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	96.5%	61.7 / ‑4.7	29	pseudogene (1317/2037 nt)	rhsE	pseudogene, Rhs family
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (16/12);  minor base G (1/0);  total (17/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.40e-01

ACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCG  >  NC_000913_3_bme_pgi/1529131‑1529364                                                                                        |                                                                                                                                                   cggggCCCGACCGGTGGAGCCGGAATACACCCCGGCGCGCATCGGTCATCTTTCGCACGCCGTCCACCGGTGTCTGCCGCGGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTaa                                                                                      <  2:601044/147‑1 (MQ=11)                            cacacCGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCa                                                           >  2:610283/1‑150 (MQ=11)                               acCGGCGCGAAAAGCTCATCTTTATCACGGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGcc                                                        <  2:561423/150‑1 (MQ=11)                                 cGGCGCGAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCCGGCGCTTAACAGCGAAGACGGCAATACGGCGTGCCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGt                                                      >  1:447523/1‑150 (MQ=11)                                      cgAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCCCCTGCAACAGCCGTACCGt                                                 >  2:342660/1‑150 (MQ=11)                                      cgAAAAGCTCATCTTTATCACTGCGACCACCGGGGACTGCCGCTGGCGATTATCAGCGAAGACGGCAATAAGCCGAGGCGCGGGGAGTATGATCAATGGGGCAAGCCGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCga                                                 >  1:83923/1‑149 (MQ=11)                                                 tctttctcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGTCGGCAATACGGCGTGGCGCGGGGAGGAGGATGACTGGGGCAACCAGCTTACTGAGGAGAACCCGCAGCACCTGCACCAGCCGGCCCGTCTGCCAGGgca                                      <  1:156588/143‑1 (MQ=11)                                                   tttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCCGCTTAATGAGGAGAACCCGCCTCACCTGCACCCGCCGTACCGTCTGCCAGGgccgc                                    >  1:534877/1‑150 (MQ=14)                                                   tttATCACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGGATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCAACAGCCGGACCGTCTGCCAGGgcagc                                    >  1:922994/1‑150 (MQ=11)                                                       tcACTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGgcagcagca                                <  1:158859/149‑1 (MQ=255)                                                         aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCCCCAGCCGTACCGTCTGCCAGGgcagccgcagg                              >  1:208252/1‑148 (MQ=255)                                                         aCTGCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCTGCCGTACCGGCTGCCAGGGCAGCAGCatg                              >  1:211561/1‑150 (MQ=255)                                                            gCGACCACCGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCACCCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCatgatg                           >  1:279110/1‑150 (MQ=255)                                                              gACCACCGGGGAGTGCCGCTGGGGCTTATCTGCGTAGACGGCAATACGGGGTGGCGCGGGGAGTTTGTTGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCTCCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgag                         <  2:625075/150‑1 (MQ=14)                                                               accaccCGGGACTGCCGCTGGCGCTTATCAGCGACGACGGCAATACGGCGGGGAGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATgagg                        <  1:849657/150‑1 (MQ=11)                                                                  accGGGGACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGt                     <  1:149040/150‑1 (MQ=255)                                                                      gggACTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCCCCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGAGGAGGAGTCggg                 >  1:673863/1‑150 (MQ=255)                                                                       tgacTGCCGCTGTCGCTTATCAGCGAAGTAGGCAATACGGAGTGGCGCGTGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGGCgggg                <  2:656677/147‑1 (MQ=14)                                                                       ggacTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGG‑‑‑GCAGCATGATGAGGAGTCGGGGCTg             <  2:263508/147‑1 (MQ=14)                                                                       ggacTGCCGCTGGCGCTTAGCAGCGAAGACGGCAATACTGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGACCCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCgggg                <  1:724343/147‑1 (MQ=14)                                                                          cTGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTg             <  1:923251/150‑1 (MQ=255)                                                                           tGCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGt            >  1:40816/1‑150 (MQ=255)                                                                            gCCGCTGTCGATTAACAGAGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGTGGCTGTa           <  2:751814/150‑1 (MQ=17)                                                                            gCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTa           >  1:287196/1‑150 (MQ=255)                                                                            gCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTa           >  2:454774/1‑150 (MQ=255)                                                                            gCCGCTGGCGCTTATCAGCGAAGACGGCAATACGGCGGGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACACGCATCACCTGCACAAGCCGTACCGTCAGCCAGGTCAGCAGCATGATGAGGAGTCGAGGCTGTa           >  1:514179/1‑150 (MQ=17)                                                                                    cgcTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAAcc   >  2:315928/1‑150 (MQ=255)                                                                                    cgcTTATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGACAGGGCAGCAGAATGATGAGGAGTCGGGGCTGTACTATAAcc   >  2:114537/1‑150 (MQ=255)                                                                                     gcTGATAAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCCCCAGCCGTACCGTCTGCCAGGGCAGCAGCATGCTGAGGAGTCGGGGCTGTACTAGAACCg  >  1:695552/1‑150 (MQ=17)                                                                                        |                                                                                                                                                   ACTGGCCAGACAGGTGGAGCCGGAATACACACCGGCGCGAAAAGTTCATTTTTACCACTGCGACCACCGGGGCCTGCCGCTGGCGCTCATCAGCGAAGACGGCAATACGGCGTGGCGCGGGGAGTATGATGAATGGGGCAACCAGCTTAATGAGGAGAACCCGCATCACCTGCACCAGCCGTACCGTCTGCCAGGGCAGCAGCATGATGAGGAGTCGGGGCTGTACTATAACCG  >  NC_000913_3_bme_pgi/1529131‑1529364

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑