Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,281,808	T→C	11.8%	D120D (GAT→GAC)	yraI →	putative periplasmic pilin chaperone

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,281,808	0	T	C	11.8%	87.4 / 4.6	34	D120D (GAT→GAC)	yraI	putative periplasmic pilin chaperone
Reads supporting (aligned to +/- strand):  ref base T (15/15);  new base C (2/2);  total (17/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.21e-01

ACAAAGGCGCAGAAACGCCTTATTTACTGCAATCATGGGTAGATAATATAGATGGTAAAAGCCGTGCCCCATTTATTATAACCCCACCGCTATTTCGTCTTGAGGCTGGCGATGACTCATCACTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCAAAATGTTTTATCGCCCCGCACACCTGAAGGGACGGGTAAACGATGCGTGGAAATCACTGGAATTTAAACGTAGTGACCATTCACTCAATATATATAACCCAACTGAATATTACGTCGTATTTGCCGGACTGGCAGTCGATAAAACCGATCTCACAAGCAAAATTGAATATATCGC  >  CP009273/3281591‑3282029                                                                                                                                                                                                                          |                                                                                                                                                                                                                              tcaacatgctgcaaaCGCCTTATTTACTGCAATCATGGGTAGATAATATAGATGGTAAAAGCCGTGCCCCATTTATTATAACCCCACCGCTATTTCGTCTTGAGGCTGGCGATGACTCATCACTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTGCATTAATGTTTGTGCCATTCCATCAAAGAAAAAATAAGATCATGTTAATGCTAACGAGTTGAACCTGTTATTTAAAACACTAAACAAAATTTTTAAt                                                                                                                                                                      >  1:302886/13‑275 (MQ=255)                                             aataTAGATGGTAAAAGCCGTGCCCCATTTATTATAACCCCACCGCTATTTCGTCTTGAGGCTGGCGATGACTCATCACTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCAAAATGTTTTATCGCACCGCACACCTGAAGGGACGGGTAAACAATGCGTGGAAAta                                                                                                                          >  1:39981/1‑274 (MQ=255)                                                      ggTAAAAGCCGTGCCCCATTTATTATAACCCCACCGCTATTTCGTCTTGAGGCTGGCGATGACTCATCACTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTaaa                                                                                                                                                                                           >  2:291639/1‑201 (MQ=255)                                                        tAAAAGCCGTGCCCCATTTATTATAACCCCACCGCTATTTCGTCTTGAGGCTGGCGATGACTCATCACTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCAAAATGTTTTATCGCCCCg                                                                                                                                                               <  1:325996/227‑1 (MQ=255)                                                          aaaGCCGTGCCCCATTTATTATAACCCCACCGCTATTTCGTCTTGAGGCTGGCGATGACTCATCACTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAacac                                                                                                                                                                                       <  1:291643/201‑1 (MQ=255)                                                                       aTTTATTATAACCCCACCGCTATTTCGTCTTGAGGCTGGCGATGACTCATCACTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCAAAATGTTTTATCGCCCCGCACACCTGAAGGGACGGGTAAACGATGCGTGGAAATCACTGGAATTTAAACGTAGTGACCAtt                                                                                                <  1:157563/275‑1 (MQ=255)                                                                                     cACCGCTATTTCGTCTTGAGGCTGGCGATGACTCATCACTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGc                                                                                                                                                                                                      >  2:46500/1‑159 (MQ=255)                                                                                     cACCGCTATTTCGTCTTGAGGCTGGCGATGACTCATCACTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCAAAATGTTTTATCGCCCCGc                                                                                                                                                              >  2:224625/1‑199 (MQ=255)                                                                                      aCCGCTATTTCGTCTTGAGGCTGGCGATGACTCATCACTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGACATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCAAAATGTTTTATCGCCCCGCACACATGAAGGGACGGGTAAACGATGCGTGGAAATCACTGGAATTTAAACGTAGTGACCATTCACTCAatatataaa                                                                                 >  1:194510/1‑273 (MQ=255)                                                                                         gCTATTTCGTCTTGAGGCTGGCGATGACTCATCACTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGt                                                                                                                                                                                                  <  1:46500/159‑1 (MQ=255)                                                                                         gCTATTTCGTCTTGAGGCTGGCGATGACTCATCACTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCAAAATGTTTTATCGCCCCGCacac                                                                                                                                                          <  1:224627/199‑1 (MQ=255)                                                                                                  tCTTGAGGCTGGCGATGACTCATCACTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGACGATGTTAATGCTAACGAGTTGACGc                                                                                                                                                                                                      >  1:93571/1‑146 (MQ=255)                                                                                                      gAGGCTGGCGATGACTCATCACTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGACGATGTTAATGCTAACGAGTTGACGCTGGt                                                                                                                                                                                                  <  2:93571/146‑1 (MQ=255)                                                                                                                       atcaCTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAgatg                                                                                                                                                                                                                              >  2:43343/1‑101 (MQ=255)                                                                                                                           cTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGt                                                                                                                                                                                                                          <  1:43343/101‑1 (MQ=255)                                                                                                                                             gCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAAc                                                                                                                                                                                                                >  2:416349/1‑93 (MQ=255)                                                                                                                                             gCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACgg                                                                                                                                                                                     >  1:277525/1‑120 (MQ=255)                                                                                                                                              cTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGtt                                                                                                                                                                                                                         >  2:31462/1‑83 (MQ=255)                                                                                                                                                 aTAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGTCATTCCAGCAAAGAACAAATCAGATGATGTTAATGCTGACGAGt                                                                                                                                                                                                            <  1:416356/93‑1 (MQ=255)                                                                                                                                                 aTAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCa                                                                                                                                                                                 <  2:277523/120‑1 (MQ=255)                                                                                                                                                  tAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATg                                                                                                                                                                                                                     <  1:31462/83‑1 (MQ=255)                                                                                                                                                        gcctgAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCATAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCAAAATGTTTTATCGCCCCGCACACCTGAAGGGACGGCTACACGATGCGTGGACATCACTGGCATTTAACCGTAGTGACCATTCACGCAATATATATAACCCAACTGAAAATTACGACGTATTTCCCGCCCTGGCAGCCTATAACACCAATCTCTCAAGaaaca               >  2:18712/1‑273 (MQ=255)                                                                                                                                                                     gagTCTCTGTTCTACAGTAAGGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGATAACGAGTTGACGCTGGTATTTAAAANACGGATCAAAATGTTTTATCGCCCCGCACACCTGAAGGGACGGGTAAACGATGCGTGGAAATCACTGGAATTTAAACGTAGTGACCATTCACTCAATATATATAACCCAACTGAATATTACGTCGTATTTGCCGGACTGGCAGTCGATAAAACCGATCTCACAAGCAAAATTGAATATATcgc  <  1:417018/275‑1 (MQ=255)                                                                                                                                                                                      tAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGACGATGTTAATGCTAACGAGtt                                                                                                                                                                                                           >  1:217617/1‑57 (MQ=255)                                                                                                                                                                                        aTGTTCGTGCCATTCCAGCAATGAAAAAATCAGATGATGTTAATGCTCACGCGTTGACGCTGGTATTTACAacac                                                                                                                                                                                       >  2:488889/1‑75 (MQ=255)                                                                                                                                                                                          gTTCGTGCCATTCCAGCAAAGAAAAAATCAGACGATGTTAATGCTAACGAGTTGACg                                                                                                                                                                                                       <  2:217615/57‑1 (MQ=255)                                                                                                                                                                                            tCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGAt                                                                                                                                                                                   <  1:488896/75‑1 (MQ=255)                                                                                                                                                                                             cGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCAAAATGTTTTATCGCCCCGCACACCTg                                                                                                                                                       >  2:328214/1‑102 (MQ=255)                                                                                                                                                                                              gTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCAAAATGTTTTATCGccc                                                                                                                                                                 >  2:522240/1‑91 (MQ=255)                                                                                                                                                                                                 ccATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCAAAATGTTTTATCGCCCCGCACACCTGAAgg                                                                                                                                                   <  1:328219/102‑1 (MQ=255)                                                                                                                                                                                                  cATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCAAAATGTTTTATCGCCCCGca                                                                                                                                                             <  1:522248/91‑1 (MQ=255)                                                                                                                                                                                                    ttCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCAAAATGTTTTATCGCCCCGCACACCTGAAGGGACGGGTAAACGATGCGTGGAAATCACTGGAATTTAAACGTAGTGACCa                                                                                                  >  1:237975/1‑148 (MQ=255)                                                                                                                                                                                                        aGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCAAAATGTTTTATCGCCCCGCACACCTGAAGGGACGGGTAAACGATGCGTGGAAATCACTGGAATTTAAACGTAGTGACCATTCa                                                                                              <  2:237973/148‑1 (MQ=255)                                                                                                                                                                                                          cAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCAAAATGTTTTATCGCCCCGCACACCTGAAGGGACGGGTAAACGATGCGTGGAAATCACTGGAATTTAAACGTAGTGACCATTCACTCAATATATATAAccc                                                                             >  1:229917/1‑163 (MQ=255)                                                                                                                                                                                                              gAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTGAAAACACGGATCAAAATGTTTTATCGCCCCGCACACCTGAAGGGACGGGTAAACGATGCGTGGAAATCACTGGAATTTAAACGTAGTGACCATTCACTCAATATATATAACCCAACt                                                                         <  2:229915/163‑1 (MQ=255)                                                                                                                                                                                                                          |                                                                                                                                                                                                                              ACAAAGGCGCAGAAACGCCTTATTTACTGCAATCATGGGTAGATAATATAGATGGTAAAAGCCGTGCCCCATTTATTATAACCCCACCGCTATTTCGTCTTGAGGCTGGCGATGACTCATCACTGCGAATTATTAAAACAGCTGATAACCTGCCTGAAAATAAAGAGTCGCTGTTCTACATTAATGTTCGTGCCATTCCAGCAAAGAAAAAATCAGATGATGTTAATGCTAACGAGTTGACGCTGGTATTTAAAACACGGATCAAAATGTTTTATCGCCCCGCACACCTGAAGGGACGGGTAAACGATGCGTGGAAATCACTGGAATTTAAACGTAGTGACCATTCACTCAATATATATAACCCAACTGAATATTACGTCGTATTTGCCGGACTGGCAGTCGATAAAACCGATCTCACAAGCAAAATTGAATATATCGC  >  CP009273/3281591‑3282029

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑