Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	887,959	G→A	*179* (TAG→TAA)	rcdA →	transcriptional regulator of csgD and ybiJI, autoregulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	887,959	0	G	A	100.0%	109.5 / NA	35	*179* (TAG→TAA)	rcdA	transcriptional regulator of csgD and ybiJI, autoregulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (16/19);  total (16/19)

AACAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGAA  >  NC_000913/887826‑888084                                                                                                                                      |                                                                                                                              aaCAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                          <  1:909649/139‑1 (MQ=255)     aTGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGt                                                                                                                      >  2:1173860/1‑139 (MQ=255)                           cgcgcgCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATc                                                                                                <  1:1173860/139‑1 (MQ=255)                                 cTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                          <  2:548317/107‑1 (MQ=255)                                 cTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                          >  1:548317/1‑107 (MQ=255)                                          tttATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGATATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGaaa                                                                                 >  1:930592/1‑139 (MQ=255)                                               tGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCg                                                                            <  2:1120281/139‑1 (MQ=255)                                                    ggATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACaaaa                                                                                                        <  2:396242/106‑1 (MQ=255)                                                    ggATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACaaaa                                                                                                        >  1:396242/1‑106 (MQ=255)                                                    ggATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGtt                                                                       >  1:160470/1‑139 (MQ=255)                                                          cGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATggg                                                                 <  2:160470/139‑1 (MQ=255)                                                             tGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGc                                                                             >  1:673705/1‑124 (MQ=255)                                                             tGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGc                                                                             <  2:673705/124‑1 (MQ=255)                                                               cATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGc                                                                <  1:270769/135‑1 (MQ=255)                                                               cATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACATTGAACCGAAATGGCGGGGTTGATGGGc                                                                >  2:270769/1‑135 (MQ=255)                                                                aTTTTGTCACCGACCGTAAGCCGCTATCGTGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCcac                                                           <  2:1089626/139‑1 (MQ=255)                                                                 ttttGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGc                                                                >  2:1196807/1‑133 (MQ=255)                                                                 ttttGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGc                                                                <  1:1196807/133‑1 (MQ=255)                                                                         ccgaccgTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATgggg                                                  >  1:631772/1‑139 (MQ=255)                                                                            accgTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCgggg                                                                         >  2:14466/1‑113 (MQ=255)                                                                            accgTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCgggg                                                                         <  1:14466/113‑1 (MQ=255)                                                                                tAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                          <  1:44276/60‑1 (MQ=255)                                                                                tAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                          >  2:44276/1‑60 (MQ=255)                                                                                tAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAAc                                                                                                            >  1:724100/1‑74 (MQ=255)                                                                                tAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAAc                                                                                                            <  2:724100/74‑1 (MQ=255)                                                                                      gCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATgg                                                                  >  2:729203/1‑110 (MQ=255)                                                                                      gCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATgg                                                                  <  1:729203/110‑1 (MQ=255)                                                                                          tCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATggg                                                                 >  1:445615/1‑107 (MQ=255)                                                                                          tCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATggg                                                                 <  2:445615/107‑1 (MQ=255)                                                                                               cgAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCa                            <  1:184052/139‑1 (MQ=255)                                                                                               cgAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCa                            <  2:631772/139‑1 (MQ=255)                                                                                                                   ttGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCt        >  2:1310785/1‑139 (MQ=255)                                                                                                                         gggTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGaa  <  2:930592/139‑1 (MQ=255)                                                                                                                            ttGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAAtt                      >  1:1307322/1‑116 (MQ=255)                                                                                                                            ttGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAAtt                      <  2:1307322/116‑1 (MQ=255)                                                                                                                                      |                                                                                                                              AACAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGAA  >  NC_000913/887826‑888084

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑