Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,131,139	T→A	L309Q (CTG→CAG)	insH9 →	IS5 family transposase and trans‑activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,131,139	0	T	A	90.0%	13.2 / ‑2.7	10	L309Q (CTG→CAG)	insH9	IS5 family transposase and trans‑activator
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base A (6/3);  total (6/4)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.01e-01

GTTGCTGAAAAACGATAACCAACTGGCGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAACGCCAAACAC  >  NC_000913/3131098‑3131382                                          |                                                                                                                                                                                                                                                    gTTGCTGAAAAACGATAACCAACTGGCGATGTTATTCACGCAGGCCAACCTGTTTCGGGCGGACAAAATGATACGTCAGTGAGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGTAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATc                                     >  2:254876/1‑250 (MQ=2)      tGAAAAACGATAACCAACTGGCGATGTTATTCACGCAGGCCAACCTGTTTCGGGCGGACCAAATGATACGTAAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATAGCGAAGAAAAGGTCGAAATAGGCAGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCACTAAATCAGGTc                                >  1:60026/1‑250 (MQ=11)       gAAAAACGATAACCAACTGGCGATGTTATTCACGCAGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAAATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCAt                              >  1:364525/1‑251 (MQ=18)        aaaaaCGATAACCAACTGGCGATGTTATTCACGCAGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAAGTGCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATa                             <  2:343727/251‑1 (MQ=18)             cGATAACCAACTGGCGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCtt                        <  2:1173/251‑1 (MQ=35)               aTAACCCACTGGCGATGTTATTCACGCAGGCCACCCTGTTTAGGGCGGACCAACTGATACGTCAGTGGCCGAGCTCTCACTAAACCCTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAAGCCAAACGCTTCg                      >  2:167087/1‑251 (MQ=11)                 aaCCAACTGGCGATGTTATTCACGCAGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCgag                    <  1:115247/251‑1 (MQ=38)                    cagcTGGCGATGTTATTCACGCAGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGAt                  >  1:67580/4‑250 (MQ=255)                    cAACTGGCGATGTTATTCACGCAGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGAt                  >  1:67573/1‑250 (MQ=39)                                    tCACGCAGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAACGCCAAacac  <  2:339532/250‑1 (MQ=255)                                          |                                                                                                                                                                                                                                                    GTTGCTGAAAAACGATAACCAACTGGCGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATCAGGTCATACGCTTCGAGATACTTAACGCCAAACAC  >  NC_000913/3131098‑3131382

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑