGAACATCTGACTCCGAATCCGACCCCAGCCTCGACTGTCATCAATGAc                                                                                    >  1:500680/1‑170 (MQ=255)                                                                                                                                     atcaCCGTTGAAGCAGGCACAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACGGGCGGCAACTTCGAACATCTGACTCCGAATCCGACCCCAGCCTCGACTGTCATCAATGACAGCATCGATACCGTCACCGTAAGTATTGTCAGCAATGGCAATGTGACCGaa                                 <  2:145458/216‑1 (MQ=255)                                                                                                                                           ggtGAAGCGGGCAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACGGGCGGCAACTTCGAACATCTGACTCCGAATCCGACCCCAGCCTCGACTGTCATCaa                                                                                        <  2:501899/156‑1 (MQ=255)                                                                                                                                                aGCGGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCTTCACCATCGAGAGCGCCACGGGCGGCAACTTCGAACa                                                                                                                               <  2:248973/114‑1 (MQ=17)                                                                                                                                                aGCGGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACGGGCGGCAACTTCGAACa                                                                                                                               >  1:248977/1‑114 (MQ=32)                                                                                                                                                 gCGGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACGGGCGGCAACTTCGAACATCTGACTCCGAATCCGACCCCAGCCTCGACTGTCATCAATGACAGc                                                                                 >  2:157130/1‑159 (MQ=255)                                                                                                                                                     gTAAAACCCAGGGCAGCGTCGATGTCCAGCCCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACGGGCGGCAACTTCGAACATCTGACTCCGAATCCGACCCCAGCCTCGACTGTCATCAATGACAGCATCGATACCGTCACCGTAAGTATTGTCAGCAATGGCAATGTGACCGAAGACCAGCAGCCTTCCTTTACTGTGAAAGTaa  <  1:525/234‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                                                                                                         TCGGTCGACACCACTACTGCGACCCTGACCGCCTCGCCAAGCGTGACCGAAGGCGGCGTGATCACCTACACCGTGACCCTGAGCAATCCTGCCCAGACGCCGGTAACCGTGACCTTGTCCAACGGCCAAACCATTACCGTTGAAGCGGGTAAAACCCAGGGCAGCGTCGATTTCCAGACCCCGGCCAATGACGTCTACAACAACGGCTCGACCGTCAGCGTCACCATCGAGAGCGCCACGGGCGGCAACTTCGAACATCTGACTCCGAATCCGACCCCAGCCTCGACTGTCATCAATGACAGCATCGATACCGTCACCGTAAGTATTGTCAGCAATGGCAATGTGACCGAAGACCAGCAGCCTTCCTTTACTGTGAAAGTAA  >  AE015451/197720‑198101

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑