Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_bme_pgi	1,529,218	C→T	pseudogene (1317/2037 nt)	rhsE →	pseudogene, Rhs family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_bme_pgi	1,529,218	0	C	T	94.4%	40.6 / NA	18	pseudogene (1317/2037 nt)	rhsE	pseudogene, Rhs family
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (9/8);  minor base G (1/0);  total (10/8)
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

GAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGG  >  NC_000913_3_bme_pgi/1529153‑1529350                                                                  |                                                                                                                                     gAATACACACCGGCGCGAAACGATCTACTTTATCACTGCGAACCCTGCGGCGTCCTGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCt                                                   <  1:716237/149‑1 (MQ=11)          ccGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGcc                                          >  1:38508/1‑149 (MQ=11)                       ctCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCa                             >  1:286750/2‑149 (MQ=11)                             tttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGAGGCGAGGGATGTATGATGAATGGGGCAACCAGATGAAAAAGAAGAAGCGGCCTCAACTGCACAAGCCTTAACGTCAGCCACGgcgg                       >  1:335409/1‑147 (MQ=2)                                   aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGc                                           <  2:98310/123‑1 (MQ=255)                                   aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGc                                           >  1:98310/1‑123 (MQ=255)                                        gACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCAtgatga            <  1:498066/149‑1 (MQ=255)                                         accaccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTGAATGAGGAGAACCCGCATCACCTGCCCCCGCCGTACCGCCTGCCAGGGCAGCAGCATGATgag           <  1:572774/149‑1 (MQ=14)                                           caccGGGGACTGCCGCTGTCGCTGATCAGCGAAGACGGCAATACGGCGTGGCGCGCGGAGTATGATGAATGGGGCAACTAGCTTAATGAGGAGAACTCGCATCACCTGCACCAGCCGTACCGTTAGCACAGGCAGCAGCATGATgagga         >  1:675467/1‑149 (MQ=11)                                           caccGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGAGTGGCGCGGGGAGTATGATACATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTATGCCAGGGCACCAGCATGATgagga         >  1:661771/1‑149 (MQ=14)                                            accGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgaggag        >  2:679372/1‑149 (MQ=255)                                                gggACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCgg    >  1:262037/1‑149 (MQ=255)                                                gggACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGCGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCgg    <  1:202178/149‑1 (MQ=255)                                                  gacTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCgggg  <  2:628698/147‑1 (MQ=255)                                                     tGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCAc                                                     >  1:612756/1‑95 (MQ=255)                                                     tGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCAc                                                     <  2:612756/95‑1 (MQ=255)                                                             gcgcTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAAcc                                                             >  1:8950/1‑79 (MQ=255)                                                             gcgcTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAAcc                                                             <  2:8950/79‑1 (MQ=255)                                                                  |                                                                                                                                     GAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGG  >  NC_000913_3_bme_pgi/1529153‑1529350

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑