Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,001,251	A→C	Q679P (CAA→CCA)	elfC →	putative fimbrial usher protein ElfC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,001,251	0	A	C	100.0%	84.5 / NA	28	Q679P (CAA→CCA)	elfC	putative fimbrial usher protein ElfC
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (19/9);  total (19/9)

CCAGGAAAAAAAATTACGCCTGGATGACCTCTAACACCAGTATCGATAACGAAGGGCACACTACACAAAACCTGGGTTTAACGGAGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAAC‑AGGGATATAACA‑GCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACAACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGCACTTGATGCGGCGTCGTTAAAACGTAACGTGGATCTTGAAAAT  >  NC_000913/1001011‑1001495                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                     ccAGGAAAAAAAATTACGCCTGGATGACCTCTAACACCAGTATCGATAACGAAGGGCACACTACACAAAACCTGGGTTTAACGGAGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAAC‑AGGGATATAACA‑GCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTAc                                                                                                                                                                                                                                            <  1:366261/251‑1 (MQ=255)        aaaaaaTTACGCCTGGATGACCTCTAACACCAGGATCGATAACGAATGGCACACTACACAAAACCTGGGTTTAACGGAGACATTACTCTATGACGGTAACCTGAACTACAGCGTGCAAC‑AGGGATATAACA‑GCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCttt                                                                                                                                                                                                                                     <  2:197201/251‑1 (MQ=255)              ttACGCCTGGATGACCTCTAACACCAGTATCGATAACGAAGGGCACACTACACAAAACCTGGGTTTAACGGCGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAAC‑AGGGATATAACA‑GCGAGGGGCAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCCCTTTCAGGc                                                                                                                                                                                                                                >  2:342637/1‑250 (MQ=255)                  gcatGGATGAACTCTAACACCAGTATCGATAACGACGGGCACACCACACAAAACCTGGGTTTAACGGAGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAAC‑AGGGATATAACA‑GCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTACGGCAGttt                                                                                                                                                                                                                           >  2:145172/4‑251 (MQ=255)                               ctAACACAAGTATCGATAACGAAGGGCACCCTACACACAACCTGGGTTTAACGGAGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAAC‑AGGGATATAACA‑GCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTc                                                                                                                                                                                                               >  2:456753/1‑250 (MQ=255)                                 aaCACCAGTATCGATAACGAAGGGCACACTACACAAAACCTGGGTTTAACGGAGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAAC‑AGGGATATAACA‑GCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGTCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTcac                                                                                                                                                                                                             <  2:410457/250‑1 (MQ=255)                                                           cacTACACAAAACCTGGGTTTAACGGAGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAAC‑AGGGATATAACA‑GCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTgg                                                                                                                                                                                  <  1:283337/251‑1 (MQ=255)                                                               acacAAAACCTGGGTTTAACGGAGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAAC‑AGGGATATAACA‑GCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTggggg                                                                                                                                                                               >  2:328758/1‑250 (MQ=255)                                                                      aCCTGGCTTTAACGGAGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAAC‑AGGGATATAACA‑GCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGAGGGATACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCCGGCAGTTTAGTTGCCCCTTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAAc                                                                                                                                                                       >  2:171920/1‑251 (MQ=255)                                                                       ccTGGGATTAACGGAGACATTACTCGATGCCGGTACCCTGAGCTACAGCGTGCAAC‑AGGGATATAACA‑GCGCGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGAGGCCATCGCTGGGGGAAACTAACg                                                                                                                                                                      >  2:186938/1‑251 (MQ=255)                                                                            gTTTAACGGAGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAAC‑AGGGATATAACA‑GCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGAGAACGGCATTCAACAACCACTTAAGGACTCTCTTGCAGGCAGTTTAGTGTCCGATTCACAGGGCAGTAGCCTTGGGGGATCGCTTGGGGAAACTGACGTTCTg                                                                                                                                                                 <  2:198580/251‑1 (MQ=255)                                                                                        cATTACTCGATGACGGTAACCTGAGCTACAGCGT‑CAACCAGGGATATAACA‑GCGAGGGGAAAACGGCTAATGGTAGCGCCAACCTGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACCACTACCGCGATAACGGCAGTCAACAACCCCTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGAATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGAt                                                                                                                                                               >  1:415124/1‑241 (MQ=255)                                                                                                     cGGTAACCTGAGCTACAGCGTGCAAC‑AGGGATATAACA‑GCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAACCTAACGTTCTGGTTGCAGCACCAGGCGCAgagact                                                                                                                                         >  2:306573/1‑248 (MQ=255)                                                                                                      ggTAACCTGAGCTACAGCGTGCAAC‑AGGGATATAACA‑GCGAGGGGAAAGCGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGCTTGAAGCACCAGGCGCAGAGAATAc                                                                                                                                       >  2:339337/1‑251 (MQ=255)                                                                                                           ccTGAGCTACAGCGAGCAAC‑ACGGATATA‑CACGCGCGGGCAAACCGGCTCATGGTCGCGCCAGCATGGATTCCAAAGAGCCGTTTGCCGATGCCCGAGTGGGCTACAACTACAGCGATCACGGCAGTCAACAACCACAGAACTACGCTCATTCAGGCAGTTTAGTTGCCCATTCAAAGGGCATTACCCTGGGGCAATCGCTGGGGGTAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCgtg                                                                                                                                  >  2:60297/1‑251 (MQ=255)                                                                                                                                                        aCGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATAc                                                                                       >  1:161165/1‑251 (MQ=255)                                                                                                                                                           gCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCgt                                                                                    >  1:342205/1‑251 (MQ=255)                                                                                                                                                                       gcCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACACTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGGTGTTCCTTATGc                                                                        >  2:371158/1‑251 (MQ=255)                                                                                                                                                                          aGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCAc                                                                     <  1:348512/251‑1 (MQ=255)                                                                                                                                                                                                 tGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAaatcgaatcg                                              >  1:339401/1‑251 (MQ=255)                                                                                                                                                                                                   cGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGc                                             >  2:56362/1‑250 (MQ=255)                                                                                                                                                                                                             aGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGCACTTGATgcgg                                  >  1:144713/1‑251 (MQ=255)                                                                                                                                                                                                                gggCTACCACTACACCGATAACGACAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGAACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTCTGCCACTTCTTCTCGGGAAAATCGAATCGCACTTGATGCGGcgt                               >  2:175320/1‑251 (MQ=255)                                                                                                                                                                                                                               cGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGCACTTGATGCGGCGTCGTTAAaacgtaacg                <  1:306573/251‑1 (MQ=255)                                                                                                                                                                                                                                gATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGCACTTGATGCGGCGTCGTTAAaacgtaacgt               <  1:401347/251‑1 (MQ=255)                                                                                                                                                                                                                                 aTAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGCACTTGATGCGGCGTCGTTAAAACGTAACGTg              <  1:75653/251‑1 (MQ=255)                                                                                                                                                                                                                                  tAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCCGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGCACTTGATGCGGCGTCGTTAAAACGTAACGTgg             >  2:349325/1‑251 (MQ=255)                                                                                                                                                                                                                                      ggCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGCACTTGATGCGGCGTCGTTAAAACGTAACGTGGATCt         >  1:204209/1‑251 (MQ=255)                                                                                                                                                                                                                                            caacaaccaCTGAACTACGCTCTTTCAGGCAGTTTAGGTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGCACTTGATGCGGCGTCGTTAAAACGTAACGTGGATCTTGaaa    <  2:161165/250‑1 (MQ=255)                                                                                                                                                                                                                                             aacaaccacTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGCACTTGATGCGGCGTCGTTAAAACGTAACGTTGATCTTGAAAAt  <  2:200377/251‑1 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                     CCAGGAAAAAAAATTACGCCTGGATGACCTCTAACACCAGTATCGATAACGAAGGGCACACTACACAAAACCTGGGTTTAACGGAGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAAC‑AGGGATATAACA‑GCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACAACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGCACTTGATGCGGCGTCGTTAAAACGTAACGTGGATCTTGAAAAT  >  NC_000913/1001011‑1001495

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑