Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,472,037	A→G	pseudogene (1521/3497 nt)	ydbA →	pseudogene, autotransporter homolog, interrupted by IS2 and IS30

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,472,037	0	A	G	100.0%	148.2 / NA	42	pseudogene (1521/3497 nt)	ydbA	pseudogene, autotransporter homolog, interrupted by IS2 and IS30
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (24/18);  total (24/18)

TGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGAATGCCTTCTTCT  >  NC_000913/1471918‑1472172                                                                                                                        |                                                                                                                                        tGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACgg                                                                                                                      <  2:287370/139‑1 (MQ=255)          ataataatTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCGGGTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTaa                                                                                                             >  1:1337213/1‑139 (MQ=255)              taatTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATAtg                                                                                                         <  2:979787/139‑1 (MQ=255)                 ttCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAg                                                                                                                    >  2:992313/1‑125 (MQ=255)                 ttCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAg                                                                                                                    <  1:992313/125‑1 (MQ=255)                 ttCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTgg                                                                                                      >  2:379431/1‑139 (MQ=255)                           aaTAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATg                                                                                            >  1:771766/1‑139 (MQ=255)                                   cggcgAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCGGTAAtt                                                                                                                                   <  1:1213774/92‑1 (MQ=255)                                   cggcgAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCGGTAAtt                                                                                                                                   >  2:1213774/1‑92 (MQ=255)                                                                 tGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCg                                                      <  1:435135/139‑1 (MQ=255)                                                                           aTCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCg                                                                                        <  2:1139978/95‑1 (MQ=255)                                                                           aTCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCg                                                                                        >  1:1139978/1‑95 (MQ=255)                                                                             cAACCAGTCCGGTAGGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAg                                                                                                                    <  2:1289760/65‑1 (MQ=255)                                                                             cAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAg                                                                                                                    >  1:1289760/1‑65 (MQ=255)                                                                                  aGTTCGGTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGc                                                                                                                   <  1:242549/61‑1 (MQ=255)                                                                                  aGTCCGGTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGc                                                                                                                   >  2:242549/1‑61 (MQ=255)                                                                                     ccGGTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCg                                                                                                                 >  2:716435/1‑60 (MQ=255)                                                                                     ccGGTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCg                                                                                                                 <  1:716435/60‑1 (MQ=255)                                                                                      cGGTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCt                                 <  2:771766/139‑1 (MQ=255)                                                                                       ggTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAg                                                                                                                    <  1:1030603/55‑1 (MQ=255)                                                                                       ggTACGCTTTATAATACCGGTCACATGAACATCGGTAATTCTTCCCACAACGGAg                                                                                                                    >  2:1030603/1‑55 (MQ=255)                                                                                                       ccGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGa                                                                        >  1:251920/1‑83 (MQ=255)                                                                                                       ccGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGa                                                                        <  2:251920/83‑1 (MQ=255)                                                                                                        cGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAgcg                                   >  2:153008/1‑119 (MQ=255)                                                                                                        cGGTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAgcg                                   <  1:153008/119‑1 (MQ=255)                                                                                                          gTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGa                                                                        <  1:31402/80‑1 (MQ=255)                                                                                                          gTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGa                                                                        >  2:31402/1‑80 (MQ=255)                                                                                                          gTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTg                                                        <  1:578608/96‑1 (MQ=255)                                                                                                          gTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTg                                                        >  2:578608/1‑96 (MQ=255)                                                                                                          gTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGt                                        <  1:1150675/112‑1 (MQ=255)                                                                                                          gTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGt                                        >  2:1150675/1‑112 (MQ=255)                                                                                                          gTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGaa             >  1:9438/1‑139 (MQ=255)                                                                                                          gTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGaa             >  1:910308/1‑139 (MQ=255)                                                                                                          gTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGaa             >  1:377417/1‑139 (MQ=255)                                                                                                          gTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGaa             >  1:1107331/1‑139 (MQ=255)                                                                                                          gTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGaa             >  2:368226/1‑139 (MQ=255)                                                                                                          gTCACATGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGCAGTCAGCGCTAATAATGCCGGCGATCAGaa             >  1:947931/1‑139 (MQ=255)                                                                                                               aTGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGAATGCct        >  2:361752/1‑139 (MQ=255)                                                                                                                tGAACATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGAATGCctt       >  1:656160/1‑139 (MQ=255)                                                                                                                    cATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGt                                                  <  2:1050084/92‑1 (MQ=255)                                                                                                                    cATCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGt                                                  >  1:1050084/1‑92 (MQ=255)                                                                                                                     aTCGGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGAATGCCTtcttct  <  1:361752/139‑1 (MQ=255)                                                                                                                        |                                                                                                                                        TGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGCTAATAATGCCGGCGATCAGAATGCCTTCTTCT  >  NC_000913/1471918‑1472172

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑