Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	233,579	C→T	S126N (AGC→AAC)	mltD ←	membrane‑bound lytic murein transglycosylase D

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	233,579	0	C	T	90.0%	20.1 / ‑5.9	10	S126N (AGC→AAC)	mltD	membrane‑bound lytic murein transglycosylase D
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (4/5);  total (5/5)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGACCTTCGCCGCTGTTATAAGCCGCTACGGTCAGAAGCCAGTCGCCGTCAAACATTTTGTTCAGACGCTGCATCATATTCAGCGCGGCAGTTGTTGAAGCAACAACATCGCGACGCGCGTCATAATTGCGGGTCTGTTTCAAACCATAATTGCGCCCCGTGCTCGGAATGATCTGCCAGATGCCTGCGGCATTGGCGCCAGACGTTGCGTGAGGATCAAAAGCGCTCTCCACTATGGGTAGTAGTACCAGTTCCATAGGCATGTTACGTTTTTTAACTTGCCCTGCTATCCAGTACATATACGGCTCTGCCCGTAAAGTTACATCGTGGAGATAGCTCTTATTGCGTAAATATTTCTGTTTCTGTTCGCGAATCCGGTCATTTTCCGGAATTCCCATCTTTAGCTCGTCGCCAATGAAAGCCCACAAGTCACCATCTGGCGCGATAGACGTCCCATCGTCCATCC  >  NC_000913/233353‑233819                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                 ncGACCTTCGCCGCTGTTATAAGCCGCTACGGTCAGAAGCCAGTCGCCGTCAAACATTTTGTTCAGACGCTGCATCATATTCAGCGCGGCAGTTGTTGAAGCAACAACATCGCGACGCGCGTCATAATTGCGGGTCTGTTTCAAACCATAATTGCGCCCCGTGCTCGGAATGATCTGCCAGATGCCTGCGGCATTGGCGCCAGACGTTGCGTGAGGATCAAAAGCGTTCTCCACTATGGGTAGTAGTAcc                                                                                                                                                                                                                           >  1:135697/2‑250 (MQ=255)                 ttATAAGCCGCTACGGTCAGAAGCCAGTCGCCGTCAAACATTTTGTTCAGACGCTGCATCATATTCAGCGCGGCAGGTGTTGAAGCAACAACATCGCGACGCGCGTCATAATTGCGGGTCTGTTTCAAACCATAATTGCGCCCCGTGCTCGGAATGATCTGCCAGATGCCTGCGGCATTGGCGCCAGACGTTGCGTGAGGATCAAAAGCGTTCTCCACTAGGGGTAGTAGTACCAGTTCCATAGGCATgn                                                                                                                                                                                                           <  1:48108/250‑2 (MQ=255)                                                                                                     gCAACAACATCGCGACGCGCGTCATAATTGCGGGTCTGTTTCAAACCATAATTGCGCCCCGTGCTCGGAATGATCTGCCAGATGCCTGCGGCATTGGCGCCAGACGTTGCGTGAGGATCAAAAGCGTTCTCCACTATGGGTAGTAGTACCAGTTCCATAGGCATGTTACGttttt                                                                                                                                                                                                  <  1:2001/175‑1 (MQ=255)                                                                                                                     gcgcgTCATAATTGCGGGTCTGTTTCAAACCATAATTGCGCCCCGTGCTCGGAATGATCTGCCAGATGCCTGCGGCATTGGCGCCAGACGTTGCGTGAGGATCAAAAGCGTTCTCCACTATGGGTAGTAGTACCAGTTCCATAGGCATGTTACGtttttt                                                                                                                                                                                                 >  1:44861/1‑160 (MQ=255)                                                                                                                                                                              tCTGCNCGATGNCNNCGGCATTGGCGCCAGACGTNGCGTGAGGATCAAAANCGTTNTCCACNATngn                                                                                                                                                                                                                                     >  2:61698/1‑66 (MQ=255)                                                                                                                                                                              tCTGCCAGATGCCTGCGGCATTGGCGCCAGACGTTGCGTGAGGATCAAAAGCGTTCTCCACTATGGGTAGTAGTACCAGTTCCATAGGCATGTTACGTTTTTTAACTTGCCCTGCTATCCAGTACATATACGGCTCTGCCCGTAAAGTTACATCGTGGAGATAGCTCTTATTGCGTAAATAtttctgtttc                                                                                                         <  1:61698/191‑1 (MQ=255)                                                                                                                                                                                 gCCAGATGCCTGCGGCATTGGCGCCAGACGTTGCGTGAGTATCAAAAGCGTTCTCCACTATGGGTAGTAGTACCAGTTCCAGAGGCATGTTACGTTTTTTAACTTGCCCTGCTATCCAGTACATATACGGCTCTGCCCGTAAAGTTACATCGTGGAGATAGCTCTTATTGCTTAAATATTTCTGTTTCTGTTCGCGAATCCGGTCATTTTCCGGAAGTCCCATCTTTAGCTCGTCGCCAATGAAAGccc                                            <  1:106936/249‑1 (MQ=255)                                                                                                                                                                                                     gcgcCAGACGTTGCGTGAGGATCAAAAGCGCTCTCCACTATGGGTAGTAGTACAAGTTCCATCGGCATGCTACGGTTTTTAACTTGCCCTGCTATCCAGCACCTATACGGCTCTGCCCGTAACGTTACATCGTGGAGATAGCTCTTATTGAGTAAATATTTCTGTTTCTGTTCACGAATCCGGTCATTTTCCGGAATTCCCATCTTTAGCTCGTTGCCAATCAAAGCCCACAAGTCACCACCTGGCGCGAt                      >  1:66250/1‑251 (MQ=255)                                                                                                                                                                                                                        gATCAAAAGCGTTCTCCACTATGGGTAGTAGTACCAGTTCCATAGGCATGTTACGTTTTTTAACTTGCCCTGCTATCCAGTACATATACGGCGCTGCCCGTAAAGTTACATCGTGTAGATAGCTCTTATTGCGTAAATATTTCTGTTTCTGTTcgc                                                                                                  <  1:26053/156‑1 (MQ=255)                                                                                                                                                                                                                         aTCAAAAGCGTTCTCCACTATGGGTAGTAGTACCAGTTCCATAGGCATGTTACGTTTTTTAACTTGCCCTGCTATCCAGTACATATACGGCTCTGACCGTAAAGTTAAATCGTGGAGATAGATCTTATTGCGTAAATATTTCTGTTTCTGTTCGCGAATCCGGTCATTTTCCGGAATTCCCATCTTTAGCTCGTCGCCAATGAAAGCCCACAAGTCACCATCTGGCGCGATATACGTCCCATCGtccatcc  >  1:140246/1‑251 (MQ=255)                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                 CCGACCTTCGCCGCTGTTATAAGCCGCTACGGTCAGAAGCCAGTCGCCGTCAAACATTTTGTTCAGACGCTGCATCATATTCAGCGCGGCAGTTGTTGAAGCAACAACATCGCGACGCGCGTCATAATTGCGGGTCTGTTTCAAACCATAATTGCGCCCCGTGCTCGGAATGATCTGCCAGATGCCTGCGGCATTGGCGCCAGACGTTGCGTGAGGATCAAAAGCGCTCTCCACTATGGGTAGTAGTACCAGTTCCATAGGCATGTTACGTTTTTTAACTTGCCCTGCTATCCAGTACATATACGGCTCTGCCCGTAAAGTTACATCGTGGAGATAGCTCTTATTGCGTAAATATTTCTGTTTCTGTTCGCGAATCCGGTCATTTTCCGGAATTCCCATCTTTAGCTCGTCGCCAATGAAAGCCCACAAGTCACCATCTGGCGCGATAGACGTCCCATCGTCCATCC  >  NC_000913/233353‑233819

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑