Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	3	121	T→C	intergenic (–/‑1126)	– / → unknown	–/DNA transformation protein TfoX

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	3	121	0	T	C	100.0%	83.7 / NA	32	intergenic (–/‑1126)	–/unknown	–/DNA transformation protein TfoX
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (8/24);  total (8/24)

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GAGGTACGCCTTTTTGTTTATGAAATCTTTAATAAATACTATGCTGTACTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTATCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGCCTGATAAAACCAATCATTAGTTAAATTAACAAGTTAATGTGCAGGCAAAAACCGGGGGGGTAGGCAGGTGACATTATTTATGCATAGCTATGCTGACTGTATTTAGCCATAGTCATTGACCTTTACTCCTGTCAAATTGTGGGTTGACGC  >  3/1‑360                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                                caaggtttacgtttcgctatccgtgaaggtggccgtacagtgggtgccggcgtggtagctaaaattatcaaataattgataagacaaaccaaagtaaaactgaaaaggcgtatcgaGAGGTACGCCTTTTTGTTTATGAAATCTTTAATAAATACTATGCTGTACTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATg                                                                                                                                                                                                                                   <  1:76015‑M2/135‑1 (MQ=255)         acgtttcgctatccgtgaaggtggccgtacagtgggtgccggcgtggtagctaaaattatcaaataattgataagacaaaccaaagtaaaactgaaaaggcgtatcgaGAGGTACGCCTTTTTGTTTATGAAATCTTTAATAAATACTATGCTGTACTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATc                                                                                                                                                                                                                           <  1:64600‑M2/143‑1 (MQ=255)                 ctatccgtgaaggtggccgtacagtgggtgccggcgtggtagctaaaattatcaaataattgataagacaaaccaaagtaaaactgaaaaggcgtatcgaGAGGTACGCCTTTTTGTTTATGAAATCTTTAATAAATACTATGCTGTACTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTatat                                                                                                                                                                                                                    <  1:658488‑M2/150‑1 (MQ=255)                                gccgtacagtgggtgccggcgtggtagctaaaattatcaaataattgataagacaaaccaaagtaaaactgaaaaggcgtatcgaGAGGTACGCCTTTTTGTTTATGAAATCTTTAATAAATACTATGCTGTACTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATc                                                                                                                                                                                                                           <  1:82516‑M2/143‑1 (MQ=255)                                                                attatcaaataattgataagacaaaccaaagtaaaactgaaaaggcgtatcgaGAGGTACGCCTTTTTGTTTATGAAATCTTTAATAAATACTATGCTGTACTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGc                                                                                                                                                                    <  1:85975‑M2/198‑1 (MQ=255)                                                                          aattgataagacaaaccaaagtaaaactgaaaaggcgtatcgaGAGGTACGCCTTTTTGTTTATGAAATCTTTAATAAATACTATGCTGTACTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTCTCAGCAACACCTCaa                                                                                                                                                          >  1:458591‑M2/44‑251 (MQ=255)                                                                            ttgataagacaaaccaaagtaaaactgaaaaggcgtatcgaGAGGTACGCCTTTTTGTTTATGAAATCTTTAATAAATACTATGCTGTACTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTc                                                                                                                                                                                                               <  1:211356‑M2/155‑1 (MQ=255)                                                                             tgataagacaaaccaaagtaaaactgaaaaggcgtattgaGAGGTACGCCTTTTTGTTTATGAAATCTTTAATAAATACTAGGCTGTACTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGcc                                                                                                                                                       <  1:424828‑M2/211‑1 (MQ=255)                                                                             tgataagacaaaccaaagtaaaactgaaaaggcgtatcgaGAGGTACGCCTTTTTGTTTATGAAATCTTTAATAAATACTATGCTGTACTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGaataat                                                                                                                                                                                                  <  1:712266‑M2/168‑1 (MQ=255)                                                                                    acaaaccaaagtaaaactgaaaaggcgtatcgaGAGGTACGCCTTTTTGTTTATGAAATCTTTAATAAATACTATGCTGTACTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGCCTGATa                                                                                                                                                  <  1:385342‑M2/216‑1 (MQ=255)                                                                                                                atcgaGAGGTACGCCTTTTTGTTTATGAAATCTTTAATAAATACTATGCTGTACTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATc                                                                                                                                                                                                                           <  1:889600‑M2/143‑1 (MQ=255)                                                                                                                                                   aataaataCTATGCTGTACTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGCCTGATAAAACCAATCATTAGTTAAATTAACAAGTTAATGTGCAGGCAAAAAc                                                                                                    <  1:571439/232‑1 (MQ=255)                                                                                                                                                        ataCTATGCTGTACTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGaat                                                                                                                                                                                                     <  1:469120/130‑1 (MQ=255)                                                                                                                                                             aTGCTGTACTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGCCTGATAAAACCAATCATTAGTTAAATTAACAAGTTAATGTGCAGGCAAAAACCGGGGGAGTAGGCAGGTGACAttattta                                                                        <  1:813837/250‑1 (MQ=255)                                                                                                                                                                    aCTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGCCTGATAAAACCAATCATTAGTTAAATTAACAAGTTAATGTGCAGGCAAAAACCGGGGGAGTAGGCAGGTGACATTATTTATGCATAGc                                                                <  1:802522/251‑1 (MQ=255)                                                                                                                                                                         cTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGCCTGATAAAACCAATCATTAGTTAAATTAACAAGTTAATGTGCAGGCAAAAACCGGGGGAGTAGGCAGGTGACATTATTTATGCATAGCTATGc                                                           <  1:499380/251‑1 (MQ=255)                                                                                                                                                                                   cATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTaa                                                                                                                                                                                    <  1:97304/120‑1 (MQ=255)                                                                                                                                                                                       ataCACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGCCTGATAAAACCAATCATTAGTTAAATTAACAAGTTAATGTGCAGGCAAAAACCGGGGGAGTAGGCAGGTGACATTATTTATGCATAGCTATGCTGACTGTATTTAGc                                             <  1:29716/251‑1 (MQ=255)                                                                                                                                                                                          cacGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGCCTGATAAAACCAATCATTAGTTAAATTAACAAGTTAATGTGCAGGCAAAAACCGGGGGAGTAGGCAGGTGACatta                                                                            <  1:112643/217‑1 (MQ=255)                                                                                                                                                                                              aCTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGCCTGATAAAACCAATCATTAGTTAAATTAACAAGTTAATGTGCAGGCAAAAACCGGGGGAGTAGGCAGGTGACATTATTTATGCATAGCTATGCTGACTGTATTTAGCCATAGt                                       >  1:224533/1‑250 (MQ=255)                                                                                                                                                                                                                   aTTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTg                                                                                                                                                                                       <  1:707771/85‑1 (MQ=255)                                                                                                                                                                                                                   aTTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGt                                                                                                                                                                                      <  1:378160/86‑1 (MQ=255)                                                                                                                                                                                                                   aTTAAATAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACAcc                                                                                                                                                              >  1:261102/1‑110 (MQ=255)                                                                                                                                                                                                                      aaaTAATCATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGCCTGATAAAACCAATCATTAGTTAAATTAACAAGTTAATGTGCAGGCAAAAACCGGGGGAGTAGGCAGGTGACATTATTTATGCATAGCTATGCTGACTGTATTTAGCCATAGTCATTGACCTTTACTc                        >  1:394065/1‑241 (MQ=255)                                                                                                                                                                                                                             cATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGa                                                                                                                                                                                                            <  1:94997/54‑1 (MQ=255)                                                                                                                                                                                                                             cATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGCCTGATAAAACCAATCATTAGTTAAATTAACAAGTTAATGTGCAGGCAAAAACCGGGGGAGTAGGCAGGTGACATTATTTATGCATAGCTATGCTGACTGTATTTAGCCATAGTCATTGACCTTTACTc                        >  1:376165/1‑234 (MQ=255)                                                                                                                                                                                                                             cATTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGCCTAACTTTCAGCAACACCTCAAGCCTGATAAAACCAATCATTAGTTAAATTAACAAGTTAATGTGCAGGCAAAAACCGGGGGAGTAGGCAGGTGACATTATTTATGCATAGCTATGCTGACTGTATTTAGCCATAGTc                                      >  1:302132/1‑220 (MQ=255)                                                                                                                                                                                                                             attcatcgCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGCCTGATAAAACCAATCATTAGTTAAATTAACAAGTTAATGTGCAGGCAAAAACCGGGGGAGTAGGCAGGTGACATTATTTATGCATAGCTATGCTGACTGTATTTAGCCATAGTCATTGACCTTTACTCCTGTCAAATTGTGGGt        <  1:597137/243‑1 (MQ=255)                                                                                                                                                                                                                              aTTTAAGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGCCTGATAAAACCAATCATTAGTTAAATTAACAAGTTAATGTGCAGGCAAAAACCGGGGGAGTAGGCAGGTGACATTATTTATGCATAGc                                                                <  1:411958/193‑1 (MQ=255)                                                                                                                                                                                                                                  aaGCCGATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGCCTGATAAAACCAATCATTAGTTAAATTAACAAGTTAATGTGCAGGCAAAAACCGGGGGAGTAGGCAGGTGACATTATTTATGCATAGCTATGCTGACTGTATTTAGCCATAGTCATTGACCTTTACTCCTGTCAAATTGTGGGTTGACGc  <  1:26591/251‑1 (MQ=255)                                                                                                                                                                                                                                       gATTTACCGTATTTTTCAATGTCTGAATCTGTatat                                                                                                                                                                                                                    >  1:388573/1‑36 (MQ=255)                                                                                                                                                                                                                                       gATTTACCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGCCTGATAAAACCAATCAt                                                                                                                                       >  1:279924/1‑113 (MQ=255)                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                                ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GAGGTACGCCTTTTTGTTTATGAAATCTTTAATAAATACTATGCTGTACTTCCTTTTTAATTCATTATACACGACTAATTTTTATTTTAATTCTATTAAATAATCATTTAAGCCGATTTATCGTATTTTTCAATGTCTGAATCTGTATATCGTTCAGACGTGAATAATAGTCCATATTGTAACGGTCTAACTTTCAGCAACACCTCAAGCCTGATAAAACCAATCATTAGTTAAATTAACAAGTTAATGTGCAGGCAAAAACCGGGGGGGTAGGCAGGTGACATTATTTATGCATAGCTATGCTGACTGTATTTAGCCATAGTCATTGACCTTTACTCCTGTCAAATTGTGGGTTGACGC  >  3/1‑360

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑