Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_vch_pgi	1,503,354	C→T	pseudogene (296/432 nt)	insP ←	pseudogene, IS609 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_vch_pgi	1,503,354	0	C	T	100.0%	99.6 / NA	32	pseudogene (296/432 nt)	insP	pseudogene, IS609 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (17/15);  total (17/15)

TTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTGGCAAAATAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTCGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAGTTAATTAACAAATGGACGTGATCTGGTTCGCCATCCATTTCAACCAGTTCAGCTTCAAAATCAGCACAT  >  NC_000913_3_vch_pgi/1503212‑1503494                                                                                                                                               |                                                                                                                                             ttCCACCTGACCAGGTGTTCGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTGGCAAAATAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCa                                                                                                                                        <  1:186384/149‑1 (MQ=255)     aCCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTGGCAAAATAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCa                                                                                                                                    <  1:342937/149‑1 (MQ=255)     aCCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTGGCAAAATAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCa                                                                                                                                    >  1:554021/1‑149 (MQ=255)     aCCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTGGCAAAATAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCa                                                                                                                                    >  1:554302/1‑149 (MQ=255)                tgtTTGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTGGCAAAATAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATa                                                                                                                         >  1:118754/1‑149 (MQ=255)                            ttCAATGTATTGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTGGCAAAATAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGc                                                                                                             >  1:310416/1‑149 (MQ=255)                              aaaTGTATTGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTGGCGGAATAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGCTCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTg                                                                                                           >  2:406513/2‑149 (MQ=255)                                     ttGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTGGCAAAATAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCa                                                                                                    >  2:389801/1‑149 (MQ=255)                                         cGGATGATGGATATTGGCCCACCTCCGCAGCTACCGGCAAAATAGCCAGGACTCCTCAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACt                                                                                                <  2:248390/149‑1 (MQ=255)                                                 ggATATTGGCGCACCTCCGCAGCTACTGGCAAAATAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCg                                                                                        >  2:497718/1‑149 (MQ=255)                                                           gcACCTCCGCAGCTACTGGCAAAATAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCATTGAGGCTGTTTCCCAGACTTGATATCGCCAGTGTggg                                                                              >  2:124556/1‑149 (MQ=255)                                                            cACCTGCGCAGCTACTGGCAAAATAGCCAGGACTCCACGAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGgga                                                                             <  2:461805/149‑1 (MQ=255)                                                            cACCTCCGCAGCTACTGGCAAAATAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACTCCTTGGAGCCTGTTTACCAGACTGGATATCGCCAGTTTGgga                                                                             <  2:372669/149‑1 (MQ=255)                                                             aCCTCCGCAGCTACTGGCAAAATAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGCGGCTGTTTACCAGACTGCATATCGCCCGTTCGggag                                                                            >  2:489137/1‑149 (MQ=255)                                                                  cGCAGCTACTGGCAAAATAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAg                                                                       <  1:150002/149‑1 (MQ=255)                                                                   gCAGCTACTGGCAAAATAGCCAGGACTCCACAAATCGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAGt                                                                      <  2:554302/149‑1 (MQ=255)                                                                   gCAGCTACTGGCAAAATAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAGt                                                                      <  2:554021/149‑1 (MQ=255)                                                                                 aaTAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTCGGAGGATAGTTAATTAACAAATgg                                                        <  1:479781/149‑1 (MQ=255)                                                                                      ccAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAGTTAATTAACAAATGGACGTg                                                   >  2:522089/1‑149 (MQ=255)                                                                                            cTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAGTTAATTAACAAATGGACGTGATCTgg                                             <  1:512336/149‑1 (MQ=255)                                                                                             tCCACCAAACGCCTTTGTAGAAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAGTTAATTAACAAATGGACGTGATCTGGt                                            <  1:147510/149‑1 (MQ=255)                                                                                             tCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAGTTAATTAACAAATGGACGTGATCTGGt                                            >  1:145794/1‑149 (MQ=255)                                                                                                       gCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTCGGGAGGAACGTTAATTAACAAATGGACGTGAGCTGGTTCGccatgca                                  >  2:293565/1‑149 (MQ=255)                                                                                                                   aTACCTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAGTTAATTAACAAATCGACGTGATCTGGTTCGCCCTCCATTTCAACCAGtt                      >  2:221341/1‑149 (MQ=255)                                                                                                                      ccTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAGTTAATTAACAAATGGACGTGATCTGGTTCGCCATCCATTTCAACCAGTTCAg                   >  1:487377/1‑149 (MQ=255)                                                                                                                      ccTGAATGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAGTTAATTAACAAATGGACGTGATCTGGTTCGCCATCCATTTCAACCAGTTCAg                   <  2:310416/149‑1 (MQ=255)                                                                                                                            tGCAATATCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAGTTAATTAACAAATGGACGTGATCTGGTTCGCCATCCATTTCAACCAGTTCAGCTTCaa             >  2:550958/1‑149 (MQ=255)                                                                                                                                 gttgaggTCGGTGTTGTCGCAGTCACCTACCCGCTGCGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTGTGGGAGGATAGTTAATTAACAAATGGACGTGATCTGGTTCGCCATCCATTTCAACCAGTTCAGCTTCAACATCa        <  2:303616/144‑1 (MQ=255)                                                                                                                                  atCTGGTCGATCTTGTCGCAGTCACCTACTCGCTTCCCATTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAGTTAATTAACAAATGGACGTGATCTGGTTCGCCATCCATTTCAACCAGTTCAGCTTCAAAATCAg       <  1:431354/149‑1 (MQ=255)                                                                                                                                   tCTGGTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAGTTAATTAACAAATGGACGTGATCTGGTTCGCCATCCATTTCAACCAGTTCAGCTTCAAAATCAGc      <  1:377264/149‑1 (MQ=255)                                                                                                                                       gTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAGTTAATTAACAAATGGACGTGATCTGGTTCGCCATCCATTTCAACCAGTTCAGCTTCAAAATCAGCacat  >  1:335070/1‑149 (MQ=255)                                                                                                                                       gTCGATCTTGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAGTTAATTAACAAATGGACGTGATCTGGTTCGCCATCCATTTCAACCAGTTCAGCTTCAAAATCAGCacat  >  1:31221/1‑149 (MQ=255)                                                                                                                                               |                                                                                                                                             TTCCACCTGACCAGGTGTTTGCTGTTGTTCAATGTATTGGCGGATGACGGATATTGGCGCACCTCCGCAGCTACTGGCAAAATAGCCAGGACTCCACAAAACGCCTTTGTAGTAATACCTGAATGCAATATCTGGTCGATCTCGTCGCAGTCACCTACCCGATACGCCTTTGAGGCTGTTTACCAGACTGGATATCGCCAGTTTGGGAGGATAGTTAATTAACAAATGGACGTGATCTGGTTCGCCATCCATTTCAACCAGTTCAGCTTCAAAATCAGCACAT  >  NC_000913_3_vch_pgi/1503212‑1503494

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: ‑