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%	97.4 / NA	31	*179* (TAG→TAA)	rcdA	transcriptional regulator of csgD and ybiJI, autoregulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (13/18);  total (13/18)

AACAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAA  >  NC_000913/887826‑888066                                                                                                                                      |                                                                                                            aaCAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGGTATCGCTCGAGGAGATTTTGAGAATGGTTGAGAGGGTTGCAGGGTAATAGAt                                                                                                        <  2:643111/139‑1 (MQ=255)                                    gATGCGTTTATTGAAGGGATGACGCTGCATATTGTCACCGACCGTAAGCCGCTTTCGCGCGAGGAGATTGTGAGGATGGTTGAGAGGGTTGCAGGGTAAGAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGaa                                                                     <  2:388736/139‑1 (MQ=255)                                            tATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATg                                                             >  2:84077/1‑139 (MQ=255)                                            tATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATg                                                             >  2:84076/1‑139 (MQ=255)                                             aTTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATgg                                                            <  2:180736/139‑1 (MQ=255)                                                gAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCAt                                                                               <  1:552027/117‑1 (MQ=255)                                                gAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCAt                                                                               >  2:552027/1‑117 (MQ=255)                                                     gATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTg                                                    <  2:971876/139‑1 (MQ=255)                                                     gATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTg                                                    <  1:888567/139‑1 (MQ=255)                                                       tGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCAt                                                                               <  2:868315/110‑1 (MQ=255)                                                       tGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCAt                                                                               >  1:868315/1‑110 (MQ=255)                                                        gACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATg                                                 >  1:925550/1‑139 (MQ=255)                                                                           gaccgTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCg                                                          >  2:256350/1‑111 (MQ=255)                                                                           gaccgTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCg                                                          <  1:256350/111‑1 (MQ=255)                                                                             ccgTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACAt                            <  2:171243/139‑1 (MQ=255)                                                                             ccgTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACAt                            <  2:925550/139‑1 (MQ=255)                                                                              cgTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATc                           >  1:527333/1‑139 (MQ=255)                                                                                tAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGAt                                                  >  2:482958/1‑114 (MQ=255)                                                                                tAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGAt                                                  <  1:482958/114‑1 (MQ=255)                                                                                tAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATggg                                               >  2:350764/1‑117 (MQ=255)                                                                                tAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATggg                                               <  1:350764/117‑1 (MQ=255)                                                                                            gcgcgAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGt              <  2:909899/138‑1 (MQ=255)                                                                                            gcgcgAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGAGAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGt              >  1:909899/1‑138 (MQ=255)                                                                                               cgAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCa          <  1:580449/139‑1 (MQ=255)                                                                                               cgAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCa          >  2:580449/1‑139 (MQ=255)                                                                                                       ttttGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTaa  <  1:70750/139‑1 (MQ=255)                                                                                                       ttttGAGGATGGTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTaa  <  2:527333/139‑1 (MQ=255)                                                                                                                 ggTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACaaa                                      <  2:772024/93‑1 (MQ=255)                                                                                                                 ggTTGAGAGGGTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACaaa                                      >  1:772024/1‑93 (MQ=255)                                                                                                                           gTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCg                                                          <  2:720895/63‑1 (MQ=255)                                                                                                                           gTTGCAGGGTAATAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCg                                                          >  1:720895/1‑63 (MQ=255)                                                                                                                                      |                                                                                                            AACAATGGTTTGAACCCGGAACCGCCCGCGCGCTTGATGCGTTTATTGAGGGGATGACGCTGCATTTTGTCACCGACCGTAAGCCGCTATCGCGCGAGGAGATTTTGAGGATGGTTGAGAGGGTTGCAGGGTAGTAGATAAGTTTTAGATAACAAAAAACCCATCAACCTTGAACCGAAATGGCGGGGTTGATGGGCTCCACAAAATGGGGACATCAAAGAAAAGCAGTGGCACTAATTAA  >  NC_000913/887826‑888066

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: ‑