Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,597,873	T→C	pseudogene (214/5422 nt)	yneO ←	AIDA‑I family autotransporter YneO

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,597,873	0	T	C	100.0%	200.2 / NA	56	pseudogene (214/5422 nt)	yneO	AIDA‑I family autotransporter YneO
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (39/17);  total (39/17)

GTCCTCATTAGCGCCAATGACGCTGGTAGTAATAGTGGTTAAGGAGGCATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGTAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCAGAGGATTTACGCAAATTAACCGTCGATGT  >  NC_000913/1597739‑1598002                                                                                                                                       |                                                                                                                                  gTCCTCATTAGCGCCAATGACGCTGGTAGTAATAGTGGTTAAGGAGGCATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCt                                                                                                                              <  1:585965/140‑1 (MQ=255)    cTCATTAGCGCCAATGACGCTGGTAGTAATAGTGGTTAAGGAGGCATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAGCCAGGTAGACATAATAAGCAACATCGGTATTAATATTGGCAATCTGAt                                                                                                                           >  2:224559/1‑140 (MQ=255)      cATTAGCGCCAATGACGCTGGTAGTAATAGTGGTTAAGGAGGCATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCa                                                                                                                         >  1:62922/1‑140 (MQ=255)                          gtagtaATAGTGGTTAAGGAGGCATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTc                                                                                                              <  1:738736/131‑1 (MQ=255)                          gtagtaATAGTGGTTAAGGAGGCATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTc                                                                                                              >  2:738736/1‑131 (MQ=255)                             gtaATAGTGGTTAAGGAGGCATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCAcc                                                                                                  <  2:414292/140‑1 (MQ=255)                             gtaATAGTGGTTAAGGAAGCATAACCGCCAGTCTAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCAcc                                                                                                  <  2:349796/140‑1 (MQ=255)                                    tGGTTAAGGAGGCATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATTAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCt                                                                                           >  2:653498/1‑140 (MQ=255)                                    tGGTTAAGGAGGCATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCt                                                                                           >  2:583470/1‑140 (MQ=255)                                        tAAGGAGGCATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGGTCATTATCAACTTCCAGACTTCCACCAGACGCTGAAc                                                                                       >  1:371224/1‑140 (MQ=255)                                         aaGGAGGCATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCAcc                                                                                                  >  1:547054/1‑128 (MQ=255)                                         aaGGAGGCATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCAcc                                                                                                  <  2:547054/128‑1 (MQ=255)                                         aaGGAGGCATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTAATCGTTACCAACTTCCAGACTTGCACCAGACGCTGAAcc                                                                                      >  2:325877/1‑140 (MQ=255)                                          aggaggCATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCg                                                                                     >  2:134956/1‑140 (MQ=255)                                              ggCATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTa                                                                                 >  1:45757/1‑140 (MQ=255)                                                cATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGt                                                                               <  1:530030/140‑1 (MQ=255)                                                        ccagccaAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCaa                                                                       >  2:7833/1‑140 (MQ=255)                                                        ccagccaAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCaa                                                                       <  2:45757/140‑1 (MQ=255)                                                           gccaAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGAATTGCACCTGACACTGAACCGCGTAGTGCCAGCAAAac                                                                    >  1:215197/1‑140 (MQ=255)                                                                   atTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCg                                                            <  1:696650/140‑1 (MQ=255)                                                                    ttAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGt                                                           >  2:496291/1‑140 (MQ=255)                                                                      aaGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACAcc                                                                 >  1:668845/1‑132 (MQ=255)                                                                      aaGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACAcc                                                                 <  2:668845/132‑1 (MQ=255)                                                                        gCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAAt                                                       <  1:583470/140‑1 (MQ=255)                                                                          aCTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCt                                                     >  2:579033/1‑140 (MQ=255)                                                                          aCTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCt                                                     >  1:598991/1‑140 (MQ=255)                                                                            tCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGACCCGCTTAGTGCAAGCAAAACATCCAGCGTCAATCTAc                                                   >  1:399342/1‑140 (MQ=255)                                                                            tCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTAc                                                   >  1:77879/1‑140 (MQ=255)                                                                            tCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTAc                                                   >  2:438010/1‑140 (MQ=255)                                                                              cAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTg                                                 >  2:49144/1‑140 (MQ=255)                                                                                 tGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAAt                                              >  1:666849/1‑140 (MQ=255)                                                                                      tACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGt                                         >  1:643077/1‑140 (MQ=255)                                                                                      tACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGt                                         >  1:582885/1‑140 (MQ=255)                                                                                          aGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTc                                     <  2:643077/140‑1 (MQ=255)                                                                                           gCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCa                                    >  2:485333/1‑140 (MQ=255)                                                                                             cAACCAGGTAGGCATCATAAGCAACATCAGTGTCATTATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGt                                  <  2:371224/140‑1 (MQ=255)                                                                                                ccAGGTAGGCATCATGAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCa                               <  1:341789/140‑1 (MQ=255)                                                                                                ccAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCa                               >  1:788027/1‑140 (MQ=255)                                                                                                    gTAGGCATCATAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCAGAgg                           >  2:32305/1‑140 (MQ=255)                                                                                                          atcatAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAGTCTGCTGAATTTCGTTGACAGTCCAGAGGATTTAc                     >  2:240524/1‑140 (MQ=255)                                                                                                           tcatAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCAGAGGATTTACg                    <  2:788027/140‑1 (MQ=255)                                                                                                           tcatAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTAAATGTCTTTGTCACTCCAGAGGATTTACg                    >  1:273758/1‑140 (MQ=255)                                                                                                           tcatAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGACAATCTAATGAATTTCATTGTAAGTCCAGAGGATTTACg                    >  2:341789/1‑140 (MQ=255)                                                                                                              tAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCAGAGGATTTACGCaa                 >  2:25028/1‑140 (MQ=255)                                                                                                              tAAGCAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAAATTCATTGTCAGTCTAGAGGATTTACGCaa                 >  1:385062/1‑140 (MQ=255)                                                                                                                  cAACATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCAGAGGATTTACGCAAATTa             >  1:590920/1‑140 (MQ=255)                                                                                                                    aCATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCAGAGGATTTACGCAAATTAAc           >  2:662684/1‑140 (MQ=255)                                                                                                                     cATCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCAGAGGATTTACGCAAATTAAcc          >  2:678567/1‑140 (MQ=255)                                                                                                                      aTCAGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCAGAGGATTTACGCAAATTAACCg         >  2:557638/1‑140 (MQ=255)                                                                                                                       tCAGTATCAATATTGGCAATCTTATCATTCTCAACTTTCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCAGAGGATTTACGCAAATTAACCGt        <  1:216013/140‑1 (MQ=255)                                                                                                                         aGTATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCAGAGGATTTACGCAAATTAACCGTCg      <  1:662684/140‑1 (MQ=255)                                                                                                                           tATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCAGAGGATTTACGCCAATTAACCGt        >  1:788726/1‑136 (MQ=255)                                                                                                                           tATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCAGAGGATTTACGCAAATTAACCGt        <  2:788726/136‑1 (MQ=255)                                                                                                                           tATCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCAGAGGATTTACGCAAATTAACCGTCGAt    >  1:474143/1‑140 (MQ=255)                                                                                                                            aTCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCAGAGGATTTACGCAAATTAACCGTCGATg   >  1:548037/1‑140 (MQ=255)                                                                                                                             tCAATATTGGCAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCAGAGGATTTACGCAAATTAACCGTCGATGt  >  1:81289/1‑140 (MQ=255)                                                                                                                                       |                                                                                                                                  GTCCTCATTAGCGCCAATGACGCTGGTAGTAATAGTGGTTAAGGAGGCATTACCGCCAGCCAAAATATTAAGCACTCCAGTGCCATACCAGCCAACCAGGTAGGCATCATAAGCAACATCAGTATCAATATTGGTAATCTGATCATTATCAACTTCCAGACTTGCACCAGACGCTGAACCGCTTAGTGCCAGCAAAACACCCAGCGTCAATCTACTGAATTTCGTTGTCAGTCCAGAGGATTTACGCAAATTAACCGTCGATGT  >  NC_000913/1597739‑1598002

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑