Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,479,864	T→C	A225A (GCT→GCC)	unknown →	Flp pilus assembly protein RcpC/CpaB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,479,864	0	T	C	100.0%	99.3 / NA	37	A225A (GCT→GCC)	unknown	Flp pilus assembly protein RcpC/CpaB
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (23/14);  total (23/14)

TAAATACTATTTTAAGTGGAGACTATGTTGCTATCTATAGCCAACAAATTGCTTCAGATTCGCGCAACACTTATGATCGTAAAGATTTAGTTAAAATTTTAGGTAAAGTATTGGTTTTACAAGCAAGAAACTTTACTCAATCAACAGAACAAGGTGCTCCTGAAGCTGAAAAGGCAGCA‑GA‑CGGGATTCCAAACAATCAAGAATATGCTGGTTATGTAGCACTAAAAATAACTGCTGAACAAGCAAAAAAATTCTATTCACTGGATAGAGAATCAAAGTTAGTTATATTACCTGCCGAAAATAATACTCAAGAAGTTGATTCACGCGGTGTATTCATCAGAAAATTAAGAGGTCAATAAGATGCAAAATTGGAATCATACTTTTGGCAAAAAACAATTAATATGCTGTGCAGTTCTCGGGGCAATGTTCTCATTAAATGCGTACGCACAAA  >  1/1479656‑1480106                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                   tAAATACTATTTTAAGCGGAGACTATGTATCTGTTTATAGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTc                                                                                                                                                                                                       <  1:543537/251‑1 (MQ=255) tAAATACTATTTTAAGCGGAGACTATGTATCTGTTTATAGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTc                                                                                                                                                                                                       <  1:2960/251‑1 (MQ=255)         aTTTTAAGCGGAGACTATGTATCTGTTTATAGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTA‑GATCTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCa                                                                                                                                                                                                 >  1:454188/1‑249 (MQ=255)         aTTTTAAGCGGAGACTATGTATCTGTTTATAGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTA‑GATCTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCa                                                                                                                                                                                                 >  1:448427/1‑249 (MQ=255)                 cggAGACTATGTATCTGTTTATAGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATagag                                                                                                                                                                                       <  1:885580/250‑1 (MQ=255)                   gagaCTATGTATCTGTTTATAGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTGTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAgaga                                                                                                                                                                                      <  1:453155/250‑1 (MQ=255)                     gactatgtatctgtttataGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTc                                                                                                                                                                                                       >  1:279359/16‑231 (MQ=255)                       ctatgtatctgtttataGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGAt                                                                                                                                                                                           <  1:459579/228‑1 (MQ=255)                       ctatgtatctgtttataGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATcga                                                                                                                                                                                 >  1:773401/14‑249 (MQ=255)                       ctatgtatctgtttataGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATcga                                                                                                                                                                                 >  1:62278/14‑249 (MQ=255)                       ctatgtatctgtttataGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATcga                                                                                                                                                                                 >  1:479787/14‑249 (MQ=255)                       ctatgtatctgtttataGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATcga                                                                                                                                                                                 >  1:894938/14‑249 (MQ=255)                         atgtatctgtttataGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAag                                                                                                                                                                               <  1:551970/240‑1 (MQ=255)                         atgtatctgtttataGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAag                                                                                                                                                                               >  1:780671/12‑251 (MQ=255)                           gtatctgtttataGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAagtt                                                                                                                                                                             >  1:606079/10‑251 (MQ=255)                                 gtttataGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAagttagtcat                                                                                                                                                                       >  1:877339/4‑248 (MQ=255)                                 gtttataGCCAGCAAACCGCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAagttagtcat                                                                                                                                                                       >  1:464845/4‑248 (MQ=255)                                           agcaaaccgCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAgaga                                                                                                                                                                                      >  1:445055/9‑226 (MQ=255)                                                 ccgCTTCAGATTCCCGCAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAAGTTAGTCATATTACCTGTCGAAaat                                                                                                                                                       <  1:725284/249‑1 (MQ=255)                                                             cccgcAATACTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAAAAAGCTAAAAAATTCTATTc                                                                                                                                                                                                  >  1:63357/3‑196 (MQ=255)                                                                 caatacTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAAGTTAGTCATATTACCTGTCGAAAATAATACTCAAGAAGTTg                                                                                                                                       >  1:410931/5‑251 (MQ=255)                                                                   atacTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAAt                                                                                                                                                                                    <  1:857967/202‑1 (MQ=255)                                                                     acTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACGAGCTAAAAAATTCTATTCACTGGATagag                                                                                                                                                                                       >  1:454210/1‑199 (MQ=255)                                                                      cTTATGATCGTAAAGATTTAGTTAAAGTTTTAGGTAAGGCAGTGGTTCTACAAGCACGGAATTTTGCTCAAGTAGCAGAACAAG‑‑GC‑ACTGAAACTGAGAAAGCGTTAGGT‑CTGG‑CTCCAAATAGTGAAGTATATGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAAGTTAGTCATATTGCCTGTCGAAAATAATACTCAAGAAGTTGATTCa                                                                                                                                  >  1:108817/1‑251 (MQ=255)                                                                                                                                                                                            gctccaaatagtgaagtatatGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAAGTTAGTCATATTACCTGTCGAAAATAATACTCAAGAAGTTGATTCACGCGGTGTATTCATCAGAAAATTAAGAGGTCAATAAGATGCAAAATTGGAATCATACTTTTGGCAAAAAACAATTGATATGCTGTGCAGTTCTCGGAGCAATGTTCTCATTaa                 >  1:155145/18‑251 (MQ=255)                                                                                                                                                                                            gctccaaatagtgaagtatatGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAAGTTAGTCATATTACCTGTCGAAAATAATACTCAAGAAGTTGATTCACGCGGTGTATTCATCAGAAAATTAAGAGGTCAATAAGATGCAAAATTGGAATCATACTTTTGGCAAAAAACAATTGATATGCTGTGCAGTTCTCGGAGCAATGTTCTCATTaa                 >  1:75646/18‑251 (MQ=255)                                                                                                                                                                                               ccaaatagtgaagtatatGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAAGTTAGTCATATTACCTGTCGAAAATAATACTCAAGAAGTTGATTCACGCGGTGTATTCATCAGAAAATTAAGAGGTCAATAAGATGCAAAATTGGAATCATACTTTTGGCAAAAAACAATTGATATGCTGTGCAGTTCTCGGAGCAATGTTCTCATTAAATg              <  1:695876/237‑1 (MQ=255)                                                                                                                                                                                                 aaatagtgaagtatatGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAAGTTAGTCATATTACCTGTCGAAAATAATACTCAAGAAGTTGATTCACGCGGTGTATTCATCAGAAAATTAAGAGGTCAATAAGATGCAAAATTGGAATCATACTTTTGGCAAAAAACAATTGATATGCTGTGCAg                                         <  1:68651/210‑1 (MQ=255)                                                                                                                                                                                                   atagtgaagtatatGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAAGTTAGTCATATTACCTGTCGAAAATAATACTCAAGAAGTTGATTCACGCGGTGTATTCATCAGAAAATTAAGAGGTCAATAAGATGCAAAATTGGAATCATACTTTTGGCAAAAAACAATTGATATGCTGTGCAGTTCTCGGAGCAATGTTCTCATTAAATGCGTa          <  1:92237/241‑1 (MQ=255)                                                                                                                                                                                                      gtgaagtatatGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAAGTTAGTCATATTACCTGTCGAAAATAATACTCAAGAAGTTGATTCACGCGGTGTATTCATCAGAAAATTAag                                                                                                        >  1:123365/8‑154 (MQ=255)                                                                                                                                                                                                      gtgaagtatatGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAAGTTAGTCATATTACCTGTCGAAAATAATACTCAAGAAGTTGATTCACGCGGTGTATTCATCAGAAAATTAAGAGGTCAATAAGATGCAAAATTGGAATCATACTTTTGGCAAAAAACAATTGATATGCTGTGCAGTTCTCGGAGCAATGTTCTCATTAAATGCGTACg        >  1:269798/8‑250 (MQ=255)                                                                                                                                                                                                          agtatatGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAAGTTAGTCATATTACCTGTCGAAAATAATACTCAAGAAGTTGATTCACGCGGTGTATtca                                                                                                                     <  1:421842/134‑1 (MQ=255)                                                                                                                                                                                                          agtatatGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAAGTTAGTCATATTACCTGTCGAAAATAATACTCAAGAAGTTGATTCACGCGGTGTATtca                                                                                                                     <  1:238118/134‑1 (MQ=255)                                                                                                                                                                                                           gtatatGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAAGTTAGTCATATTACCTGTCGAAAATAATACTCAAGAAGTTGATTCACGCGGTGTATtcatc                                                                                                                   <  1:61838/136‑1 (MQ=255)                                                                                                                                                                                                           gtatatGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAAGTTAGTCATATTACCTGTCGAAAATAATACTCAAGAAGTTGATTCACGCGGTGTATTCATCAGAAAATTAAGAGGTCAATAAGATGCAAAATTGGAATCATACTTTTGGCAAAAAACAATTGATATGc                                                >  1:806659/3‑205 (MQ=255)                                                                                                                                                                                                           gtatatGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAAGTTAGTCATATTACCTGTCGAAAATAATACTCAAGAAGTTGATTCACGCGGTGTATTCATCAGAAAATTAAGAGGTCAATAAGATGCAAAATTGGAATCATACTTTTGGCAAAAAACAATTGATATGCTGTGCAGTTCTCGGAGCAATGTTCTCATTAAATGCGTACGCACaaa  >  1:484353/3‑251 (MQ=255)                                                                                                                                                                                                             atatGCCGGTTATGTAGCATTAAAAATAACTGCTGAACAAGCTAAAAAATTCTATTCACTGGATAGAGAATCGAAGTTAGTCATATTACCTGTCGAAAATAATACTCAAGAAGTTGATTCACGCGGTGTATTCATCAGAAAATTAAGAGGTCAATAAGATGCAAAATTGGAATCATACTTTTGGCAAAAAACAATTGATATGCTGTGCAGTTCTCGGAGCAATGTtc                        >  1:625327/1‑227 (MQ=255)                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                   TAAATACTATTTTAAGTGGAGACTATGTTGCTATCTATAGCCAACAAATTGCTTCAGATTCGCGCAACACTTATGATCGTAAAGATTTAGTTAAAATTTTAGGTAAAGTATTGGTTTTACAAGCAAGAAACTTTACTCAATCAACAGAACAAGGTGCTCCTGAAGCTGAAAAGGCAGCA‑GA‑CGGGATTCCAAACAATCAAGAATATGCTGGTTATGTAGCACTAAAAATAACTGCTGAACAAGCAAAAAAATTCTATTCACTGGATAGAGAATCAAAGTTAGTTATATTACCTGCCGAAAATAATACTCAAGAAGTTGATTCACGCGGTGTATTCATCAGAAAATTAAGAGGTCAATAAGATGCAAAATTGGAATCATACTTTTGGCAAAAAACAATTAATATGCTGTGCAGTTCTCGGGGCAATGTTCTCATTAAATGCGTACGCACAAA  >  1/1479656‑1480106

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑