Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,756,356	C→T	V66V (GTC→GTT)	intA →	integrase IntA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,756,356	0	C	T	100.0%	38.0 / NA	12	V66V (GTC→GTT)	intA	integrase IntA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (9/3);  total (9/3)

TACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGTGACGGGCTTACTCTGTTAATCAAGTCCAGTGGCAGTAAGCTTTGGCAATTCCGTTACTATCGGCCTTTGACCAAGCAGCGAACCAAACAGAGCTTCGGTGCCTATCCTGCCGTCTCGCTTTCTGATGCACGTAAACTCAGAGCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATC  >  NC_000913/2756128‑2756593                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                              tACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGTGACGGGCTTACTCTGTTAATCAAGTCCAGTGGCAGTAAGCTTTGGCAATTCCGTTACTATCGGCCTTTGACCAAGCAGCGAACCAAACAGAGCTTCGGTGCCTATCCTGCCGTTTCGCTTTCTGATGCACGTAAAc                                                                                                                                                                                                                         >  2:89101/1‑251 (MQ=255)                                                                    aTCAAAGCCCCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGCGACGGGCTTACTCTGTTAAGCAAGTCCAGTGGCAGTAAGCTTTGGCAATTCCGTTACTATCGGCCTTTGCCCAAGCATCGACCCAAACACAGCTTCGGTGCCTATCCTGCCGTTTCGCTTTCGGATGCACGTAAACTCAGAGCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGt                                                                                                                                                      <  2:44260/251‑1 (MQ=255)                                                                      cAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGTGACGGGCTTACTCTGTTAATCAAGTCCAGTGGCAGTAAGCTTTGGCAATTCCGTTACTATCGGCCTTTGACCAAGCAGCGAACCAAACAGAGCTTCGGTGCCTATCCTGCCGTTTCGCTTTCTGATGCACGTAAACTCAGAGCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTg                                                                                                                                                     <  1:258375/250‑1 (MQ=255)                                                                         aGCCGACACACCTAAAGATACAGATTACCAGCTTTATGACGGTGAAGGGCTTACTATGTTAATCAAGTCCAGTGGCAGTAAGCTTTGGCCATTCCGTTACTATCGGCCTTTGACCAAGCAGCGAAACAAACAGAGATTCGGTGCCGATCCTGCCGTTTCGCTTTCTGATGCAAGTAAACCTATGGCCGTATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAAACTCAGAAAGTACAGATGAgg                                                                                                                                                  >  2:258997/1‑250 (MQ=255)                                                                                                aTTACCAGCTTTATGACGGTGACGGGCTTACTCTGTTAATCAAGTCCAGTGGCAGTAAGCTTTGGCAATTCCGTTACTATCGGCCTTTGACCAAGCAGCGAACCAAACAGAGCTTCGGTGCCTATCCTGCCGTTTCGCTTTCTGATGCACGTAAACTCAGAGCCGAATCTTAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAATGAACAGGTGAGGAATTCTCAAGAGGCCAAAAACAAt                                                                                                                          >  1:117998/1‑251 (MQ=255)                                                                                                                           ttACTCTGTTAATCAAGTCCAGTGGCAGGAAGCTTTGGCAATTCCGTTACTATCGGCCTTTGACCAAGCAGCGAACCAAACAGAGCTTCGGTGCCTATCCTGCCGTTTCGCTTTCTGATGCACGTAAACTCAGAGCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGACAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTtgg                                                                                               >  1:36855/1‑251 (MQ=255)                                                                                                                                               aGTGGCAGTAAGCTTTGGCAATTCCGTTACTATCGGCCTTTGACCAAGCAGCGAACCAAACAGAGCTTCGGTGCCTATCCTGCCGTTTCGCTTTCTGATGCACGTAAACTCCGAGCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTCGTTGCCGAGCGTTGGTGGAATGTGAAGAAAAcc                                                                             >  1:255077/1‑249 (MQ=255)                                                                                                                                                gTGGCAGTAAGCTTTGGCAATTCCGTTACTATCGGCCTTTGACCAAGCCGCGAACCAAACAGAGCTTCGGCGCCTCTCCTGCCGTTCCGCCTTCTGATGCACGAAAAATCAGAGCCGACTCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGCACATCAGCAAGAACAGGCGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGc                                                                          >  1:165674/1‑251 (MQ=255)                                                                                                                                                                                               cagcGAACCAAACAGAGCTTCGGTGCCTATCCTGCCGTTTCGCTTTCTGATGCACGTAAACTCAGAGCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTgagag                              >  2:182190/1‑248 (MQ=255)                                                                                                                                                                                                               gCTTCGGTGCCTATCCTGCCGTTTCGCTTTCTGATGCACGTAAACTCAGAGCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATc           <  2:71485/251‑1 (MQ=255)                                                                                                                                                                                                                    ggTGCCTATCCTGCCGTTTCGCTTTCTGATGCACGTAAACTCAGAGCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTg       >  2:157389/1‑250 (MQ=255)                                                                                                                                                                                                                         cTATCCTGCCGTTTCGCTTTCTGATGCACGTAAACTCAGAGCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGatctc  >  1:94823/1‑247 (MQ=255)                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                              TACGTTGGGCCTAAACGCAGGGAGACTCCCCATGGCAAGAAAAACCAAGCCGTTAACTGATACGGAAATCAAAGCCGCCAAACCTAAAGATGCCGATTACCAGCTTTATGACGGTGACGGGCTTACTCTGTTAATCAAGTCCAGTGGCAGTAAGCTTTGGCAATTCCGTTACTATCGGCCTTTGACCAAGCAGCGAACCAAACAGAGCTTCGGTGCCTATCCTGCCGTCTCGCTTTCTGATGCACGTAAACTCAGAGCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATC  >  NC_000913/2756128‑2756593

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑