Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,261,358	T→A	9.8%	intergenic (+52/‑311)	yjbM → / → dusA	uncharacterized protein/tRNA‑dihydrouridine synthase A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,261,358	0	T	A	9.8%	164.6 / 8.4	51	intergenic (+52/‑311)	yjbM/dusA	uncharacterized protein/tRNA‑dihydrouridine synthase A
Reads supporting (aligned to +/- strand):  ref base T (23/23);  new base A (3/2);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

GTTTGACCCAACCTCAAAGGAAGAGATTAAAATACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACAAAGTTAACGGCTAATAAGATTATTTC  >  NC_000913/4261216‑4261499                                                                                                                                                |                                                                                                                                              gTTTGACCCAACCTTAAAGGAAGAGATTAAAATACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTg                                                                                                                                         >  3:35578/1‑149 (MQ=255) gTTTGACCCAACCTCAAAGGAAGAGATTAAAATACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTg                                                                                                                                         <  1:80106/149‑1 (MQ=255)     gACCCAACCTCAAAGGAAGAGATTAAAATACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATATAAAAAGAACCCAATAAATATTGGGt                                                                                                                                      <  1:363910/149‑1 (MQ=255)        ccAACCTCAAAGGAAGAGATTAAAATACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCtt                                                                                                                                  <  3:12677/149‑1 (MQ=255)        ccAACCTCAAAGGAAGAGATTAAAATACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGAACCCAATAAATATTGGGtcc                                                                                                                                    >  1:161157/1‑145 (MQ=255)        ccAACCTCAAAGGAAGAGATTAAAATACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGAACCCAATAAATATTGGGtcc                                                                                                                                    <  2:161157/147‑3 (MQ=255)         cAACCTCAAAGGAAGAGATTAAAATACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCttt                                                                                                                                 <  4:204969/149‑1 (MQ=255)            ccTCAAAGGAAGAGATTAAAATACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCtttttt                                                                                                                              <  1:66832/149‑1 (MQ=255)             cTCAAAGGAAGAGATTAAAATACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTg                                                                                                                                         >  1:273241/1‑137 (MQ=255)             cTCAAAGGAAGAGATTAAAATACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTg                                                                                                                                         <  2:273241/137‑1 (MQ=255)                  aGGAAGAGATTAAAATACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTAt                                                                                                                        <  4:102294/149‑1 (MQ=255)                     aaGAGATTAAAATACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCaa                                                                                                                     <  2:4060/149‑1 (MQ=255)                          aTTAAAATACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTa                                                                                                                >  3:209783/1‑149 (MQ=255)                                 tACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATc                                                                                                                       >  3:336552/1‑135 (MQ=255)                                 tACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATc                                                                                                                       <  4:336552/135‑1 (MQ=255)                                  aCTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAgg                                                                                                        >  3:396509/1‑149 (MQ=255)                                    ttACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGga                                                                                                      <  2:25366/149‑1 (MQ=255)                                     gaCAGACACTTATAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCAATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGaag                                                                                                     <  4:232373/148‑1 (MQ=255)                                       cAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGat                                                                                                   <  4:35578/149‑1 (MQ=255)                                              ttCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCAc                                                                                            >  4:320360/1‑149 (MQ=255)                                              ttCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCAc                                                                                            <  1:303950/149‑1 (MQ=255)                                                            aTGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAAtgtg                                                                              <  3:320360/149‑1 (MQ=255)                                                              gATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAAtgtgtg                                                                            >  2:216092/1‑149 (MQ=255)                                                                    ttCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGa                                                                           <  4:228990/144‑1 (MQ=255)                                                                    ttCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGa                                                                           >  3:228990/1‑144 (MQ=255)                                                                        gggTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAAtattta                                                                                                                                            >  2:395370/1‑75 (MQ=255)                                                                        gggTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAAtattta                                                                                                                                            <  1:395370/75‑1 (MQ=255)                                                                        gggTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTtttatt                                                                  >  3:117580/1‑149 (MQ=255)                                                                          gTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGa                                                                           <  4:125360/138‑1 (MQ=255)                                                                          gTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGa                                                                           >  3:125360/1‑138 (MQ=255)                                                                           ttAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTttta                                                                    <  3:361086/144‑1 (MQ=255)                                                                           ttAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTttta                                                                    >  4:361086/1‑144 (MQ=255)                                                                                        ataataTGAGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGa                                                  >  4:40848/1‑149 (MQ=255)                                                                                               gtgAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGgaga                                                                                                    >  3:249600/1‑92 (MQ=255)                                                                                               gtgAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGgaga                                                                                                    <  4:249600/92‑1 (MQ=255)                                                                                                     ttcttcGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTg                                     >  3:63120/1‑149 (MQ=255)                                                                                                                tATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACaaa                          <  3:40848/149‑1 (MQ=255)                                                                                                                tATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACaaa                          >  4:14498/1‑149 (MQ=255)                                                                                                                tATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACaaa                          <  3:14498/149‑1 (MQ=255)                                                                                                                  tGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACAAAGt                        >  1:314738/1‑149 (MQ=255)                                                                                                                        gCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACAAAGTTAACgg                  >  1:299589/1‑149 (MQ=255)                                                                                                                           ttATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGc                                   >  3:44/1‑129 (MQ=255)                                                                                                                           ttATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGc                                   <  4:44/129‑1 (MQ=255)                                                                                                                           ttATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACAAAGTTAACGGCta               >  3:67085/1‑149 (MQ=255)                                                                                                                               at‑aAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACAAAGTTAACGGCtaataa           <  4:209783/149‑1 (MQ=255)                                                                                                                                  aaaaGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACAAAGTTAACGGCTAATAAGa         <  4:117580/149‑1 (MQ=255)                                                                                                                                  aaaaGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACAAAGTTAACGGCTAATAAGa         >  3:83672/1‑149 (MQ=255)                                                                                                                                       gACCCAATATTTATTGGTTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACAAAGTTAACGGCTAATAAGattatt    >  3:155746/1‑149 (MQ=255)                                                                                                                                       aaCCCAATAAATATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACAAAGTTAACGGCTAATAAGattatt    >  4:92818/2‑149 (MQ=255)                                                                                                                                        aCCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACAAAGTTAACGGCtaat             >  4:32982/1‑139 (MQ=255)                                                                                                                                        aCCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACAAAGTTAACGGCtaat             <  3:32982/139‑1 (MQ=255)                                                                                                                                         cccAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACAAAGTTAACGGCTAATAAGATTATTTc  >  1:122162/1‑149 (MQ=255)                                                                                                                                         cccAATAAATATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACAAAGTTAACGGCTAATAAGATTATTTc  >  3:55441/1‑149 (MQ=255)                                                                                                                                                |                                                                                                                                              GTTTGACCCAACCTCAAAGGAAGAGATTAAAATACTTACAGACACTTCTAAATTAATTTATGATTTGTTCGGGGTTAAATCGGAGAAATAATATGTGAAGTTCTTCGATAGTATGGAAGGCATTATAT‑AAAAGGACCCAATATTTATTGGGTTCTTTTTTCTCTATCAATACTATTAGCAGGGAGATATATCACCAGAGTTTAATGTGTGATTTTTTATTTATCGTCGAACCTGGATTGTTTATCATTGGCCTTAACAAAGTTAACGGCTAATAAGATTATTTC  >  NC_000913/4261216‑4261499

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑