Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AE015451	3,904,004	T→G	9.1%	I247L (ATC→CTC)	ilvA‑I ←	threonine deaminase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451	3,904,004	0	T	G	9.1%	109.2 / 4.4	37	I247L (ATC→CTC)	ilvA‑I	threonine deaminase
Reads supporting (aligned to +/- strand):  ref base T (15/18);  new base G (2/2);  total (17/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.27e-01

CACACCTTCACGCGCCACGTACTTCTTGATACCGGCCACGGCCAAGGCCCCGGACGGCTCGGTGATCGAACGGGTGTCGTCGTAGATATCCTTGATCGCCGCGCACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAGGTACTTCACATAGGCGGCGATCCCGGCGATCAAGCCGCCACCGCCCACGGGCACAAAGATCGCGTCCAACGCCCCAGGGCGCTGACGGAGGATTTCCATGGC  >  AE015451/3903780‑3904190                                                                                                                                                                                                                                 |                                                                                                                                                                                           cacaCCTTCACGCGCCACGTACTTCTTGATACCGGCCACGGCCAAGGCCCCGGACGGCTCGGTGATCGAACGGGTGTCGTCGTAGATATCCTTGATCGCCGCGCACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCg                                                                                                                                                                                  <  1:296724/235‑1 (MQ=255)         cACGCGCCACGTACTTCTTGATACCGGCCACGGCCAAGGCCCCGGACGGCTCGGTGATCGAACGGGTGTCGTCGTAGATATCCTTGATCGCCGCGCACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCAc                                                                                                                                                                                         >  1:494860/1‑220 (MQ=255)         cACGCGCCACGTACTTCTTGATACCGGCCACGGCCAAGGCCCCGGACGGCTCGGTGATCGAACGGGTGTCGTCGTAGATATCCTTGATCGCCGCGCACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCAc                                                                                                                                                                                         <  2:494859/220‑1 (MQ=255)            gcgcCACGTACTTCTTGATACCGGCCACGGCCAAGGCCCCGGACGGCTCGGTGATCGAACGGGTGTCGTCGTAGATATCCTTGATCGCCGCGCACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGcgtgg                                                                                                                                                                      <  1:478124/236‑5 (MQ=255)                               aCCGGCCACGGCCAAGGCCCCGGACGGCTCGGTGATCGAACGGGTGTCGTCGTAGATATCCTTGATCGCCGCGCACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTg                                                                                                                                                    >  1:455625/1‑235 (MQ=255)                                      acggccaAGGCCCCGGACGGCTCGGTGATCGAACGGGTGTCGTCGTAGATATCCTTGATCGCCGCGCACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGCTCACGCGCCCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGact                                                                                                                                                >  1:197008/1‑230 (MQ=255)                                                   cGGACGGCTCGGTGATCGAACGGGTGTCGTCGTAGATATCCTTGATCGCCGCGCACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCg                                                                                                                               <  1:354357/236‑1 (MQ=255)                                                      aCGGCTCGGTGATCGAACGGGTGTCGTCGTAGATATCCTTGATCGCCGCGCACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCg                                                                                                                                                                                  <  1:309243/182‑1 (MQ=255)                                                            cGGTGATCGAACGGGTGTCGTCGTAGATATCCTTGATCGCCGCGCACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCt                                                                                                                        >  1:515170/1‑234 (MQ=255)                                                                                           cTTGATCGCCGCGCACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCt                                                                                                                                                               <  2:291729/164‑1 (MQ=255)                                                                                           cTTGATCGCCGCGCACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCt                                                                                                                                                               >  1:291730/1‑164 (MQ=255)                                                                                                     gcgcACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCt                                                                                                                                       <  1:511503/178‑1 (MQ=255)                                                                                                      cgcACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCGAGCGCGTGATCCTGCCGCAGGTGGGCACCTTTGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAGGTACTTCACATAGGCGGCGATCCCGGc                                                                             >  1:744797/1‑235 (MQ=255)                                                                                                       gcACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTgc                                                                                                                                                             >  2:369123/1‑154 (MQ=255)                                                                                                       gcACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTgc                                                                                                                                                             <  1:369124/154‑1 (MQ=255)                                                                                                              tCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAGGTACTTCACATAGGCGGCGATCCCGGCGATCAAg                                                                      <  1:403763/234‑1 (MQ=255)                                                                                                                          aCCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGc                                                                                                                                                                          >  2:26734/1‑122 (MQ=255)                                                                                                                          aCCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACCCCgct                                                                                                                             >  2:39557/1‑165 (MQ=255)                                                                                                                                    ccTCGTCGACGAAGTGGCGGCACAGCTCGAAGCCATGGGCGCCGCTCTGCCCCACCGCCACGCCGTCGACAAAGGTGCCCACCTGCGGCAGGATCAcg                                                                                                                                                                                        >  2:34828/1‑98 (MQ=255)                                                                                                                                           gacgaAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCGAGCGCGTGATCCTGCCGCAGGTGGGCACCTTTGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAGGTACTTCACATAGGCGGCGATCCCGGCGATCAAGCCGCCACCGccc                                                          >  1:271205/1‑217 (MQ=37)                                                                                                                                           gacgaAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCGAGCGCGTGATCCTGCCGCAGGTGGGCACCTTTGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAGGTACTTCACATAGGCGGCGATCCCGGCGATCAAGCCGCCACCGccc                                                          <  2:271204/217‑1 (MQ=25)                                                                                                                                                             cgcGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCAc                                                                                                                    <  2:12780/139‑1 (MQ=255)                                                                                                                                                               cGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAGGTACTTCACATAGGCGGCGATcc                                                                                 >  1:381133/1‑174 (MQ=255)                                                                                                                                                                    cAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAGGTACTTCACATAGGCGGCGATCCCGGCGATCAAGCCGCCACCGCCCACGGGCACAAAGATCGCGTCCAACGc                                <  1:455222/218‑1 (MQ=255)                                                                                                                                                                          gcgcCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAGGTACTTCACATAGGCGGCGATCCCGGCGATCAAGCCGCCACCGc                                                            <  2:348376/184‑1 (MQ=255)                                                                                                                                                                          gcgcCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGAAGGTACTTCACATAGGCGGCGATccc                                                                                >  1:49163/1‑164 (MQ=255)                                                                                                                                                                             ccGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCAt                                                                                                                                                                       <  1:164256/74‑1 (MQ=255)                                                                                                                                                                                       ccaccgccacGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAGGTACTTCACATAGGCGGCGATCCCGGCGATCAAGCCGCCACCGCCCACGGGCACAAAGATCGCGTCCAACGCCCCAGGGCGCTGACGGAGGATTTCCa      <  1:39557/225‑1 (MQ=255)                                                                                                                                                                                        ccccgccacGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGt                                                                                                                  <  1:225232/114‑1 (MQ=255)                                                                                                                                                                                          ccgccacGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAGGTACTTCACATAGGCGGCGATCCCGGCGATCAAGCCGCCACCGCCCACGGGCACAAAGATCGCGTCCAACGc                                <  1:203180/196‑1 (MQ=255)                                                                                                                                                                                          ccgccacGCCGTCGGCAAAGGTGCCCACCGGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAg                                                                                                        <  2:145706/124‑1 (MQ=255)                                                                                                                                                                                            gccacGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAGGTACTTCACATAGGCGGCGATCCCGGCGATCAAGCCGCCACCGCCCACGGGCACAAAGATCGCGTCCAACGCCCCAGGGCGCTGACGGAGGATTTCCATGGc  <  1:475983/224‑1 (MQ=255)                                                                                                                                                                                                  ccGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAGGTACTTCACATAGGCGGCGATCCCGGCGATCAAGCCGCCACCGCCCACGGGCACAAAGATCGCGTCCAACGCCCCAGGGCGCTGACg                 >  1:608300/1‑203 (MQ=255)                                                                                                                                                                                                       ggCAAAGGTGCCCACCTGCGGCAGGAGCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAGGTACTTCACATAGGCGGCGATCCCGGCGATCAAgccg                                                                   <  2:193736/148‑1 (MQ=255)                                                                                                                                                                                                         cAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAGGTACTTCACATAGGCGGCGATCCCGGCGATCAAGCCGCCACCGCCCACGGGca                                                   >  2:410996/1‑162 (MQ=255)                                                                                                                                                                                                              gTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAGGTACTTCACATAGGCGGCGATccc                                                                                >  2:315861/1‑128 (MQ=255)                                                                                                                                                                                                                    aCCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACCTCAGGGCCCAGGTACTTCACATa                                                                                            >  2:30871/1‑110 (MQ=255)                                                                                                                                                                                                                                 |                                                                                                                                                                                           CACACCTTCACGCGCCACGTACTTCTTGATACCGGCCACGGCCAAGGCCCCGGACGGCTCGGTGATCGAACGGGTGTCGTCGTAGATATCCTTGATCGCCGCGCACAGCTCGTCACTGCTCACCGTCACCACCTCGTCGACGAAGTGGCGGCACAGCTCGAAGCAATGGGCGCCGATCTGCGCCACCGCCACGCCGTCGGCAAAGGTGCCCACCTGCGGCAGGATCACGCGCTCGCCGACGGCCATGGCAGCCTGCAGGCAGTTGGAATCTGCCGGCTCGACACCGATCACCTTCACGTCAGGGCGCAGGTACTTCACATAGGCGGCGATCCCGGCGATCAAGCCGCCACCGCCCACGGGCACAAAGATCGCGTCCAACGCCCCAGGGCGCTGACGGAGGATTTCCATGGC  >  AE015451/3903780‑3904190

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑