Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,453,540	T→C	pseudogene (1462/2646 nt)	yfcU ←	putative outer membrane usher protein YfcU

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,453,540	0	T	C	100.0%	127.6 / NA	36	pseudogene (1462/2646 nt)	yfcU	putative outer membrane usher protein YfcU
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (20/16);  total (20/16)

TATGGCGGGTATAGTTGAGATAAACCGAAACACCCGCATCGCGGAAGTTCTGGTTATAAGTGGCGGTGTACATCTCTTTGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGTCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACGGAAGGAGTTACCGTCCAGCGAACCTTTGCCATAAGCGGTGTCTTTAT  >  NC_000913/2453405‑2453671                                                                                                                                        |                                                                                                                                    tATGGCGGGTATAGTTGAGATAAACCGAAACACCCGCATCGCGGAAGTTCTGGTTATAAGTGGCGGTGTACATCTCTTTGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATa                                                                                                                                 <  2:266805/140‑1 (MQ=255)      cGGGTATAGTTGAGATAAACCGAAACACCCGCATCGCGGAAGTTCTGGTTATAAGTGGCGGTGTACATCTCTTTGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGtt                                                                                                                            <  1:629426/140‑1 (MQ=255)           ataGTTGAGATAAACCGAAACACCCGCATCGCGGAAGTTCTGGTTATAAGTGGCGGTGTACATCTCTTTGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCtt                                                                                                                       <  1:395340/140‑1 (MQ=255)              gTTGAGATAAACCGATACACCCTCATCGCAGAAGTTCTGGTTATAAGTGGCGGTGTACATCTCTTTGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCg                                                                                                                    <  1:258277/140‑1 (MQ=255)                  agaTAAACCGAAACACCCGCATCGCGGAAGTTCTGGTTATAAGTGGCGGCGTACATCTCTTTGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGaa                                                                                                                >  2:344049/1‑140 (MQ=255)                         ccGAAACACCCGCATCGCGGAAGTTCTGGTTATAAGTGGCGGTGTACATCTCTTTGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGatat                                                                                                         >  1:550146/1‑140 (MQ=255)                                          cgGAAGTTCTGGTTATAAGTGGCGGTGTACATCTCTTTGTCGTTGCCCATACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGATCTCTTCCGAGAAGCGATATCGAGCGAAAGTGAcgcg                                                                                        >  1:235075/1‑140 (MQ=255)                                               gTTCTGGTTATAAGTGGCGGTGTACATCTCTTTGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGt                                                                                   >  2:476397/1‑140 (MQ=255)                                                ttCTGGTTATAAGTGGCGGTGTACATCTCTTTGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCAGAAAGTTCTGTTCGGAGGAGCGATATGCAGCGAAAGTGACGCGGCTGtt                                                                                  >  2:188587/1‑140 (MQ=255)                                                ttCTGGTTATAAGTGGCGGTGTACATCTCTTTGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCAAAAAGTTCTCTTCCGAGTAGCGATATGCAGCGAAAGTGACGCGGCTGtt                                                                                  >  2:273362/1‑140 (MQ=255)                                                    ggTTATAAGTGGCGGTGTACATCTCTTTGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGc                                                                              <  2:550146/140‑1 (MQ=255)                                                    ggTTATAAGTGGCGGTGTACATCTCATTGTCGTTGCCAGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGc                                                                              <  1:264648/140‑1 (MQ=255)                                                         taAGTGGCGGTGTACATCTCTTTGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGACGCGCTATACAGCGAAAGTGACTCGGCTGTTGAGCTGGTc                                                                         >  2:264648/1‑140 (MQ=255)                                                          aaGTGGCGGTGTACATCTCTTTGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCa                                                                        <  1:444174/140‑1 (MQ=255)                                                           aGTGGCGGTGTACATCTCTTTGACGCTGCTCGTACGGCCAATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCaa                                                                       <  1:175762/140‑1 (MQ=255)                                                               gCGGTGTACATCTCTTTGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTc                                                                   >  2:440580/1‑140 (MQ=255)                                                               gCGGTGTACATCTCTTTGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTATTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAATc                                                                   >  2:410321/1‑140 (MQ=255)                                                                               tGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTcaca                                                   >  2:503074/1‑140 (MQ=255)                                                                               tGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTcaca                                                   >  1:234845/1‑140 (MQ=255)                                                                                  cGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCATATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACgg                                                <  2:234845/140‑1 (MQ=255)                                                                                    ttGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACGGaa                                              <  1:461965/140‑1 (MQ=255)                                                                                     tGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGGGCTCGTCAAAGTATTTGGAATAACTCACACGGAAg                                             >  2:270759/1‑140 (MQ=255)                                                                                      gCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACGGAAgg                                            >  1:75158/1‑140 (MQ=255)                                                                                           tACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACGGAAGGAGTTa                                       <  1:344049/140‑1 (MQ=255)                                                                                                aCCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACGGAAGGAGTTACCGTc                                  >  1:134612/1‑140 (MQ=255)                                                                                                     ttCGCTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATCACTAACACGGAAGAAGTTACCGTCCAGCg                             >  1:263819/1‑140 (MQ=255)                                                                                                         cTGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTATTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACGGAAGGAGTTACCGTCCAGCGAAcc                         <  1:410321/140‑1 (MQ=255)                                                                                                          tGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACGGAAGGAGTTACCGTCCAGCGAACCt                        >  1:54893/1‑140 (MQ=255)                                                                                                          tGTCACTGGCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACGGAAGGAGTTACCGTCCAGCGAACCt                        <  1:545529/140‑1 (MQ=255)                                                                                                                 ggCATCCAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACGGAAGGAGTTACCGTCCAGCGAACCTTTGCCAt                 <  2:75158/140‑1 (MQ=255)                                                                                                                      ccAGATACTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACGGAAGGAGTTACCGTCCAGCGAACCTTTGCCATAAGCg            >  2:643855/1‑140 (MQ=255)                                                                                                                             cTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACGGAAGGAGTTACCGTCCAGCGAACCTTTGCCATAAGCGGTGTCt      <  2:387378/139‑1 (MQ=255)                                                                                                                             cTCGCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACGGAAGGAGTTACCGTCCAGCGAACCTTTGCCATAAGCGGTGTCt      >  1:387378/1‑139 (MQ=255)                                                                                                                                gCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACGGAAGGAGTTACCGTCCAGCGAACCTTTGCCATAAGCgg           <  2:25658/131‑1 (MQ=255)                                                                                                                                gCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACGGAAGGAGTTACCGTCCAGCGAACCTTTGCCATAAGCgg           >  1:25658/1‑131 (MQ=255)                                                                                                                                gCTCATGGCCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACGGAAGGAGTTACCGTCCAGCGAACCTTTGCCATAAGCGGTGTCTTTAt  >  1:133461/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                    TATGGCGGGTATAGTTGAGATAAACCGAAACACCCGCATCGCGGAAGTTCTGGTTATAAGTGGCGGTGTACATCTCTTTGTCGTTGCCCGTACGGACCATTTCGCTGTCACTGGCATCCAGATACTCGCTCATGGTCATAAAGTTCTCTTCCGAGAAGCGATATCCAGCGAAAGTGACGCGGCTGTTGAGCTGGTCAAAGTCTTTGGAATAACTCACACGGAAGGAGTTACCGTCCAGCGAACCTTTGCCATAAGCGGTGTCTTTAT  >  NC_000913/2453405‑2453671

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑