Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AE015451	211,465	T→C	13.1%	V5657V (GTT→GTC)	PP_0168 →	putative surface adhesion protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451	211,465	0	T	C	13.1%	78.4 / 2.9	30	V5657V (GTT→GTC)	PP_0168	putative surface adhesion protein
Reads supporting (aligned to +/- strand):  ref base T (12/14);  new base C (2/2);  total (14/16)
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

GGCACCCCAGGCAACCCGGGCGGCAGCAACGAAGGCGACCTGGTCAAGGTCACCATCACGGCCGACCAGACTTCGTTGGCCGAGAACGTCAAACCGACGTTCACCGTACACGTCAACCAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCAAGTGACCGATACCACCGACGAAGTGGTGGCCAAGCTGACCGCGACGCCTTCGGTGACCGAAGGTGGTGAGATCACCTACACCATCACCCTGACCAACAAA  >  AE015451/211238‑211666                                                                                                                                                                                                                                    |                                                                                                                                                                                                          ggCACCCCAGGCAACCCGGGCGGCAGCAACGAAGGCGACCTGGTCAAGGTCACCATCACGGCCGACCAGACTTCGTTGGCCGAGAACGTCAAACCGACGTTCACCGTACACGTCAACCAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAacga                                                                                                                                                                                                   >  1:679003/1‑236 (MQ=33)            cAACCCGGGCGGCAGCAACGAAGGCGACCTGGTCAAGGTCACCATCACGGCCGACCAGACTTCGTTGGCCGAGAACGTCAAACCGACGTTCACCGTACACGTCAACCAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGTGAAACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTCTACAACGATGCTGGcc                                                                                                                                                                                           <  2:720309/233‑1 (MQ=16)              aCCCGGGCGGCAGCAACGAAGGCGACCTGGTCAAGGTCACCATCACGGCCGACCAGACTTCGTTGGCCGAGAACGTCAAACCGACGTTCACCGTACACGTCAACCAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGAt                                                                                                                                                                                       >  1:425223/1‑235 (MQ=32)                                   gCGACCTGGTCAAGGTCACCATCACGGCCGACCAGACTTCGTTGGCCGAGAACGTCAAACCGACGTTCACCGTACACGTCAACCAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTcggc                                                                                                                                                                  <  1:326982/235‑1 (MQ=31)                                             cAAGGTCACCATCACGGCCGACCAGACTTCGTTGGCCGAGAACGTCAAACCGACGTTCACCGTACACGTCAACCAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTCTACa                                                                                                                                                                                                       >  2:683817/1‑188 (MQ=17)                                                    aCCATCACGGCCGACCAGACTTCGTTGGCCGAGAACGTCAAACCGACGTTCACCGTACACGTCAACCAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTg                                                                                                                                                    <  2:268764/232‑1 (MQ=31)                                                              ccGACCAGACTTCGTTGGCCGAGAACGTCAAACCGACGTTCACCGTACACGTCAACCAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTCTACAACGATGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGt                                                                                                                                                  >  2:402098/1‑224 (MQ=14)                                                               cGACCAGACTTCGTTGGCCGAGAACGTCAAACCGACGTTCACCGTACACGTCAACCAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCgaga                                                                                                                                     <  1:672790/236‑1 (MQ=31)                                                                gACCAGACTTCGTTGGCCGAGAACGTCAAACCGACGTTCACCGTACAAGTCAACCAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGAc                                                                                                                                                           <  1:173894/213‑1 (MQ=14)                                                                    agccTTCGTTGGCCGAGAACTCCAAACCGACGTTCACCGTACACGTCAACCAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTc                                                                                                                                <  1:116421/233‑1 (MQ=14)                                                                                            aaCCGACGTTCACCGTACACGTCAACCAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGt                                                                                                         >  1:277919/1‑235 (MQ=37)                                                                                               cGACGTTCACCGTACACGTCAACCAGCCGCTGGCCCACGGCCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGtt                                                                                                        <  1:157938/233‑1 (MQ=37)                                                                                               cGACGTTCACCGTACACGTCAACCAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCaa                                                                                                     <  1:456160/236‑1 (MQ=38)                                                                                                     tCACCGTACACGTCAACCAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCAAGTGAcc                                                                                               <  1:554322/236‑1 (MQ=37)                                                                                                                      cAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGGCGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCAAGTg                                                                                                  >  1:251530/1‑216 (MQ=21)                                                                                                                      cAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTCCAAGTGACCGACACCACCGACGaa                                                                                >  1:575182/1‑234 (MQ=18)                                                                                                                                       ccTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCAAGTGACCGATACCACCGACGAAGTGGTGGCCAAGCTGAcc                                                              <  1:367461/235‑1 (MQ=37)                                                                                                                                                                  ccAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCAAGTGACCGATACCACCGACGAAGTGGTGGCCAAGCTGACCGCGACGCCTTCGGTGACCGAAGgtggtg                                  <  1:237277/236‑1 (MQ=255)                                                                                                                                                                            aTCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCAAGTGACCGATACCACCGACGAAGTGGTGGCCAAGCTGACCGCGACGCCTTCGGTGACCGAAGGTGGTGAGATCAc                           >  2:497564/1‑233 (MQ=255)                                                                                                                                                                                  gccggCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGCGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCAAGTGACCGATACCACCGACGAAGTGGTGGCCAAGCTGACCGCGACGCCTTCGGTGACCGAAGGTGGTGAGATCACCTACACCa                   <  1:486885/232‑1 (MQ=255)                                                                                                                                                                                  gCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCAAGTGACCGATACCACCGACGAAgtg                                                                             >  2:609391/1‑177 (MQ=38)                                                                                                                                                                                        gagaCCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCAAGTGACCGATACCACCGACGAAGTGGTGGCCAAGCTGACCGCGACGCCt                                                     <  1:725995/195‑1 (MQ=255)                                                                                                                                                                                        gagaCCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCAAGTGACCGATACCACCGACGAAGTGGTGGCCAAGCTGACCGCGACGCCt                                                     >  2:725994/1‑195 (MQ=255)                                                                                                                                                                                        gagaCCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTCCAAGTGACCGaca                                                                                           >  2:733143/1‑155 (MQ=21)                                                                                                                                                                                                                  tGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCAAGTGACCGATACCACCGACGAAGTGGTGGCCAAGCTGACCGCGACGCCTTCGGTGACCGAAGGTGGTGAGATCACCTACACCATCACCCTGACcaaca    <  1:709574/218‑1 (MQ=255)                                                                                                                                                                                                                  tGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCAAGTGACCGATACCACCGACGAAGTGGTGGCCAAGCTGACCGCGACGCCTTCGGTGACCGAAGGTGGTGAGATCACCTACACCATCACCCTGACcaaca    >  2:709573/1‑218 (MQ=255)                                                                                                                                                                                                                    cgcAGGGTGATGACGTCTACAACGACGCTGGCCAGATCAGCCTGGGTATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCAAGTGACCGATACCACCGACGAAGTGGTGGCCAAGCTGACCGCGACGCCTTCGGTGACCGAAggtggt                                   <  1:473282/185‑1 (MQ=255)                                                                                                                                                                                                                       aGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGTGCGGTGCGGCTTCGGTTCTAGTGACCGATACCACCGACGAAGTGGTGGCCAAGCTGACCGCGACGCCGTCGGTGACCTAAGGCGGTGAGATCACCTACACCATCACCCTGACcaaccac  >  2:697418/1‑212 (MQ=255)                                                                                                                                                                                                                       aGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCAAGTGACCGATACCACCGACGAAGTGGTGGCCAAGCTGACCGCGACGCCTTCGGTGACCGAAGGTGGTGAGATCACCTACACCATc                 <  2:664747/200‑1 (MQ=255)                                                                                                                                                                                                                       aGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCAAGTGACCGATACCACCGACGAAGTGGTGGCCAAGCTGACCGCGACGCCTTCGGTGACCGAAGGTGGTGAGATCACCTACACCATc                 >  1:664748/1‑200 (MQ=255)                                                                                                                                                                                                                                    |                                                                                                                                                                                                          GGCACCCCAGGCAACCCGGGCGGCAGCAACGAAGGCGACCTGGTCAAGGTCACCATCACGGCCGACCAGACTTCGTTGGCCGAGAACGTCAAACCGACGTTCACCGTACACGTCAACCAGCCGCTGGCCCACGACCTGGTCGTGACCCTGAGCAACAACGCCCAGGTCACCATCAAGGCTGGCGAGACCAGCGCGCCGTACACCCACGCTGCGCAGGGTGATGACGTTTACAACGACGCTGGCCAGATCAGCCTGGGCATCAACTCGGCGGTGGACGCCACTGGTGCGACCTTCGAGAACCTCGAGCTGGGCGGTGCGGCTTCGGTTCAAGTGACCGATACCACCGACGAAGTGGTGGCCAAGCTGACCGCGACGCCTTCGGTGACCGAAGGTGGTGAGATCACCTACACCATCACCCTGACCAACAAA  >  AE015451/211238‑211666

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑