Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,186,138	A→T	9.5%	intergenic (+48/‑49)	yqiG → / → insC1	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein/IS2 repressor TnpA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,186,138	0	A	T	9.5%	132.4 / 6.3	42	intergenic (+48/‑49)	yqiG/insC1	pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein/IS2 repressor TnpA
Reads supporting (aligned to +/- strand):  ref base A (17/21);  new base T (2/2);  total (19/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.97e-01

ACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAATGATAAGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCCAGCCAGTTATTTCT  >  NC_000913/3185872‑3186329                                                                                                                                                                                                                                                                           |                                                                                                                                                                                                aCTCAATTTCAAACTTCCCATGGATACCCCAAGCAAAAATGCCACCCCGGGCAACGTTTACGCTCATGCTGACTACACGATTGCATACGATTAATCGCATTTGGCCGTGTTCGCCCGGCCACATCATTAACTGATTAATGATAAGTGGATAAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATGAAAAATAGTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACAAGTATCACTTAAATAAGTGAt                                                                                                                                                                                         <  4:154387/275‑1 (MQ=255)                                        tGCGACCCCGGGCAACGTTGACGCTCAGGCTGACTACAAGATTGTTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAATGATAAGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGGACCCCTGAATCTCCAGACAACAAATATCGCTTAAATAAGTGATAGTCTTAATACTAGTTGTTAGACTAGTCATTGGAGAACa                                                                                                                                                  <  2:525572/275‑1 (MQ=255)                                                 gggCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAATGATAAGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGAtgattga                                                                                                                                         <  2:445445/275‑1 (MQ=255)                                                                                      tACGAGTAAGCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAATGATAAGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTg                                                                                                                                                         <  1:113469/222‑1 (MQ=255)                                                                                                                      gCCACATCATTAACGGATTAATGATAAGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGAACGAAATTGTTcagcaggtctt                                                                    >  4:432390/1‑270 (MQ=255)                                                                                                                             catTAACGGATTAATGATAAGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTATTTAAGt                                                                                                                                                                                            >  6:1111368/1‑148 (MQ=255)                                                                                                                                  aCGGATTAATGATAAGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTATTTAAGTGATat                                                                                                                                                                                       <  5:1111368/148‑2 (MQ=255)                                                                                                                                                                                        aGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTGATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCCAGCCAGTTATTtct  <  2:432391/275‑1 (MQ=255)                                                                                                                                                                                            aaTTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGAtgattga                                                                                                                                         <  6:837320/136‑1 (MQ=255)                                                                                                                                                                                            aaTTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGAtgattga                                                                                                                                         >  5:837320/1‑136 (MQ=255)                                                                                                                                                                                                  ttAAAAATATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTa                                                                                                                                                                                  >  8:489049/1‑89 (MQ=255)                                                                                                                                                                                                  ttAAAAATATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTa                                                                                                                                                                                  <  7:489049/89‑1 (MQ=255)                                                                                                                                                                                                  ttAAAAATATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAga                                                                                                                                                >  8:440770/1‑123 (MQ=255)                                                                                                                                                                                                  ttAAAAATATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAga                                                                                                                                                <  7:440770/123‑1 (MQ=255)                                                                                                                                                                                                       aaTATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTa                                                                                                                                                                                  <  5:603895/84‑1 (MQ=255)                                                                                                                                                                                                       aaTATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTa                                                                                                                                                                                  >  6:603895/1‑84 (MQ=255)                                                                                                                                                                                                            ttattGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAg                                                                                                                                                                    >  5:1014725/1‑93 (MQ=255)                                                                                                                                                                                                            ttattGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAg                                                                                                                                                                    <  6:1014725/93‑1 (MQ=255)                                                                                                                                                                                                                tGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGAt                                                                                                                                                                                         >  8:914183/1‑68 (MQ=255)                                                                                                                                                                                                                tGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGAt                                                                                                                                                                                         <  7:914183/68‑1 (MQ=255)                                                                                                                                                                                                                   tCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTATTTAAGTGAt                                                                                                                                                                                         <  7:250233/65‑1 (MQ=17)                                                                                                                                                                                                                   tCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTATTTAAGTGAt                                                                                                                                                                                         >  8:250233/1‑65 (MQ=17)                                                                                                                                                                                                                   tCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGaa                                                                                                                       >  7:132833/1‑131 (MQ=40)                                                                                                                                                                                                                   tCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTAc                                                                                                        >  2:8577/1‑146 (MQ=40)                                                                                                                                                                                                                   tCATTATCCGTTATTAGACTGGCCCCCTGAATCGCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGaa                                                                                                                       <  8:132833/131‑1 (MQ=255)                                                                                                                                                                                                                     aTTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGc                                                                                                                              >  8:784732/1‑122 (MQ=40)                                                                                                                                                                                                                     aTTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGc                                                                                                                              <  7:784732/122‑1 (MQ=40)                                                                                                                                                                                                                      ttATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAgatga                                                                                                                                             <  7:48645/106‑1 (MQ=40)                                                                                                                                                                                                                      ttATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAgatga                                                                                                                                             >  8:48645/1‑106 (MQ=40)                                                                                                                                                                                                                       tATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAg                                                                                                                                                                    >  5:545991/1‑82 (MQ=255)                                                                                                                                                                                                                       tATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAg                                                                                                                                                                    <  6:545991/82‑1 (MQ=255)                                                                                                                                                                                                                       tATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAgatga                                                                                                                                             >  5:150165/1‑105 (MQ=40)                                                                                                                                                                                                                       tATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAgatga                                                                                                                                             <  6:150165/105‑1 (MQ=40)                                                                                                                                                                                                                       tATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAggg                                                                                                                               <  8:285088/119‑1 (MQ=39)                                                                                                                                                                                                                       tATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAggg                                                                                                                               >  7:285088/1‑119 (MQ=39)                                                                                                                                                                                                                       tATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACcaca                                                                                                    <  4:8577/146‑1 (MQ=37)                                                                                                                                                                                                                            gTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGttttt                                                                                                                                                                      <  5:824382/75‑1 (MQ=35)                                                                                                                                                                                                                            gTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGttttt                                                                                                                                                                      >  6:824382/1‑75 (MQ=35)                                                                                                                                                                                                                            gTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGt                                                                                                          >  7:628413/1‑135 (MQ=33)                                                                                                                                                                                                                            gTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGt                                                                                                          <  8:628413/135‑1 (MQ=33)                                                                                                                                                                                                                              tattaGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCtt                                                                                                                                   <  8:419860/108‑1 (MQ=31)                                                                                                                                                                                                                              tattaGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCtt                                                                                                                                   >  7:419860/1‑108 (MQ=31)                                                                                                                                                                                                                                                                           |                                                                                                                                                                                                ACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAATGATAAGTGGATCAGATGTATAAAAAATTAAAATTAACCACAATAAGCGAATTGATTAAAAATATTTATTGTTCATTATCCGTTATTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCCAGCCAGTTATTTCT  >  NC_000913/3185872‑3186329

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑