Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,648,331	G→A	15.1%	P45L (CCT→CTT)	lipM ←	Octanoyltransferase LipM

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,648,331	0	G	A	15.1%	55.3 / 2.3	25	P45L (CCT→CTT)	lipM	Octanoyltransferase LipM
Reads supporting (aligned to +/- strand):  ref base G (11/10);  new base A (2/2);  total (13/12)
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

ACTGTAAGTTAACTCTTTATCATGTAGCACCCCACGGCCACCAGTTTGACGCCTTACGAGACCAAAACCTTTCTCTTTAACCTTATCAATATCAATTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGATTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTCATCCATTGCCATATTATAATATGGGTCTTTACTTCCTGTATTAATAAAATTCCAAGTTTCAGTCATA  >  USA300TCH1516_ALE/1648192‑1648465                                                                                                                                            |                                                                                                                                       acTGTACGTTAACTCCTTATCATGTAGCACCCCACGGCCACCAGTTTGACGCCTTACGAGACCAAAACCTTTCTCTTTAACCTTATCAATATCAATTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAgg                                                                                                                                       <  1:222619/141‑1 (MQ=255) acTGTAAGTTCACTCTTTATCATGTAGCACCCCACGGCCACCAGTTTGACGCCTTACGAGACCAAAACCTTTCTCTTTAACCTTATCAATATCAATTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAgg                                                                                                                                       <  1:255494/141‑1 (MQ=255)                  tATCATGTAGCACCCCACGGCCACCAGTTTGACGCCTTACGAGACCAAAACCTTTCTCTTTAACCTTATCAATATCAATTTCTTTTTTTTTTTTTTTTAAATACCCTATTGATTATTTTGCAAGTTTCCTTGTGTTAAAAc                                                                                                                      >  2:165471/1‑141 (MQ=255)                  tATCATGTAGCACCCCACGGCCACCAGTTTGACGCCTTACGAGACCAAAACCTTTCTCTTTAACCTTATCAATATCAATTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAAGATTCCATGTGTAAAAAc                                                                                                                      >  2:165493/1‑141 (MQ=255)                            cACCCCACGGCCACCAGTTTGACGCCTTACGAGACCAAAACCTTTCTCTTTAACCTTATCAATATCAATTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGATTCCATGTGTAAAAACGTATAACTgg                                                                                                            <  2:26294/141‑1 (MQ=255)                                ccACGGCCGCCAGTTTGACGCCTTACGAGACCAAACCCTTTCTCTTTAACCTTATCAATATCAATTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGCTTTCATTTTTAAAAACGTATAACTGGATCa                                                                                                        <  2:152876/141‑1 (MQ=255)                                                gACGCCTTACGAGACCAAAACCTTTCTCTTTAACCTTATCAATATCAATTTCTTTTTTTAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGCTTCCATGTGTAAAAACGTATAACTGGAACAATTTAACCCCTAgaga                                                                                        >  1:15288/1‑141 (MQ=255)                                                gACGCCTTACGAGACCAAAACCTTTCTCTTTAACCTTATCAATATCAATTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATACTGCTGCAGGATTCCATGTGTCAAAACGTATAACTGTATCAATTTCACCTCTagatt                                                                                        >  1:92368/1‑139 (MQ=255)                                                 aCGCCTTACGAGACCAAAACCTTTCTCTTTAACCTTATCAATATCAATTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGATTCCATGTGTAAAAACGTATAACTGTATCACTTTCACCTCTAGAGAc                                                                                       <  1:170584/141‑1 (MQ=255)                                                                   aCCTTTCTCTTTAACCTTATCAATATCAATTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGCTTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTc                                                                     <  2:268150/141‑1 (MQ=255)                                                                   aCCTTTCTCTTTAACCTTATCAATATCAATTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGATTCCATGTGTAACAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTc                                                                     >  1:54834/1‑141 (MQ=255)                                                                        tctcTTTAACCTTATCAATATCAATTTCTTTTTGTAGCCTTTTGAAATACCCTATTGATAATGTGGCAGGATTCCATGTGTAAAAACGTATAACTGGATCAGTTTCACCTCTAGAGACAAACTTTAATACCGCttcattca                                                                >  2:20428/1‑141 (MQ=255)                                                                        tctcTTTAACCTTATCAATATCAATTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGATTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTCATCCa                                                                >  2:15369/1‑141 (MQ=255)                                                                                  cTTATCAATATCAATTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGATTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTCATCCATTGCCAtatt                                                      <  2:261130/141‑1 (MQ=255)                                                                                    tatcaatatcaaTTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGATTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTCATCCATTGCCAtatttt                                                    >  1:289590/1‑139 (MQ=255)                                                                                    tatcaatatcaaTTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGATTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTCATCCATTGCCAtattat                                                    >  2:242168/1‑141 (MQ=255)                                                                                        aatatcaatTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGATTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTCATCCATTGCCATATTataata                                                <  2:253224/141‑1 (MQ=255)                                                                                            tcaatTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGATTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTCATCCATTGCCATATTATAATATggg                                            >  1:327235/1‑141 (MQ=255)                                                                                               atTTCTTTTTGAAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGATTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTCATCCATTGCCATATTATAATATGGGTCt                                         <  1:124728/141‑1 (MQ=255)                                                                                                   cTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGATTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTCATCCATTGCCATATTATAATATGGGTCTTTAc                                     <  2:231469/141‑1 (MQ=255)                                                                                                     ttttGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGATTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTCATCCATTGCCATATTATAATATGGGACTTTACtt                                   >  2:188715/1‑141 (MQ=255)                                                                                                                     aaTACCCTATTGATAATGTTGCAGGATTCCATGTGTAAAAACGTAAAACTGGATCAATTTCACCTCAAGAGACAAAATTTAATAACGCTTCATCCATTGCCATATTATAATATGGGTCTTTACTTCCTGTATTACTAAAAt                   >  2:107492/1‑141 (MQ=255)                                                                                                                      aTACCCTATTGATAATGTTGCAGGATTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTCATCCATTGCCATATTATAATATGGGTCTTTACTTCCTGTATTAATAAAAtt                  >  1:56655/1‑141 (MQ=255)                                                                                                                                  tAATGTTGCAGGATTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTCATCCATTGCCATATTATAATATGGGTCTTTACTTCCTGTATTAATAAAATTCCAAGTTTCAGt      <  1:15369/141‑1 (MQ=255)                                                                                                                                  tAATGTTGCAAGATTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTCATCCATTGCCATATTATAATATGGGTCTTTACTTCCTGTATTAATATAATTCCAAGTTTCAGt      <  1:165493/141‑1 (MQ=255)                                                                                                                                  aaaTGTTGCAAGATTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTCATCCATTGCCATATTATAATATGGGTCTTTACTTCCTGTATTAATATAATTCCAAGTTTCAGt      <  1:165471/140‑1 (MQ=255)                                                                                                                                      gTTCCAGGATTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTCATCCATTGCCATATTATAATATGGGTCTTTACTTCCTGTATTAATAAAATTCCAAGTTTCAGTCata  <  1:239796/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                       ACTGTAAGTTAACTCTTTATCATGTAGCACCCCACGGCCACCAGTTTGACGCCTTACGAGACCAAAACCTTTCTCTTTAACCTTATCAATATCAATTTCTTTTTGTAGCCTTTGGAAATACCCTATTGATAATGTTGCAGGATTCCATGTGTAAAAACGTATAACTGGATCAATTTCACCTCTAGAGACAAAATTTAATAACGCTTCATCCATTGCCATATTATAATATGGGTCTTTACTTCCTGTATTAATAAAATTCCAAGTTTCAGTCATA  >  USA300TCH1516_ALE/1648192‑1648465

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑