Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,529,180	T→C	pseudogene (1279/2037 nt)	rhsE →	pseudogene, Rhs family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,529,180	0	T	C	95.5%	36.9 / NA	22	pseudogene (1279/2037 nt)	rhsE	pseudogene, Rhs family
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (6/15);  minor base A (0/1);  total (6/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

CTGGACAGGCTGGAGGAAGAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTGAGAGGTGGATGGAATA  >  NC_000913/1529042‑1529438                                                                                                                                           |                                                                                                                                                                                                                                                                   ctgGACAGGCTGGAGGAAGAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCg                                                                                                                            <  1:291886/275‑1 (MQ=12)                   gaaATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCat                                                                                                         >  1:359134/1‑276 (MQ=12)                              aggccGCGGGAGGAGTGAAAGGCGAGGGGGGCTGGCGCAGGGGGGGGTGACGGTGGGGCAACTGGCCAGACATGTGGAGCCGGAATAAAAACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGt                                                                                               <  2:92109/272‑1 (MQ=11)                              agacgggttgggCAGTGAAAGCGGGGCGTGGCGTGCGCAGGGGGGGGTGAAGGGGGAGCAAATGGCCAGAAAGGTGGAGCCGGAATACACACCGGGGCGAAAAGCACAGCTTTAGCACGGCGACCAACGGGGACGGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGt                                                                                               <  2:364728/264‑1 (MQ=11)                                  cgcgtgggtgtggAAAGCCGGGGGTGGCTGGAGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCAGCTTTATCACTGCGACCACCGGGGACGGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCgggg                                                                                          <  2:396415/264‑1 (MQ=11)                                   gggTGGGCAGTGAAAGCCGGGGGTGGCGTGCGCAGGGCGGGCTGACGGGGGAGAAAATGGCCAGACAGGTGGGGCCGGAATAAACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACGGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGc                                                                                         <  2:377437/274‑1 (MQ=11)                                     gTGAGCAGTGACAGCCGGTCGTGGCTTGCGCAGTGCGGGCGCACGGTGGAGCACCTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTg                                                                                       <  1:146061/276‑1 (MQ=11)                                          caggggaaGGCGGGCGGGGCTGGCGCAGTGCGGGCAGACGTGTGAGCAACTGGCCATACAGGTGGAGCCGGATGCCACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGTGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACt                                                                                   <  1:293775/269‑1 (MQ=11)                                          cAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGCACCCGCATCACCTGCACCACCCGTACCGTCTGCCAGGGCAGCAGCATGATGCGGAGTCGGGGGGGTACt                                                                                   >  2:348356/1‑275 (MQ=11)                                                     gggCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACGGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCAc                                                                        <  1:78989/275‑1 (MQ=255)                                                        gtgggCTTGCGCAGTGCGGGCGGACGGGGGAGCAACTGGCCTGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCgg                                                                     <  2:404859/272‑1 (MQ=255)                                                        cggggatggcgcAGTGCGGACTGACTGTGAGGAAAAGGGCAAGACAGGTGGACCAGGAATACACACCGGCGCGAAACGCTCATATTTATCACGGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCgg                                                                     <  2:37299/267‑1 (MQ=11)                                                              ttGCGCAGTGCGGGCTGACGGTGGAGCAACGGGCCGGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCCCGGCGACCACCGGGGACTGCCGCTGGCGCTGATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGGCACCGGCACTACg                                                              <  1:20099/276‑1 (MQ=11)                                                                            cTGACGGTGGGGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAgggg                                                <  1:16818/276‑1 (MQ=255)                                                                             ggACGGTGGATCAACGGGCCAGACAGGTGGAGCCGGAATACACCCCGGCTCGAAAATCTCATCTCTATCACCGCGAGCACCGGGGACTGCCGCTGGCGTTTATCATCTAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAgggg                                                <  1:150579/274‑1 (MQ=11)                                                                                cGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGCAGACGGCAATACGGCGTGGCGCGGGGCGTCTGATGAATGGGGCAACCAGCTTAATGAGGAGAGCCCGCATCACCTGAACCAGCAGTACATTATGCCAGGGCAGCCGCATGATGAGCAGTCGGGTCTGACCTATACCCGGCTCAGCCACTCGCATCCGTTGCAGggggggg                                            >  2:241407/1‑275 (MQ=11)                                                                                cGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCCGCAGACTGACGCGGAGTCGGGGCTGTACTATAACCGTACCCGGCACTACGACCCGTTGCCGGGGCgg                                             >  2:252601/1‑275 (MQ=11)                                                                                            cggCCAGACAGGTGGAGCCGTAATCCACAGCGGCGAGAGAAGCTCATCTTAACCACTCCGACCGCCGAGGGCTGCCGCTGGCGCTTATCAGCGAAGACGGCAATGCGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTAGCAGGGGCGGTATATCACCCCgg                                <  1:132351/275‑1 (MQ=14)                                                                                                  caCATGTGGAGCCGAAATGACCGCCGGCTCTACAAGCGCATCTTTTGCACTGCCACCACCGGGGAGTGCCGCTGGCGCTGATCAGCGAAGACTGCAAGACGGCGTGGCGCGGGGAGTATGATGAATTGGTCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGa                          <  1:174309/275‑1 (MQ=14)                                                                                                             ccGGAATACACACCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCCCCGGCACTCCGATCCGTTGCAGGGCGGGTTTAACACCCCGTGCCCCGTAGGGTTgaga               >  2:404191/1‑276 (MQ=14)                                                                                                                  aTACACGCCGTCGCGAAAAGCGCGTCTTTGACACTGTGACCGCCGGGGGATGCGGCGGGTGCGTATCAGGGAAGCCGGCAATACGGCGGGGGGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGGGGGGAGCCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTGAGAGGtgg          <  2:332217/276‑1 (MQ=14)                                                                                                                          cGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACAGTCACCGGCACTACGCTCAGTGGCAGGGGCGGTATATCCACCCGGACCCGATTGGGGTGGGCggtgggtgtgcgc  >  2:330822/1‑271 (MQ=14)                                                                                                                                           |                                                                                                                                                                                                                                                                   CTGGACAGGCTGGAGGAAGAAATCCGGGCAGACCGCGTGAGCAGTGAAAGCCGGGCGTGGCTTGCGCAGTGCGGGCTGACGGTGGAGCAACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCGTCACCGGCACTACGATCCGTTGCAGGGGCGGTATATCACCCCGGACCCGATTGGGTTGAGAGGTGGATGGAATA  >  NC_000913/1529042‑1529438

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑