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	94.7%	56.4 / NA	19	Q679P (CAA→CCA)	elfC	putative fimbrial usher protein ElfC
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base C (9/9);  total (10/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCTGGATGACCTCTAACACCAGTATCGATAACGAAGGGCACACTACACAAAACCTGGGTTTAACGGAGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAACAGGGATATAACAGCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACAACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGCACTTGATGCGGCGTCGTTAAAACGTAACGTGG  >  NC_000913/1001028‑1001484                                                                                                                                                                                                                                |                                                                                                                                                                                                                                          gcatGGATGACCTCTCCCACCAGTCTCGTTAACGTACGGCACACTCCACAAAACCTTGGATTAACGGAGACATAAATCGATGACGGTAACCTGAGCTACAGCGTGCAACAGGGATATAACCGCGAGGGGAAAACGGCCAATGGTAGCGCCAGAATGGATTACAAAGGGGCGATTGCGGATGACCGAGTGGGCTACAACTACAGCGATAACGGCAGTACACAAAAACTGCACTACGCTCTTTCAGGCAGttt                                                                                                                                                                                                                >  2:247967/4‑251 (MQ=255)                             aTAACGAAGGGCACACTACACAAAACCTGGGTTTAACGGAGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAACAGGGATATAACAGCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTg                                                                                                                                                                                    <  2:103813/251‑1 (MQ=255)                                         acacTACACAATACCTGGGCTTAACGGAGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAACAGGGATATAACAGCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGTCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTTAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACCGGGCATTACCCTTGGGCAATCGCTg                                                                                                                                                                        <  2:189852/251‑1 (MQ=255)                                                       cTGGGTTTAACGGAGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAACAGGGATATAACAGCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGt                                                                                                                                                          >  1:190858/1‑251 (MQ=255)                                                            tttAACGCAGACCTTAATCGATGACGGGTACCCGCGCTACAGCGTGCAACCGGGATATAACAGCGAGGGGACAACGGCAATTGGCAGCGCCAGCCTGGATTACAAAGGGGCGCTTGCGGATGCCCGAGTGGGCTACCACTACAGCGATAACGGCAGTCAACAACCAATGGCCTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCAAAGGGAATTACCCTTGGGCAATCGCTGGGGGGAAATAACGTTCTgc                                                                                                                                                     >  2:36079/1‑250 (MQ=255)                                                              tAACGGAGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAACAGGGATATAACAGCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGAt                                                                                                                                                    <  1:121049/250‑1 (MQ=255)                                                                  ggAGACATTACACGATAACGGTAACCTGAGCTACAGCGTGCAACAGGGATATAACCGCGAGAGGAAAACGCCTAATGGTAGCGCGAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGAGGTCTACAACTACAGCGATAACGGCAGTCAACATCCAGTCAACTACGTCCTTTCACGCAGTTTAGTTGCACATTAACCGGGCTTAACCCTCAGCCAATCGCTGGGGGATACTAACGTTCTGATTgct                                                                                                                                                >  2:258478/1‑249 (MQ=255)                                                                                                     gCGTGCAACAGGGATATAACAGCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTGGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGTCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGCGGCGAACAGc                                                                                                            <  2:231418/251‑1 (MQ=255)                                                                                                              aGGGATATAACAGCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAAGATACTAGTGGGGCGAACAGCACCGGGCTg                                                                                                   >  1:178356/1‑251 (MQ=255)                                                                                                              aGGGATATAACAGCGAGGGGAAAACGGCTAATGGTAGCGCCAGCAGGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTg                                                                                                   <  1:235223/251‑1 (MQ=255)                                                                                                                           cGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGgc                                                                                      <  2:190858/251‑1 (MQ=255)                                                                                                                                              ggcaGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCGACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCTGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCgttgtta                                                                    <  2:263882/247‑2 (MQ=255)                                                                                                                                                   cgcCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGTTATACCGTTGTTCCTTATg                                                              >  1:281233/1‑251 (MQ=255)                                                                                                                                                                   aaaGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCggg                                               >  1:129194/1‑250 (MQ=255)                                                                                                                                                                                             gggCTACAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGCACTTGATGCGGcgt                    >  2:75391/1‑251 (MQ=255)                                                                                                                                                                                                   cAACTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGCACTTGATGCGGCGTCGTTa               >  2:185299/1‑250 (MQ=255)                                                                                                                                                                                                    aaCTACAGCGATAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTTATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCCCCGGGCTGAAAACTGACTGGCGCGGATATACCGTTTTTCCTTATGCCTCTTCTTATCGGGAAAATCGAATCTCACTTGATGCGTCGTCGTTaaa             <  1:160561/251‑1 (MQ=255)                                                                                                                                                                                                              aTAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGCACTTGATGCGGCGTCGTTAAAACGTAACGTg   <  2:129194/251‑1 (MQ=255)                                                                                                                                                                                                               tAACGGCAGTCAACAACCACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGCACTTGATGCGGCGTCGTTAAAACGTAACGTgg  >  1:312906/1‑251 (MQ=255)                                                                                                                                                                                                                                |                                                                                                                                                                                                                                          GCCTGGATGACCTCTAACACCAGTATCGATAACGAAGGGCACACTACACAAAACCTGGGTTTAACGGAGACATTACTCGATGACGGTAACCTGAGCTACAGCGTGCAACAGGGATATAACAGCGAGGGGAAAACGGCTAATGGTAGCGCCAGCATGGATTACAAAGGGGCGTTTGCGGATGCCCGAGTGGGCTACAACTACAGCGATAACGGCAGTCAACAACAACTGAACTACGCTCTTTCAGGCAGTTTAGTTGCCCATTCACAGGGCATTACCCTGGGGCAATCGCTGGGGGAAACTAACGTTCTGATTGCAGCACCAGGCGCAGAGAATACTCGTGTGGCGAACAGCACCGGGCTGAAAACTGACTGGCGCGGATATACCGTTGTTCCTTATGCCACTTCTTATCGGGAAAATCGAATCGCACTTGATGCGGCGTCGTTAAAACGTAACGTGG  >  NC_000913/1001028‑1001484

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑