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%	122.7 / NA	38	*179* (TAG→TAA)	rcdA	transcriptional regulator of csgD and ybiJI, autoregulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (20/18);  total (20/18)

AACAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGAAAAGT  >  NC_000913/887826‑888088                                                                                                                                      |                                                                                                                                  aaCAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                              <  2:963846/139‑1 (MQ=255) aaCAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                              <  1:1397777/139‑1 (MQ=255)        gTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGtttt                                                                                                                       >  2:1161960/1‑139 (MQ=255)            gAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGAt                                                                                                                   <  1:990200/139‑1 (MQ=255)                         cccgcGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                              <  2:786286/115‑1 (MQ=255)                         cccgcGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                                              >  1:786286/1‑115 (MQ=255)                         cccgcGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCa                                                                                                      >  1:844184/1‑139 (MQ=255)                                          tttATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAAc                                                                                                                <  1:1045138/112‑1 (MQ=255)                                          tttATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAAc                                                                                                                >  2:1045138/1‑112 (MQ=255)                                            tATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATg                                                                                   >  2:161055/1‑139 (MQ=255)                                                     gATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGc                                                                                 <  2:701242/132‑1 (MQ=255)                                                     gATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGc                                                                                 >  1:701242/1‑132 (MQ=255)                                                        gACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATg                                                                       >  2:552325/1‑139 (MQ=255)                                                           gCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGa                                                                                       <  1:1319199/120‑1 (MQ=255)                                                           gCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGa                                                                                       >  2:1319199/1‑120 (MQ=255)                                                                         ccgaccgTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATgggg                                                      >  2:1447254/1‑139 (MQ=255)                                                                           gaccgTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGAc                                                    >  2:1059139/1‑139 (MQ=255)                                                                                tAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCaa                                               >  1:1165073/1‑139 (MQ=255)                                                                                       cTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAg                                        >  2:1176033/1‑139 (MQ=255)                                                                                        tATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATggg                                                                     <  1:1193947/109‑1 (MQ=255)                                                                                        tATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATggg                                                                     >  2:1193947/1‑109 (MQ=255)                                                                                          tCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGa                                                                                                                    <  1:1083840/60‑1 (MQ=255)                                                                                          tCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGa                                                                                                                    >  2:1083840/1‑60 (MQ=255)                                                                                             cgcgAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTgg                                  >  2:185663/1‑139 (MQ=255)                                                                                               cgAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGTGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCa                                <  1:264536/139‑1 (MQ=255)                                                                                               cgAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCa                                <  2:501350/139‑1 (MQ=255)                                                                                               cgAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCa                                <  1:185663/139‑1 (MQ=255)                                                                                               cgAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCa                                <  2:844184/139‑1 (MQ=255)                                                                                               cgAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCa                                <  1:1182020/139‑1 (MQ=255)                                                                                                    agaTTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAAt                           >  2:393445/1‑139 (MQ=255)                                                                                                      aTTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGAt                                                                                                                   <  1:850110/49‑1 (MQ=255)                                                                                                      aTTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGAt                                                                                                                   >  2:850110/1‑49 (MQ=255)                                                                                                       ttttGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTaa                        <  2:1165073/139‑1 (MQ=255)                                                                                                                            ttGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATgg                                                                                  >  2:1436976/1‑60 (MQ=255)                                                                                                                            ttGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATgg                                                                                  <  1:1436976/60‑1 (MQ=255)                                                                                                                             tGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATggg                                                                     <  2:1215571/72‑1 (MQ=255)                                                                                                                             tGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATggg                                                                     >  1:1215571/1‑72 (MQ=255)                                                                                                                             tGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGAAAAGt  >  2:33871/1‑139 (MQ=255)                                                                                                                                      |                                                                                                                                  AACAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAAGACTGATGCCCTGCGGAAAAGT  >  NC_000913/887826‑888088

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: ‑