Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,639,269	C→A	28.9%	L472L (CTG→CTT)	pbpC ←	penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,639,269	0	C	A	28.9%	15.8 / 2.3	14	L472L (CTG→CTT)	pbpC	penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain
Reads supporting (aligned to +/- strand):  ref base C (5/5);  new base A (2/2);  total (7/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.96e-01

TTATTGACCTGATTCAACAATGGTACGGCACTGGCAAAGCCAAACTGACCAACAACGGGCGTGCCGTCCGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGCACTATCCGGCAAGGGTTGCGCTTCATCAGCCATAATCCGGCGAATGATCCACGCCGCCCCCGACGACATTAAAGGCCGTTCAAGCAGCGGATCGTCAGGCTGTAAGCGCAATTTGCCTGCCTTGCCGTGGCGAGCAAACGCGGTATACGCTGCCGCCATATCTTCCAGTTTTGCACCAGCGCCGCCGAGAATGAGTGAAAGATTCGGCGCAGCACCGTTGGGCAAATATAACGGCAATCCAACATTGCGTAACTTTGCCGCAAACCGTTTCGGTCCATAGGCTTCCAGCACCTGCACAG  >  CP009273/2639000‑2639483                                                                                                                                                                                                                                                                              |                                                                                                                                                                                                                       ttattGACCTGATTCAACAATGGTACGGCACTGGCAAAGCCAAACTGACCAACAACGGGCGTGCCGTCCGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTATCCCCAATCGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCGTGTTCCATGCCAGTGGGGCGACGCGCGGCAAGGCACTATCCGGCAAGGGTTGCGCTTCATCAGCCATAATCCGGCGAATGATCCACGCCGCCCCCGACGACATTAAAGGCCGTTCAAGCAGCgg                                                                                                                                                                                                                   >  1:298069/1‑275 (MQ=255)            aTTCAACAATGGTACGGCACTGGCAAAGCCAAACTGACCAACAACGGGCGTGCCGTCCGGTCTGCCAGTCCAGATCCCAATGACATAGAGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGCACTATCCGGCAAGGGGTGCGCTTCATCAGCCATAATCCGGCGAATGATCCACGCCGCCCCGGCCGCCATTAAAGGCCGCCCAAGCACCAGAACGtgactcg                                                                                                                                                                                                        >  2:287972/1‑269 (MQ=255)                        tACGGCACTGGCAAAGCCAAACTGACCAACAACGGGCGTGCCGTCCGGTCTGCCAGCCCAGCCCCCAACGACATAGCGAGCGTTAACCCCAACCGCCCAGGCGTCACGACAGCCATAACTGGTGCCCGTTTTCCATGCCAGTCGGGCGACTCGCGCCAAAGCCCTATCCGCCACGGGCTGCGCTTCATCAGCCACAAACCGCCGAATGATCCACGCCCCCCCACACAACATCAAAGGACGATCCAGCAGCGGACCGTCAGGCGGAGAGCGCAAt                                                                                                                                                                                             >  2:328301/1‑274 (MQ=255)                                                   aacaacGGGCGTGAACGCCCGTCTCCACGGCCAGATCCCAATGCCATGGCGGGCGTTTTCCCCAATCGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGCACTATCCGGCAAGGGTTGCGCTTCATCAGCCATAATCCGGCGAATGATCCACGCCGCCCCCGACGACATTAAAGGCCGTTCAAGCAGCGGATCGTCAGGCTGTAAGCGCAATTTGCCTGCCTTGCCGTGGCGAGCAAAcg                                                                                                                                                                 <  2:298058/275‑1 (MQ=255)                                                                             cAGTCCAGATACCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGCACTATCCGGCAAGGGTTGCGCTTCATCAGCCGTAATCCGGCGAATGATCCACGCCGCCCCCGACGACATTAAAGGCCGTTCAAGCAACGGAACGTCAGGCTGTAAGCGCAATTTGCCTGCCTTGCCGTGGCGAGCAAACGCGGCATACACTACCGCCAAATCTAcc                                                                                                                                       >  1:332563/1‑275 (MQ=255)                                                                                               cATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGCAATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGCACTATCCGGCAAGGGTTGCGCTTCATCAGCCATAATCCGGCGAATGATCCACGCCGCCCCCGACGACATTAAAGGCCGTTCAAGCAGCGGATCGTCAGGCTGTAAGCGCAATTTGCCTGCCTTGCCGTGGCGAGCAAACGCGGTATACGCTGCCGCCATATCTTCCAGTTTTGCACCAGcgccg                                                                                                                     <  1:313476/275‑1 (MQ=255)                                                                                                           tAACCCCAATCGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCNTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGCACTATCCGGCAAGGGTTGCGCTTCATCAGCCATAATCCGGCGAATGATCCACGCCGCCCCCGACGACATTAAAGGCCGTTCAAGCAGCGGATCGTCAGGCTGTAAGCGCAATTTGCCTGCCTTGCCGTGGCGGGCAAACGCGGTATACg                                                                                                                                                        <  1:246768/228‑1 (MQ=255)                                                                                                                                cACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGCACTATCCGGCAAGGGTTGCGCTTCATCAGCCATAATCCGGCGAATGATCCACGCCGCCCCCGACGACATTAAAGGCCGTTCAAGAAGCGGATCGTCAGGCTGTAAGCGCAATTTGCCTGCCTTGCCGTGGCGAGCAAACGCGGTATACGCTGCCGCCATATCTTCCAGTTTTGCACCAGCGCCGCCGAGAATGAGTGAAAGATTCGGCGCAGCAcc                                                                                     >  1:276268/1‑274 (MQ=255)                                                                                                                                                                     tGGGGCGACGCGCGGCAAGGCACTATCCGGCAAGGGTTGCGCTTCATCAGCCATAATCCGGCGAATGATCCACGCCGCCCCCGACGACATTAAAGGCCGTTCAagc                                                                                                                                                                                                                        >  2:107089/1‑106 (MQ=255)                                                                                                                                                                         gCGACGCGCGGCAAGGCACTATCCGGCAAGGGTTGCGCTTCATCAGCCATAATCCGGCGAATGATCCACGCCGCCCCCGACGACATTAAAGGCCGTTCAAGCAGCg                                                                                                                                                                                                                    <  1:107091/106‑1 (MQ=255)                                                                                                                                                                                             agacggaaggggTTGCGCTTCCTAAGCCATACGCCGGCGAATGATCCACGCCGCCCCCGACGACATTAAAGGCCGTTCAAGAAGCGGATCGTCAGGCGGTAAGCGCAATTTGCCTGCCTGGCCGTGGCGAGCAAACGCGGTATACGCTGCCGCCATATCTTCCAGTTTTGCACCAGCGCCGCCGAGAATGAGTGAAAGATTCGGCGCAGCACCGTTGGGCAAATATAACGGCAATCCAACATTGCGTAACTTTGCCGCAAACCGTTTCGGTCCa                        <  2:276257/265‑1 (MQ=255)                                                                                                                                                                                                                      gCCATAATCCGGCGAATGATCCACGCCGCCCCCGACGACATTAAAGGCCGTTCAAGCAGCGGATCGTCAGGCTGTAAGCGCAATTTGCCTGCCTTGCCGTGGCGAGCAAACGCGGTATNCGCTGCCGCCATATCTTCCAGTTTTGCACCAGCGCCGCCGAGAATGAGTGAAAGATTCGGCGCAGCACCGTTGGGCAAATATAACGGCAATCCAACATTGCGTAACTTTGCCGCAAACCGTTTCGGTCCATAGGCTTCCAGCACCTGCAcag  <  1:287983/271‑1 (MQ=255)                                                                                                                                                                                                                                     aTGATCCACGCCGCCCCCGACGCCATTAAAGGCCGTTCAagc                                                                                                                                                                                                                        <  1:272388/42‑1 (MQ=255)                                                                                                                                                                                                                                                               tAAAGGCCGTTCAAGAAGCGGATCGTCAGGCTGTAAGCGCAATTTGCCTGCCTTGCCGTGGCGAGCAAACGCGGTATACGCTGCCGCCATATCTTCCAGTTTTGCACCAGCGCCGCCGAGAATGAGTGAAAGATTCGGCGCAGCACCGTTGGGCAAATATAACGGCAATCCAACATTGCGTAACTTTGCCGCAAACCGTTTCGGTCCATAGGCTTCCAGCACCt        >  1:109142/1‑224 (MQ=255)                                                                                                                                                                                                                                                                   ggCCGTTCAAGAAGCGGATCGTCAGGCTGTAAGCGCAATTTGCCTGCCTGGCCGTGGCGAGCAAACGCGGTATACGCTGCCGCCATATCTTCCAGTTTTGCACCAGCGCCGCCGAGAATGAGTGAAAGATTCGGCGCAGCACCGTTGGGCAAATATAACGGCAATCCAACATTGCGTAACTTTGCCGCAAACCGTTTCGGTCCATAGGCTTCCAGCACCTGcac    <  2:109140/224‑1 (MQ=255)                                                                                                                                                                                                                                                                      cGTTCAAGCAGCGGATCGTCAGGCTGTAAGCGCAATTTGCCTGCCTTGCCGTGGCGAGCAAACGCGGTATACGCTGCCGCCATATCTTCCAGTTTTGCACCAGCGCCGCCGAGAATGAGTGAAAGATTCGGCGCAGCACCGTTGGGCAAATATAACGGCAATCCAACATTGCGTAACTTTGCCGCAAACCGTTTCGGTcc                         >  1:133880/1‑200 (MQ=255)                                                                                                                                                                                                                                                                              |                                                                                                                                                                                                                       TTATTGACCTGATTCAACAATGGTACGGCACTGGCAAAGCCAAACTGACCAACAACGGGCGTGCCGTCCGGTCTGCCAGTCCAGATCCCAATGACATAGCGAGCGTTAACCCCAATCGCCCAGGCGTCACGATAGCCATAGCTGGTGCCCGTTTTCCATGCCAGTGGGGCGACGCGCGGCAAGGCACTATCCGGCAAGGGTTGCGCTTCATCAGCCATAATCCGGCGAATGATCCACGCCGCCCCCGACGACATTAAAGGCCGTTCAAGCAGCGGATCGTCAGGCTGTAAGCGCAATTTGCCTGCCTTGCCGTGGCGAGCAAACGCGGTATACGCTGCCGCCATATCTTCCAGTTTTGCACCAGCGCCGCCGAGAATGAGTGAAAGATTCGGCGCAGCACCGTTGGGCAAATATAACGGCAATCCAACATTGCGTAACTTTGCCGCAAACCGTTTCGGTCCATAGGCTTCCAGCACCTGCACAG  >  CP009273/2639000‑2639483

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑